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2,339,100 | A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. | Cancer diagnosis is one of the most important emerging clinical applications of gene expression microarray technology. We are seeking to develop a computer system for powerful and reliable cancer diagnostic model creation based on microarray data. To keep a realistic perspective on clinical applications we focus on multicategory diagnosis. To equip the system with the optimum combination of classifier, gene selection and cross-validation methods, we performed a systematic and comprehensive evaluation of several major algorithms for multicategory classification, several gene selection methods, multiple ensemble classifier methods and two cross-validation designs using 11 datasets spanning 74 diagnostic categories and 41 cancer types and 12 normal tissue types.</AbstractText>Multicategory support vector machines (MC-SVMs) are the most effective classifiers in performing accurate cancer diagnosis from gene expression data. The MC-SVM techniques by Crammer and Singer, Weston and Watkins and one-versus-rest were found to be the best methods in this domain. MC-SVMs outperform other popular machine learning algorithms, such as k-nearest neighbors, backpropagation and probabilistic neural networks, often to a remarkable degree. Gene selection techniques can significantly improve the classification performance of both MC-SVMs and other non-SVM learning algorithms. Ensemble classifiers do not generally improve performance of the best non-ensemble models. These results guided the construction of a software system GEMS (Gene Expression Model Selector) that automates high-quality model construction and enforces sound optimization and performance estimation procedures. This is the first such system to be informed by a rigorous comparative analysis of the available algorithms and datasets.</AbstractText>The software system GEMS is available for download from http://www.gems-system.org for non-commercial use.</AbstractText>[email protected].</AbstractText> |
2,339,101 | [Characterisation of the gene expression profiles in the inner ear and the colliculus inferior of normal and deafened rats by gene-array-technology]. | The phenotype of deafness and its mechanisms are morphologically and electrophysiologically well characterised. However, the molecular mechanisms and the consequences of deafness are poorly understood.</AbstractText>In this study we investigated changes in gene expression profiles in subfractions of the cochlea and the colliculus inferior, a non-cochlear tissue, of normal and deafened (10 % Neomycin) rats using the gene-array-technology. RNA was prepared from modiolus (Mo) und sensorineural epithel/lateral wall (SnE/Lw) und Colliculus inferior (IC), reverse transcribed with gene specific primers, labeled with (32)P-dATP and hybridised with its complementary sequences of 1200 rat ESTs.</AbstractText>Similar gene expression profiles were detected in Mo- and SnE/Lw in normal as well in deafened rats differing significantly from those found in IC. In deafened animals differences in mRNA levels were determined in IC for 8 genes, in Mo für 17 genes and in SnE/Lw for 25 genes in comparison to those of normal rats. By using gene-arrays many genes described in the literature previously could be detected. Otherwise most of the genes found in the cochlea are unknown.</AbstractText>The gene-array-technology is a valuable tool in otological research for gene expression analysis and, therefore, for comprehensive understanding of molecular processes in the inner ear. Furthermore gene screening for candidate genes could be a big step ahead in developing therapies of diseases of the inner ear.</AbstractText> |
2,339,102 | Carrier incidence for spinal muscular atrophy in southern Chinese. | A real time quantitative PCR (QPCR) method using TaqMan technology was used to assess the copy number of the two survival motor neuron genes (SMN1 and SMN2) on chromosome 5q13. This allows the accurate determination of carriers for spinal muscular atrophy (SMA), with one copy of SMN1. Analysis of 569 normal southern Chinese individuals revealed a carrier incidence of 1.6%, similar to that found in the western society. Study of 42 obligatory carriers showed a (2 + 0) genotype in two (4.8 %). In 27 SMA patients with homozygous deletion of the SMN1 gene, the number of SMN2 gene correlated with disease phenotype, with 68% of type II and III patients carrying three or more SMN2 genes, whilst the incidence of three or more SMN2 genes in the normal population was 1.57%. |
2,339,103 | Influence of functional polymorphisms of the MDR1 gene on vincristine pharmacokinetics in childhood acute lymphoblastic leukemia. | Our objective was to investigate the effect of single nucleotide polymorphisms (SNPs) in the P-glycoprotein MDR1 gene on vincristine pharmacokinetics and side effects in childhood acute lymphoblastic leukemia.</AbstractText>From 52 of 70 children who participated in a previous study on vincristine pharmacokinetics, patient material was available for investigation of the MDR1 genetic variants. The SNPs C3435T and G2677T were determined by use of polymerase chain reaction-restriction fragment length polymorphism. Vincristine side effects were scored retrospectively from patient records.</AbstractText>No association was observed between C3435T or G2677T and vincristine pharmacokinetic variables. When haplotypes were assigned, haplotype 1/1 carriers (3435C/2677G) showed a longer elimination half-life than noncarriers (1156 versus 805 minutes, P =.038). In contrast, haplotype 1/2 carriers (3435T/2677G) had a shorter elimination half-life than noncarriers (805 versus 1180 minutes, P =.044). However, this significance was lost after Bonferroni correction for multiple testing. The haplotypes did not affect the other pharmacokinetic parameters, such as clearance and area under the concentration-time curve, suggesting that the observed effect on elimination half-life is of very limited relevance. Moreover, SNPs in the MDR1 gene did not identify patients with an increased risk for vincristine-induced constipation.</AbstractText>The genetic variants in the MDR1 gene alone cannot explain the large variability in vincristine pharmacokinetics.</AbstractText> |
2,339,104 | Practice patterns of obstetrician-gynecologists regarding preconception and prenatal screening for cystic fibrosis. | To assess practices of obstetrician-gynecologists regarding carrier screening for cystic fibrosis (CF).</AbstractText>A questionnaire investigating practice patterns and opinions pertaining to CF screening was mailed to 1165 members of the American College of Obstetricians and Gynecologists (ACOG), of whom 565 participate in the Collaborative Ambulatory Research Network (CARN) and 600 were randomly selected.</AbstractText>Of the questionnaires, 64% were returned. Statistical analyses were limited to the 632 respondents whose primary medical specialty was gynecology (Gyn Only) or obstetrics and gynecology (ObGyn). CARN membership was not a significant factor on any nondemographic measure. Almost one-half of physicians do not ask nonpregnant patients their family history of CF or provide them with information about CF screening. The majority of ObGyns (88.7%) ask obstetric patients their family history of CF, and offer CF carrier screening. Almost two-thirds (65.8%) offer screening to all prenatal patients. Among those ObGyns who selectively offer CF screening to pregnant patients, only 27.4% utilized all of the selection criteria in the guidelines. Liability for not offering screening, familiarity with CF, and the ability to interpret a positive screening test were important physician concerns.</AbstractText>The results indicate a need for minimizing the complexity of clinical guidelines for population-based genetic screening, prospective assessment of implementation and focused continuing education for providers.</AbstractText> |
2,339,105 | Bayesian analysis for cystic fibrosis risks in prenatal and carrier screening. | Risk assessment is an essential component of genetic counseling and testing, and Bayesian analysis plays a central role in complex risk calculations. We previously developed generalizable Bayesian methods to calculate the autosomal recessive disease risk of a fetus when one or no mutation is detected, and another, independent risk factor is present. Our methods are particularly useful for calculating the CF disease risk for a fetus with echogenic bowel. In genetics practice, however, there are other scenarios for which our previous methods are inadequate.</AbstractText>We provide herein methods for calculating genetic risks in a variety of common clinical scenarios. These scenarios include the following: (1) different mutation panels that have been used for the parents and for a fetus; (2) genetic testing results available on the proband or other relatives, in addition to the consultand; (3) fetal ultrasound negative for echogenic bowel with a positive family history; and (4) a consultand with a mixed ethnic background.</AbstractText>Our Bayesian methods have proven their versatility through application to many different common genetic counseling scenarios. These methods permit autosomal recessive disease and carrier probabilities to be calculated accurately, taking into account all relevant information. Our methods allow accurate genetic risk estimates for patients and their family members for CF or other autosomal recessive disorders.</AbstractText> |
2,339,106 | Cystic fibrosis carrier screening: validation of a novel method using BeadChip technology. | To validate a novel BeadChip assay system for cystic fibrosis (CF) mutation testing using the panel of 25 ACMG recommended mutations and D1152H.</AbstractText>DNA from 519 individuals originally tested for CF mutation status by allele specific oligonucleotide hybridization (ASOH) were blindly analyzed by the BeadChip assay and the results were compared. The elongation mediated multiplexed analysis of polymorphisms (eMAP) protocol, which combines multiplex amplification of genomic DNA and multiplex detection of mutations on color-coded bead arrays, was used to analyze 26 CF mutations in two separate groups.</AbstractText>The system accurately distinguished the 26 CF genotypes and had 100% concordance with the ASOH technique with an assay failure rate of 1.7%. Benign variants of exon 10 codons 506, 507, and 508 did not interfere with mutation identification and reflex testing for the 5/7/9T IVS8 polymorphism was performed on a separate array.</AbstractText>The BeadChip assay system provided accurate and rapid identification of the ACMG recommended CF mutations.</AbstractText> |
2,339,107 | Premarital and prenatal screening for cystic fibrosis: experience in the Ashkenazi Jewish population. | Since the early 1990s, Dor Yeshorim (DY) and the Mount Sinai School of Medicine (MSSM) have conducted premarital and prenatal carrier screening for cystic fibrosis (CF) in the Ashkenazi Jewish (AJ) population as part of their genetic testing programs, respectively. Together, over 170,000 screenees have been tested. In this study, we report the CF mutation frequencies in over 110,000 screenees who reportedly were of 100% AJ descent from the DY program and MSSM. In addition, the CF mutation frequencies in a group of > 7,000 screenees for AJ diseases who were of < 100% AJ descent are reported.</AbstractText>Testing for CF mutations was performed by either PCR and restriction digestion or ASO hybridization analyses at MSSM or sent to various academic and commercial laboratories by DY.</AbstractText>The overall (and individual) carrier frequency for the five common AJ mutations, W1282X (0.020), DeltaF508 (0.012), G542X (0.0024), 3849+10kb C>T (0.0020), and N1303K (0.0016), among screenees who were 100% AJ was 1 in 26; when D1152H and the rare 1717-1G>A were included, the overall carrier frequency increased to approximately 1 in 23. In four families with D1152H, five compound heterozygotes for D1152H and W1282X (n = 2), DeltaF508 (1) or 3849+10kb C>T (1) were identified. In contrast, the carrier frequency for screenees reporting < 100% AJ descent was approximately 1 in 30 for the seven mutations.</AbstractText>The carrier frequency for five common CF mutations in a large 100% AJ sample increased from 1 in 26 to 1 in 23 when D1152H was included in the panel. Addition of D1152H to mutation panels when screening the AJ population should be considered because compound heterozygosity is associated with a variable disease phenotype. Further studies to delineate the phenotype of CF patients with this mutation are needed.</AbstractText> |
2,339,108 | Clinical sensitivity of prenatal screening for cystic fibrosis via CFTR carrier testing in a United States panethnic population. | To estimate CFTR mutation frequencies, clinical sensitivities (proportions of carrier couples or affected fetuses detected), and birth prevalence estimates for broad racial/ethnic groups and for a panethnic U.S. population.</AbstractText>Published sources of information were identified, corrected when appropriate, and summarized. Combining racial/ethnic-specific mutation frequencies and birth prevalence estimates allowed the computation of panethnic estimates.</AbstractText>Two of the 25 recommended mutations do not meet the 0.1% threshold in a panethnic population set by the American College of Medical Genetics. The clinical sensitivities are estimated to be 71.9%, 51.7%, 41.6%, 88.6%, and 23.4% for non-Hispanic Caucasians, Hispanic Caucasian, African American, Ashkenazi Jewish Caucasian, and Asian American couples, respectively. Birth prevalence estimates are 1:2,500, 1:13,500, 1:15,100, 1:2,270, and 1:35,100, whereas the number of couples needed to screen to detect an affected fetus are about 3,200, 26,120; 36,040; 2,600, and 129,600, respectively, for the same racial/ethnic groups.</AbstractText>Overall, the panethnic estimates for CFTR mutation frequencies are similar to those for non-Hispanic Caucasians. However, large differences in both clinical sensitivity and birth prevalence exist between the broad racial/ethnic groups examined. Whether and how the differences in the numbers of couples needed to screen to detect an affected fetus are to be included in prenatal screening for cystic fibrosis needs to be more explicitly addressed.</AbstractText> |
2,339,109 | Analysis of 3208 cystic fibrosis prenatal diagnoses: impact of carrier screening guidelines on distribution of indications for CFTR mutation and IVS-8 poly(T) analyses. | To evaluate and quantify indications for CFTR mutation analysis of prenatal specimens, and to determine if a significant portion of tests are performed only for the identification of 5T alleles, we surveyed our laboratory data over a 3-year time period that spanned the issuance of the cystic fibrosis (CF) carrier screening guidelines.</AbstractText>Referral indications for 3208 prenatal specimens were compared for an 18-month period before (April 2000 to September 2001) and after (October 2001 to April 2003) publication of the ACMG/ACOG statement regarding prenatal and preconception testing for CF.</AbstractText>The frequency of cases received for testing when one or both parents were CF mutation carriers did not change significantly after publication of the guidelines. The most frequent indication during the entire 3-year period was fetal ultrasound abnormality, yet in the post-ACMG/ACOG period the percentage decreased significantly due to an increase in the number of prenatal screening cases. Testing indications related to parental 5T status also increased significantly in the post-ACMG/ACOG period and accounted for 2.9% of testing over the 3-year period. A small subset (1.6%) of prenatal specimens were tested for poly(T) even though the parents did not carry 5T allele(s). However, more than 40% of these cases could be attributed to parental R117H mutations.</AbstractText>These data indicate that although indications for prenatal testing shifted after the issuance of carrier screening guidelines, prenatal testing related to parental 5T alleles comprised < 3% of the total referral indications.</AbstractText> |
2,339,110 | CFTR mutation distribution among U.S. Hispanic and African American individuals: evaluation in cystic fibrosis patient and carrier screening populations. | We reviewed CFTR mutation distribution among Hispanic and African American individuals referred for CF carrier screening and compared mutation frequencies to those derived from CF patient samples.</AbstractText>Results from CFTR mutation analyses received from January 2001 through September 2003, were analyzed for four populations: Hispanic individuals with a CF diagnosis (n = 159) or carrier screening indication (n = 15,333) and African American individuals with a CF diagnosis (n = 108) or carrier screening indication (n = 8,973). All samples were tested for the same 87 mutation panel.</AbstractText>In the Hispanic population, 42 mutations were identified: 30 in the patient population (77.5% detection rate) and 33 among carrier screening referrals. Five mutations not included in the ACMG/ACOG carrier screening panel (3876delA, W1089X, R1066C, S549N, 1949del84) accounted for 7.55% detection in patients and 5.58% among carriers. Among African American referrals, 33 different mutations were identified: 21 in the patient population (74.4% detection) and 23 in the carrier screening population. Together, A559T and 711+5G>A were observed at a detection rate of 3.71% in CF patients and 6.38% in carriers. The mutation distribution seen in both the carrier screening populations reflected an increased frequency of mutations with variable expression such as D1152H, R117H, and L206W.</AbstractText>A detailed analysis of CFTR mutation distribution in the Hispanic and African American patient and carrier screening populations demonstrates that a diverse group of mutations is most appropriate for diagnostic and carrier screening in these populations. To best serve the increasingly diverse U.S. population, ethnic-specific mutations should be included in mutation panels.</AbstractText> |
2,339,111 | Early onset hereditary papillary renal carcinoma: germline missense mutations in the tyrosine kinase domain of the met proto-oncogene. | Hereditary papillary renal carcinoma (HPRC) is characterized by a predisposition to multiple, bilateral papillary type 1 renal tumors caused by inherited activating missense mutations in the tyrosine kinase domain of the MET proto-oncogene. In the current study we evaluated the clinical phenotype and germline MET mutation of 3 new HPRC families. We describe the early onset clinical features of HPRC.</AbstractText>We identified new HPRC families of Italian (family 177), Spanish (family 223) and Cuban (family 268) descent. We evaluated their clinical features, performed MET mutation analysis by denaturing high performance liquid chromatography and DNA sequencing, and estimated age dependent penetrance and survival using Kaplan-Meier analysis. We characterized renal tumors by histology and fluorescence in situ hybridization.</AbstractText>Identical germline MET c.3522G --> A mutations (V1110I) were identified in families 177 and 268 but no evidence of a founder effect was found. Affected members of family 223 carried a germline c.3906G --> C.3522G --> A MET mutation (V1238I). Age dependent penetrance but not survival was significantly earlier for the c.3522G -->A mutation than for the c.3906G --> A mutation in these HPRC families. Trisomy of chromosome 7 and papillary renal carcinoma type 1 histology were detected in papillary renal tumors.</AbstractText>HPRC can occur in an early onset form. The median age for renal tumor development in these 3 HPRC families was 46 to 63 years. HPRC associated papillary renal tumors may be aggressive and metastasize, leading to mortality. Median survival age was 60 to 70 years. Families with identical germline mutations in MET do not always share a common ancestor. HPRC is characterized by germline mutations in MET and papillary type 1 renal tumor histology.</AbstractText> |
2,339,112 | Association of Fc gamma receptor IIA polymorphisms with acute renal-allograft rejection. | Acute rejection is a leading cause of early renal-allograft failure. The human Fc gamma receptor IIA (FcgammaRIIA) forms an essential link between the humoral branch and the effector cells of the immune system. In this study, we examined FcgammaRIIA genotypes in renal-allograft recipients (rejectors) with acute graft rejection and in a number of control groups to investigate a possible association between FcgammaRIIA polymorphism and acute renal-allograft rejection. The distribution of the genotypes in the study patient group differed from the control groups. The frequency of homozygosity for FcagammaRIIA-R/R131 in the rejectors was significantly higher than that in the recipients (nonrejectors) with well-functioning renal allografts and in blood donors (P< 0.05). In comparison with the control groups, the rejectors displayed a higher R131 allele frequency (P< 0.05) and a lower H131 allele frequency (P< 0.05). These results reveal a significant association between FcgammaRIIA-R/R131 and acute renal-graft rejection, and it is likely that FcgammaRIIA polymorphisms could be useful markers for potential risk of rejection. |
2,339,113 | Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. | We use evolutionary trees of haplotypes to study phenotypic associations by exhaustively examining all possible biallelic partitions of the tree, a technique we call tree scanning. If the first scan detects significant associations, additional rounds of tree scanning are used to partition the tree into three or more allelic classes. Two worked examples are presented. The first is a reanalysis of associations between haplotypes at the Alcohol Dehydrogenase locus in Drosophila melanogaster that was previously analyzed using a nested clade analysis, a more complicated technique for using haplotype trees to detect phenotypic associations. Tree scanning and the nested clade analysis yield the same inferences when permutation testing is used with both approaches. The second example is an analysis of associations between variation in various lipid traits and genetic variation at the Apolipoprotein E (APOE) gene in three human populations. Tree scanning successfully identified phenotypic associations expected from previous analyses. Tree scanning for the most part detected more associations and provided a better biological interpretative framework than single SNP analyses. We also show how prior information can be incorporated into the tree scan by starting with the traditional three electrophoretic alleles at APOE. Tree scanning detected genetically determined phenotypic heterogeneity within all three electrophoretic allelic classes. Overall, tree scanning is a simple, powerful, and flexible method for using haplotype trees to detect phenotype/genotype associations at candidate loci. |
2,339,114 | Testing for Hardy-Weinberg equilibrium in samples with related individuals. | When the classical chi(2) goodness-of-fit test for Hardy-Weinberg (HW) equilibrium is used on samples with related individuals, the type I error can be greatly inflated. In particular the test is inappropriate in population isolates where the individuals are related through multiple lines of descent. In this article, we propose a new test for HW (the QL-HW test) suitable for any sample with related individuals, including large inbred pedigrees, provided that their genealogy is known. Performed conditional on the pedigree structure, the QL-HW test detects departures from HW that are not due to the genealogy. Because the computation of the QL-HW test becomes intractable for very polymorphic loci in large inbred pedigrees, a simpler alternative, the GCC-HW test, is also proposed. The statistical properties of the QL-HW and GCC-HW tests are studied through simulations considering a sample of independent nuclear families, a sample of extended outbred genealogies, and samples from the Hutterite population, a North American highly inbred isolate. Finally, the method is used to test a set of 143 biallelic markers spanning 82 genes in this latter population. |
2,339,115 | A novel KERA mutation associated with autosomal recessive cornea plana. | To report a novel KERA mutation associated with autosomal recessive cornea plana in members of a nuclear family and to describe their ophthalmic phenotypes.</AbstractText>Ophthalmic examination, biometry, and direct sequencing of KERA.</AbstractText>Five of the 6 siblings were affected and had small flat corneas, variable anterior chamber depths, and short axial lengths. The remaining brother and the 2 parents had normal ophthalmic examinations. Genetic testing revealed a novel homozygous nonsense mutation in exon 3 [937C>T] in the clinically affected individuals. The clinically unaffected parents were confirmed as carriers. The clinically unaffected sibling had no KERA mutation. This mutation leads to replacement of an arginine by a stop codon at position 313 of keratocan protein.</AbstractText>This novel point mutation in KERA is the fourth thus far described. The ocular phenotype is characteristic of autosomal recessive cornea plana.</AbstractText> |
2,339,116 | Translating emerging research on the genetics of smoking into clinical practice: ethical and social considerations. | Despite decades of research aimed at improving the effectiveness of smoking treatment, available treatments are only modestly effective, and smoking remains the leading cause of preventable deaths in the United States. Recent research on genetic factors related to smoking behavior eventually may lead to the design of new tobacco dependence treatments and to the individualization of treatment based on genetic factors. Although this research is in its infancy, and data on the analytic and clinical validity of genetic tests to tailor smoking treatment are not yet available, it is not too soon to begin identifying and addressing key ethical issues associated with genetic testing in the context of tobacco dependence treatment. Key concerns include (a) potential harm (e.g., stigmatization, discrimination) to patients related to inappropriate use of genetic information, (b) implications of pleiotropic associations, (c) differential prevalence of risk-conferring genotypes among racial or ethnic subpopulations, (d) preparedness of primary care physicians to incorporate genetic testing into smoking treatment, (e) informed consent, and (f) ensuring an appropriate balance between individually tailored treatment by genotype and broad-based interventions that focus on social and environmental factors affecting smoking behavior. Additional research on these ethical and social issues must be conducted simultaneously with the scientific work currently under way. Failure to address these concerns will likely undermine efforts to translate knowledge emerging from the United States' substantial investment in genetic research on smoking into clinical practice and improved patient outcomes. |
2,339,117 | Human papilloma virus type 16 infection and the early onset of cervical cancer. | Human papilloma viruses (HPV), particularly type 16, have been associated with cervical cancer. It has been noted that the average onset of cervical cancer is occurring in younger women coupled with a higher prevalence of cervical HPV infection. However, the correlation between HPV 16 infection and the early onset of cervical cancer is still unclear. We hypothesize that HPV infection is an indicator of early onset of cervical cancer. To test this hypothesis, cervical smears from 197 women were evaluated by the polymerase chain reaction for HPV 16. These data revealed that the HPV 16-positive women were significantly younger than the HPV 16-negative women. Moreover, the average age of HPV 16-positive women with CIN 3 or invasive cancer was significantly younger compared with the other groups. These data clearly suggest that HPV 16 infection is a significant risk factor for the progression for cervical cancer in a young population of women. |
2,339,118 | A high-resolution radiation hybrid map of chicken chromosome 5 and comparison with human chromosomes. | The resolution of radiation hybrid (RH) maps is intermediate between that of the genetic and BAC (Bacterial Artificial Chromosome) contig maps. Moreover, once framework RH maps of a genome have been constructed, a quick location of markers by simple PCR on the RH panel is possible. The chicken ChickRH6 panel recently produced was used here to construct a high resolution RH map of chicken GGA5. To confirm the validity of the map and to provide valuable comparative mapping information, both markers from the genetic map and a high number of ESTs (Expressed Sequence Tags) were used. Finally, this RH map was used for testing the accuracy of the chicken genome assembly for chromosome 5.</AbstractText>A total of 169 markers (21 microsatellites and 148 ESTs) were typed on the ChickRH6 RH panel, of which 134 were assigned to GGA5. The final map is composed of 73 framework markers extending over a 1315.6 cR distance. The remaining 61 markers were placed alongside the framework markers within confidence intervals.</AbstractText>The high resolution framework map obtained in this study has markers covering the entire chicken chromosome 5 and reveals the existence of a high number of rearrangements when compared to the human genome. Only two discrepancies were observed in relation to the sequence assembly recently reported for this chromosome.</AbstractText> |
2,339,119 | The role of haplotypes in candidate gene studies. | Human geneticists working on systems for which it is possible to make a strong case for a set of candidate genes face the problem of whether it is necessary to consider the variation in those genes as phased haplotypes, or whether the one-SNP-at-a-time approach might perform as well. There are three reasons why the phased haplotype route should be an improvement. First, the protein products of the candidate genes occur in polypeptide chains whose folding and other properties may depend on particular combinations of amino acids. Second, population genetic principles show us that variation in populations is inherently structured into haplotypes. Third, the statistical power of association tests with phased data is likely to be improved because of the reduction in dimension. However, in reality it takes a great deal of extra work to obtain valid haplotype phase information, and inferred phase information may simply compound the errors. In addition, if the causal connection between SNPs and a phenotype is truly driven by just a single SNP, then the haplotype-based approach may perform worse than the one-SNP-at-a-time approach. Here we examine some of the factors that affect haplotype patterns in genes, how haplotypes may be inferred, and how haplotypes have been useful in the context of testing association between candidate genes and complex traits. |
2,339,120 | An exact maternal-fetal genotype incompatibility (MFG) test. | The maternal-fetal genotype incompatibility (MFG) test can be used for a variety of genetic applications concerning disease risk in offspring including testing for the presence of alleles that act directly through offspring genotypes (child allelic effects), alleles that act through maternal genotypes (maternal allelic effects), or maternal-fetal genotype incompatibilities. The log-linear version of the MFG model divides the genotype data into many cells, where each cell represents one of the possible mother, father, and child genotype combinations. Currently, tests of hypotheses about different allelic effects are accomplished by an asymptotic MFG test, but it is unknown if this is appropriate under conditions that produce small cell counts. In this report, we develop an exact MFG test that is based on the permutation distribution of cell counts. We determine by simulation the type I error and power of both the exact MFG test and the asymptotic MFG test for four different biologically relevant scenarios: a test of child allelic effects in the presence of maternal allelic effects, a test of maternal allelic effects in the presence of child allelic effects, and tests of maternal-fetal genotype incompatibility with and without child allelic effects. These simulations show that, in general, the exact test is slightly conservative whereas the asymptotic test is slightly anti-conservative. However, the asymptotic MFG test produces significantly inflated type I error rates under conditions with extreme null allele frequencies and sample sizes of 75, 100, and 150. Under these conditions, the exact test is clearly preferred over the asymptotic test. Under all other conditions that we tested, the user can safely choose either the exact test or the asymptotic test. |
2,339,121 | Examination of the SGCE gene in Tourette syndrome patients with obsessive-compulsive disorder. | Mutations in the epsilon-sarcoglycan gene (SGCE) have been reported in families with myoclonus-dystonia (M-D). In addition to abnormal movements, obsessive-compulsive disorder (OCD) has also been described in families with M-D. OCD is a common feature in another movement disorder, namely Tourette syndrome (TS). The comorbidity of these disorders suggests that common genetic factors might be involved in their susceptibility. To evaluate this, we performed two sets of experiments. An association study using a polymorphism within an intron of the SGCE gene was assessed in patients with TS and OCD versus controls, and the SGCE gene itself was screened for mutations in all TS/OCD patients, followed by direct sequencing of the gene in a limited number of these patients. No correlation was found by either method. |
2,339,122 | Early hearing detection and intervention programs: opportunities for genetic services. | Congenital hearing loss is relatively frequent and has serious negative consequences if it is not diagnosed and treated during the first few months of life. Babies with hearing loss who are identified early and provided with appropriate intervention develop better language, cognitive, and social skills. As a result of improvements in screening equipment and procedures, newborn hearing screening programs have expanded rapidly in recent years, and almost 90% of all newborns are now screened for hearing loss before leaving the hospital. Because 50% or more of congenital hearing loss is due to genetic causes, providers of genetic services should play an increasingly important role in newborn hearing screening, diagnostic, and intervention services. For this to happen, parents, public health officials, and primary health care providers need to become better informed about the benefits of genetic services for children with hearing loss and their families. Providers of genetic services also need to become better informed about the current status of Early Hearing Detection and Intervention (EHDI) programs and how they can contribute to continued improvement of these programs. |
2,339,123 | Attitudes of deaf individuals towards genetic testing. | Recent advances have made molecular genetic testing for several forms of deafness more widely available. Previous studies have examined the attitudes of the deaf towards genetic testing, including prenatal diagnosis. This study examines the attitudes of deaf college students towards universal newborn hearing screening, including molecular testing for specific forms of deafness, as well as the utilization of genetic test results for mate selection. We found that there may be differences in the attitudes of deaf individuals who associate closely with the deaf community (DC), and those who have equal involvement with both the deaf and hearing communities (EIC). The majority perceived newborn hearing screening for deafness to be helpful. However, more members of the EIC than the DC groups support newborn testing for genes for deafness. While there was reported interest in using genetic testing for partner selection, most participants reported they would not be interested in selecting a partner to have children with a specific hearing status. The results of this study point out important differences that genetic professionals should be aware of when counseling deaf individuals. |
2,339,124 | Genetic heterogeneity in Usher syndrome. | Mutations in seven different genes have been associated with Usher syndrome, and an additional four loci have been mapped. The identified genes encode myosin VIIa, harmonin (a PDZ-domain protein), cadherin 23, protocadherin 15, sans (a scaffold-like protein), usherin and clarin. Three clinical types of Usher syndrome have been described: USH1 patients have severe to profound congenital hearing loss, vestibular dysfunction, and retinal degeneration beginning in childhood, those with USH2 have moderate to severe congenital hearing loss, normal vestibular function, and later onset of retinitis pigmentosa, and USH3 patients have progressive hearing loss, which distinguishes them from the other two types. The shaker-1, waltzer, Ames waltzer, and Jackson shaker mice provide murine models for four of the genetic forms of Usher syndrome. Ongoing studies are enabling early diagnosis of Usher syndrome in children who present with hearing loss, thus providing time to prepare for the onset of visual loss. |
2,339,125 | Clinical application of genetic testing for deafness. | Advances in the molecular biology of hearing and deafness have identified many genes essential for normal auditory function. Allele variants of these genes cause nonsyndromic deafness, making mutation screening a valuable test to unequivocally diagnose many different forms of inherited deafness. In this study, genetic testing of GJB2, SLC26A4 and WFS1 is reviewed. |
2,339,126 | Association of paraoxonase 1 gene polymorphisms with risk of Parkinson's disease: a meta-analysis. | Paraoxonase1 (PON1) gene polymorphisms were implicated as risk factors for Parkinson's disease (PD), but the results of case-control studies that investigated these associations were controversial. In order to provide an answer to these contradictory results, a meta-analysis of all available studies relating the PON1-55M/L and PON1-192Q/R polymorphisms to the risk of developing PD was conducted. The racial descent of the populations in these studies was Caucasian and Asian. The meta-analysis revealed that there was an association of the PON1-55M allele and the risk of developing PD relative to the L allele: fixed effects pooled odds ratio (OR)=1.32 [95%CI (1.10-1.59)]. In addition, there was evidence of association for the genotypic contrast PON1-55MM+LM relative to PON1-55LL: fixed effects OR=1.50 [95%CI (1.16-1.95)]. There was no significant association between PON1-192Q/R alleles and risk of developing PD: OR=1.09 [95%CI (0.93-1.26)]. There was no evidence for an association between the genotypic contrasts of PON1-192 and development of PD. The heterogeneity between studies and the publication bias were not significant ( P> or =0.10) in either polymorphism. Therefore, the pooled results of the meta-analysis supported that there was an association between PON1-55M/L polymorphism and PD and that PON1-192Q/R polymorphism was unlikely to be a major risk factor for susceptibility to PD. |
2,339,127 | A TP53-truncating germline mutation (E287X) in a family with characteristics of both hereditary diffuse gastric cancer and Li-Fraumeni syndrome. | Mutations in CDH1, which encodes E-cadherin, have been associated with hereditary diffuse gastric cancer (HDGC) in Western populations but have not been shown to play a major role in Asians. Recently, a patient with familial gastric cancer (FGC) was shown to harbor a germline mutation in the TP53 gene, which encodes p53 and has been previously associated with Li-Fraumeni Syndrome (LFS). To determine whether mutations in TP53 are associated with FGC in Asians, we screened the entire coding region of TP53 in probands from 23 Korean FGC families. We identified a nonsense (E287X) TP53 germline mutation in a family whose history is compatible with both HDGC and LFS. Two members of this family (SNU-G2) were afflicted with brain tumors, seven with gastric cancers, two with sarcomas, and one with both gastric cancer and a sarcoma. The E287X TP53 mutation segregated with the cancer phenotype in the family members from whom DNA samples were available. To our knowledge, this is the first report of a large family with both HDGC and LFS. Our results suggest that TP53 mutational screening in FGC families should be interpreted with caution because additional TP53 mutation-carrying HDGC families may also show LFS-related phenotypes. |
2,339,128 | Use of real-time PCR for determining copy number and zygosity in transgenic plants. | This review examines how real-time PCR can be used to determine copy number and zygosity in transgenic plants. Distinguishing between plants that harbor one and two copies of a transgene or are hemizygous and homozygous requires the ability to routinely distinguish twofold differences, a detection difference which approaches the resolution of PCR-based quantification methods. After explaining the basic principles, especially the threshold cycle (Ct value) as the basic measuring unit in real-time PCR, we introduce three quantitation methods currently in use. While the absolute and relative standard curve approaches are qualitative methods that distinguish high-copy from low-copy transformants, the comparative (2(-DeltaDeltaCt)) method with double-dye oligonucleotides (TaqMan probes) is able to detect twofold differences. In order to obtain reliable results, Ct values for an amplicon should be below 25 and the standard deviation below 0.3. Although real-time PCR can deliver exact copy number determinations, the procedure is not fail-safe. Therefore, real-time PCR should to be viewed as complementary to--rather than as a replacement of--other methods such as Southern analysis, but it is particularly useful as a preliminary screening tool for estimating copy numbers of a large number of transformants. |
2,339,129 | Genetic screening of infertile men. | Male infertility is an extraordinarily common medical condition, affecting 1 in 20 men. According to the World Health Organization, this condition is now considered to be a complex disease involving physical, genetic and environmental factors. With continuing advances in our understanding of male reproductive physiology and endocrinology, together with the availability of the complete sequence of the human genome and powerful functional genomic techniques, the stage is now set to identify the genes that are essential for spermatogenesis. Given that the process of spermatogenesis, from the germ cell to mature sperm, is complex, the challenge for research is to develop the strategies for identifying new genetic causes of idiopathic male infertility and defining genotypes associated with specific defects in semen parameters and testicular pathologies. Such information will form the basis of new genetic tests that will allow the clinician to make an accurate diagnosis of the male partner and a more informed decision about treatment options for the couple. |
2,339,130 | Causes of azoospermia and their management. | Azoospermia may occur because of reproductive tract obstruction (obstructive azoospermia) or inadequate production of spermatozoa, such that spermatozoa do not appear in the ejaculate (non-obstructive azoospermia). Azoospermia is diagnosed based on the absence of spermatozoa after centrifugation of complete semen specimens using microscopic analysis. History and physical examination and hormonal analysis (FSH, testosterone) are undertaken to define the cause of azoospermia. Together, these factors provide a >90% prediction of the type of azoospermia (obstructive v. non-obstructive). Full definition of the type of azoospermia is provided based on diagnostic testicular biopsy. Obstructive azoospermia may be congenital (congenital absence of the vas deferens, idiopathic epididymal obstruction) or acquired (from infections, vasectomy, or other iatrogenic injuries to the male reproductive tract). Couples in whom the man has congenital reproductive tract obstruction should have cystic fibrosis (CF) gene mutation analysis for the female partner because of the high risk of the male being a CF carrier. Patients with acquired obstruction of the male reproductive tract may be treated using microsurgical reconstruction or transurethral resection of the ejaculatory ducts, depending on the level of obstruction. Alternatively, sperm retrieval with assisted reproduction may be used to effect pregnancies, with success rates of 25-65% reported by different centres. Non-obstructive azoospermia may be treated by defining the cause of low sperm production and initiating treatment. Genetic evaluation with Y-chromosome microdeletion analysis and karyotype testing provides prognostic information in these men. For men who have had any factors potentially affecting sperm production treated and remain azoospermic, sperm retrieval from the testis may be effective in 30-70% of cases. Once sperm are found, pregnancy rates of 20-50% may be obtained at different centres with in vitro fertilisation and intracytoplasmic sperm injection. |
2,339,131 | Does heterozygosity estimate inbreeding in real populations? | Many recent studies report that individual heterozygosity at a handful of apparently neutral microsatellite markers is correlated with key components of fitness, with most studies invoking inbreeding depression as the likely underlying mechanism. The implicit assumption is that an individual's inbreeding coefficient can be estimated reliably using only 10 or so markers, but the validity of this assumption is unclear. Consequently, we have used individual-based simulations to examine the conditions under which heterozygosity and inbreeding are likely to be correlated. Our results indicate that the parameter space in which this occurs is surprisingly narrow, requiring that inbreeding events are both frequent and severe, for example, through selfing, strong population structure and/or high levels of polygyny. Even then, the correlations are strong only when large numbers of loci (~200) can be deployed to estimate heterozygosity. With the handful of markers used in most studies, correlations only become likely under the most extreme scenario we looked at, namely 20 demes of 20 individuals coupled with strong polygyny. This finding is supported by the observation that heterozygosity is only weakly correlated among markers within an individual, even in a dataset comprising 400 markers typed in diverse human populations, some of which favour consanguineous marriages. If heterozygosity and inbreeding coefficient are generally uncorrelated, then heterozygosity-fitness correlations probably have little to do with inbreeding depression. Instead, one would need to invoke chance linkage between the markers used and one or more gene(s) experiencing balancing selection. Unfortunately, both explanations sit somewhat uncomfortably with current understanding. If inbreeding is the dominant mechanism, then our simulations indicate that consanguineous mating would have to be vastly more common than is predicted for most realistic populations. Conversely, if heterosis provides the answer, there need to be many more polymorphisms with major fitness effects and higher levels of linkage disequilibrium than are generally assumed. |
2,339,132 | Germline MUTYH (MYH) mutations in Portuguese individuals with multiple colorectal adenomas. | Germinal mutations in the base excision repair (BER) gene MUTYH (MYH) have recently been described in association with predisposition to multiple colorectal adenomas and cancer. In contrast to the classic dominant condition of familial adenomatous polyposis (FAP) due to germinal mutations in the APC gene, the MYH polyposis is an autosomal recessive disease. The identification of individuals affected by MYH polyposis brings new and important implications for the diagnostic, screening, genetic counseling, follow up and therapeutic options in these patients. In this study, screening for germinal mutations in the MYH gene was performed in 53 Portuguese individuals with multiple colorectal adenomas or classic adenomatous polyposis, in whom no mutation had been identified in the APC gene. The results revealed the presence of biallelic germline MYH mutations in 21 patients. In addition, we here report 3 mutations (c.340T>C [p.Y114H]; c.503G>A [p.R168H]; and c.1186_1187insGG [p.E396fsX437]) which, to our knowledge, have not been previously described. |
2,339,133 | Identification of novel and rare mutations in California Hispanic and African American cystic fibrosis patients. | In ethnic heterogeneous California, complete genetic information is currently lacking to build solid population-based cystic fibrosis (CF) screening programs because a large proportion of mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR/ABCC7) are still unknown, especially in non-Caucasian patients. A total of 402 [46 African American+356 Hispanic] Hispanic and African American patients from California CF patient registry were included in this study. Patients with at least one unidentified mutant allele were asked to donate blood samples for further analysis, first by Genzyme Genetics for a panel of 87 known mutations, followed by temporal temperature gradient gel electrophoresis (TTGE) scanning of the entire coding exons of CFTR gene. A total of eight novel mutations; one missense mutation, one splice-site mutation and six frame-shift mutations were identified. In addition to the eight novel mutations, 20 [corrected] distinct rare mutations that are not in the current available commercial mutation panels were identified by TTGE. The overall detection rate was raised to 95.7% for African American and 94.5% for Hispanic. The discovery of recurrent rare and novel mutations improves the diagnosis and care of persons with CF and improves our ability to adequately and equitably provide screening and genetic counseling services to non-Caucasians. |
2,339,134 | GJB2: the spectrum of deafness-causing allele variants and their phenotype. | Genetic testing was completed on 1,294 persons with deafness referred to the Molecular Otolaryngology Research Laboratories to establish a diagnosis of DFNB1. Exon 2 of GJB2 was screened for coding sequence allele variants by denaturing high-performance liquid chromatography (DHPLC) complemented by bidirectional sequencing. If two deafness-causing mutations of GJB2 (encoding Connexin 26) were identified, further screening was not performed. If only a single deafness-causing mutation was identified, we screened for the g.1777179_2085947del (hereafter called del(GJB6-D13S1830); GenBank NT_024524.13) and mutations in the noncoding region of GJB2. Phenotype-genotype correlations were evaluated by categorizing mutations as either protein truncating or nontruncating. A total of 205 persons carried two GJB2 exon 2 mutations and were diagnosed as having DFNB1; 100 persons carried only a single deafness-causing allele variant of exon 2. A total of 37 of these persons were c.35delG carriers, and 51 carried other allele variants of GJB2. Persons diagnosed with DFNB1 segregating two truncating/nonsense mutations had a more severe phenotype than persons carrying two missense mutations, with mean hearing impairments being 88 and 37%, respectively (P < 0.05). The number of deaf c.35delG carriers was greater than expected when compared to the c.35delG carrier frequency in normal-hearing controls (P < 0.05), suggesting the existence of at least one other mutation outside the GJB2 coding region that does not complement GJB2 deafness-causing allele variants. |
2,339,135 | Women, pregnancy and serendipity: a personal story about the discovery of HLA. | The discovery of HLA was an adventure in many ways very much like the discovery of a new continent with many people entering it from different angles. This has been a truly global effort with laboratories from all over the world voluntarily collaborating. The picture that finally emerged of a highly complex genetic system and its role in biology and medicine was and is fascinating. I have been involved from almost the beginning in the HLA story and have watched--often from nearby--the breakthroughs insights that opened new aspects of HLA. A discovery is not a gradual process, but one, which goes with jumps and laps. I will therefore not give a chronological summing up what happened, but limit myself to turning points, the sudden flashes of insight, which made working in HLA so exciting and rewarding. |
2,339,136 | Analysis of polyglutamine-coding repeats in the TATA-binding protein in different neurodegenerative diseases. | Trinucleotide repeat (TNR) expansion in the gene for TATA binding protein (TBP) has recently been described as causal for spinocerebellar ataxia type 17. The normal number of repeats has been considered to be 42 or less. An intermediate range with reduced penetrance has been assumed to be 43-47 CAA/CAG repeats. We examined this gene in 30 patients with autosomal-dominant cerebellar ataxia (ADCA), 35 patients with sporadic ataxia, 11 patients with Huntington's disease (HD), 351 patients with idiopathic Parkinson's disease (PD), 105 patients with Alzheimer's disease (AD), and 291 controls with no history of neurodegenerative disease. Three patients (one with sporadic PD and two with AD) carrying more than 42 TNRs in the TBP gene were identified. This reveals that the phenotype associated with CAG/CAA expansion in the TBP gene may be heterogeneous. |
2,339,137 | A major QTL conditioning salt tolerance in S-100 soybean and descendent cultivars. | Deployment of salt tolerant cultivars is an effective approach to minimize yield loss in a saline soil. In soybean, Glycine max (L.) Merr., substantial genetic variation exists for salt response. However, breeding for salt tolerance is hampered because no economically viable screening method has been developed for practical breeding. To facilitate the development of an effective screening method for salt tolerance in soybean, the present study was conducted to determine the heritability of salt tolerance and to identify associated quantitative trait loci (QTL). F2:5 lines from the cross of 'S-100' (salt tolerant) x 'Tokyo' (salt sensitive) were evaluated in a saline field in Hyde County, N.C., USA, in 1999 and in a greenhouse located in Raleigh, N.C., USA, in 2001. S-100 and Tokyo are ancestors of popular soybean cultivars released for the southern USA. The visual salt tolerance ratings of the F2:5 lines ranged from 0 (complete death) to 5 (normal healthy appearance). The entry-mean heritability for salt tolerance was 0.85, 0.48, and 0.57 in the field (four replications), greenhouse (two replications), and combined environments, respectively. The genotypic correlation between field and greenhouse ratings was 0.55, indicating reasonably good agreement between the two screening environments. To identify QTL associated with salt tolerance, each line was characterized with RFLP markers and an initial QTL single-factor analysis was completed. These results were used to identify genomic regions associated with the trait and to saturate the selected genomic regions with SSR markers to improve mapping precision. Subsequently, a major QTL for salt tolerance was discovered near the Sat_091 SSR marker on linkage group (LG) N, accounting for 41, 60, and 79% of the total genetic variation for salt tolerance in the field, greenhouse, and combined environments, respectively. The QTL allele associated with tolerance was derived from S-100. Pedigree tracking was used to examine the association between the salt tolerance QTL and flanking SSR marker alleles in U.S. cultivars descended from S-100 or Tokyo through 60 years of breeding. The presence of alleles from S-100 at the Sat_091 and Satt237 marker loci was always associated with salt tolerance in descendants. Alleles from Tokyo for these same markers were generally associated with salt sensitivity in descendent cultivars. The strong relationship between the SSR marker alleles and salt tolerance suggests that these markers could be used for marker-assisted selection in commercial breeding. |
2,339,138 | Antimicrobial susceptibilities of invasive pediatric Abiotrophia and Granulicatella isolates. | Abiotrophia and Granulicatella species have been associated with various infections. Antimicrobial susceptibility data for these nutritionally variant streptococcus-like organisms, especially for pediatric isolates, are very limited. Little is known about the genetic bases of their resistance mechanisms. We report the results of identification to bacterial species level, antimicrobial susceptibility testing, macrolide resistance testing, and detection of genes encoding that resistance for a collection of 15 pediatric clinical isolates from normally sterile sites. Our results indicate that the prevalence of beta-lactam and macrolide resistance is high and that both erm and mef are found in these isolates. |
2,339,139 | Real-time fluorescence PCR assays for detection and characterization of heat-labile I and heat-stable I enterotoxin genes from enterotoxigenic Escherichia coli. | To facilitate the diagnosis of enterotoxigenic Escherichia coli (ETEC) infections in humans, we developed and evaluated real-time fluorescence PCR assays for the Roche LightCycler (LC) against the enterotoxin genes commonly present in strains associated with human illness. Separate LC-PCR assays with identical cycling conditions were designed for the type I heat-labile enterotoxin (LT I) and the type I heat-stable enterotoxin (ST I) genes, using the LC hybridization probe format. A duplex assay for ST I with two sets of amplification primers and three hybridization probes was required to detect the major nucleotide sequence variants of ST I, ST Ia and ST Ib. LC-PCR findings from the testing of 161 E. coli isolates of human origin (138 ETEC and 23 non-ETEC) were compared with those obtained by block cycler PCR analysis. The sensitivities and specificities of the LC-PCR assays were each 100% for the LT I and ST I genes. The LC-PCR and block cycler PCR assays were also compared for their abilities to detect LT I and ST I genes in spiked stool specimens with different methods of sample preparation. Findings from these experiments revealed that the limits of detection for the LC-PCR assays were the same or substantially lower than those observed for the block cycler PCR assay. Melting curve analysis of the amplified LT I and ST I genes revealed sequence variation within each gene, which for the ST I genes correlated with the presence of ST Ia and ST Ib. The rapidity, sensitivity, and specificity of the LC-PCR assays make them attractive alternatives to block cycler PCR assays for the detection and characterization of ETEC. |
2,339,140 | Plasmin deficiency does not alter endogenous murine amyloid beta levels in mice. | Deposition of amyloid beta (A beta) into extracellular plaques is a pathologic characteristic of Alzheimer's disease. Plasmin, neprilysin, endothelin-converting enzyme and insulin-degrading enzyme (IDE) have each been implicated in A beta degradation; data supporting the role of the latter three enzymes have included increased levels of endogenous murine A beta in mice genetically deficient for the respective enzyme. In this study, we sought to determine if plasminogen deficiency increases endogenous A beta. We report that plasminogen deficiency did not result in an A beta increase in the brain or in the plasma of adult mice. Hence, although plasmin is potentially important in the degradation of A beta aggregates, we interpret these data as suggesting that plasmin does not regulate steady-state A beta levels in non-pathologic conditions. |
2,339,141 | Autosomal dominant congenital nystagmus is not linked to 6p12, 7p11, and 15q11 in a German family. | Congenital nystagmus (CN) is an eye-movement disorder that usually starts within the first months of life. Autosomal dominant, autosomal recessive, and X-chromosomal pedigree patterns are observed. Causative genes are yet unknown. Several loci were implicated to contain disease-relevant genes for autosomal dominant CN (AD CN). AD CN cosegregated with a balanced translocation of 7;15 in a family. In a large black pedigree linkage was demonstrated to 6p12.</AbstractText>In this study, we describe a large German family with AD congenital nystagmus. Linkage of AD in this family was tested with previously implicated loci.</AbstractText>Affected family members and unaffected members underwent genetic analysis. Key family members underwent ophthalmologic testing and oculography.</AbstractText>No linkage of AD CN to the implicated loci on 6p12, and 7p11, and 15q11 was found in this study.</AbstractText>In the presented pedigree genes on 15q11, and on the assumption of full penetrance, 6p12 and 7p11 are not involved in the development of AD congenital nystagmus.</AbstractText> |
2,339,142 | Cell mediated immune response elicited in mice after immunization with the P64k meningococcal protein: epitope mapping. | The P64k protein of Neisseria meningitidis has been reported as an immunological carrier for weak immunogens. This investigation was aimed at characterizing the T-cell response produced in primed mice and at identifying T helper cell epitopes within this molecule. BALB/c mice subcutaneously immunized with the recombinant antigen provided inguinal lymph node cells (LNC) that proliferated in the presence of P64k in a dose-dependent manner. Proliferating cells secreted IL-4 while the concentration of IL-12 remained unaltered in the culture supernatant. By testing a panel of 59 overlapping synthetic peptides spanning the entire sequence of the antigen a T-cell determinant was localized. Prime-boost and lymphoproliferation experiments, conducted with highly purified synthetic peptides, confirmed that the segment including amino acids 470-485 comprises a T-cell epitope within the P64k molecule. |
2,339,143 | Data mining techniques for cancer detection using serum proteomic profiling. | Pathological changes in an organ or tissue may be reflected in proteomic patterns in serum. It is possible that unique serum proteomic patterns could be used to discriminate cancer samples from non-cancer ones. Due to the complexity of proteomic profiling, a higher order analysis such as data mining is needed to uncover the differences in complex proteomic patterns. The objectives of this paper are (1) to briefly review the application of data mining techniques in proteomics for cancer detection/diagnosis; (2) to explore a novel analytic method with different feature selection methods; (3) to compare the results obtained on different datasets and that reported by Petricoin et al. in terms of detection performance and selected proteomic patterns.</AbstractText>Three serum SELDI MS data sets were used in this research to identify serum proteomic patterns that distinguish the serum of ovarian cancer cases from non-cancer controls. A support vector machine-based method is applied in this study, in which statistical testing and genetic algorithm-based methods are used for feature selection respectively. Leave-one-out cross validation with receiver operating characteristic (ROC) curve is used for evaluation and comparison of cancer detection performance.</AbstractText>The results showed that (1) data mining techniques can be successfully applied to ovarian cancer detection with a reasonably high performance; (2) the classification using features selected by the genetic algorithm consistently outperformed those selected by statistical testing in terms of accuracy and robustness; (3) the discriminatory features (proteomic patterns) can be very different from one selection method to another. In other words, the pattern selection and its classification efficiency are highly classifier dependent. Therefore, when using data mining techniques, the discrimination of cancer from normal does not depend solely upon the identity and origination of cancer-related proteins.</AbstractText> |
2,339,144 | Only one of the two annotated Lactococcus lactis fabG genes encodes a functional beta-ketoacyl-acyl carrier protein reductase. | The small genome of the Gram-positive bacterium Lactococcus lactis ssp. lactis IL1403 contains two genes that encode proteins annotated as homologues of Escherichia coli beta-hydroxyacyl-acyl carrier protein (ACP) reductase. E. coli fabG encodes beta-ketoacyl-acyl carrier protein (ACP) reductase, the enzyme responsible for the first reductive step of the fatty acid synthetic cycle. Both of the L. lactis genes are adjacent to (and predicted to be cotranscribed with) other genes that encode proteins having homology to known fatty acid synthetic enzymes. Such relationships have often been used to strengthen annotations based on sequence alignments. Annotation in the case of beta-ketoacyl-ACP reductase is particularly problematic because the protein is a member of a vast protein family, the short-chain alcohol dehydrogenase/reductase (SDR) family. The recent isolation of an E. coli fabG mutant strain encoding a conditionally active beta-ketoacyl-ACP reductase allowed physiological and biochemical testing of the putative L. lactishomologues. We report that expression of only one of the two L. lactis proteins (that annotated as FabG1) allows growth of the E. coli fabG strain under nonpermissive conditions and restores in vitro fatty acid synthetic ability to extracts of the mutant strain. Therefore, like E. coli, L. lactis has a single beta-ketoacyl-ACP reductase active with substrates of all fatty acid chain lengths. The second protein (annotated as FabG2), although inactive in fatty acid synthesis both in vivo and in vitro, was highly active in reduction of the model substrate, beta-ketobutyryl-CoA. As expected from work on the E. coli enzyme, the FabG1 beta-ketobutyryl-CoA reductase activity was inhibited by ACP (which blocks access to the active site) whereas the activity of FabG2 was unaffected by the presence of ACP. These results seem to be an example of a gene duplication event followed by divergence of one copy of the gene to encode a protein having a new function. |
2,339,145 | Characterization of the human nasal embryonic LHRH factor gene, NELF, and a mutation screening among 65 patients with idiopathic hypogonadotropic hypogonadism (IHH). | As the mouse nasal embryonic LHRH factor gene (Nelf) encodes a guidance molecule for the migration of the olfactory axon and gonadotropin-releasing hormone neurons, its human homolog, NELF, is a candidate gene for Kallmann syndrome, a disease of idiopathic hypogonadotropic hypogonadism (IHH) with anosmia or hyposmia. We report here characterization of NELF and results of mutation analysis in 65 IHH patients. Assembling EST clones, RACE, and sequencing showed that NELF mapped to 9q34.3 is composed of 16 exons and 15 introns with a 1,590-bp ORF encoding 530 amino acids. RT-PCR on a fetal brain cDNA library revealed five alternatively spliced variants. Among them, NELF-v1 has 93-94% identity at the amino acid level to mouse/rat Nelf, and four other transcripts are also highly conserved among the three species. A 3.0-kb transcript is expressed most highly in the adult and fetal brain, testis, and kidney, indicating that NELF plays a role in the function of these tissues. Mutation screening detected in a patient with IHH one novel heterozygous missense mutation (1438A>G, T480A) at the donor-splice site in exon 15 of NELF. As this mutation was not found in 100 normal control individuals, T480A may be associated with IHH. Four other novel SNPs (102C > T and 1029C > T within the coding region, and two IVS14+47C > T and IVS15+41G > A) were also identified in NELF. |
2,339,146 | Relational ethics and genetic counseling. | Genetic counseling is viewed as a therapeutic interrelationship between genetic counselors and their clients. In a previous relational ethics research project, various themes were identified as key components of relational ethics practice grounded in everyday health situations. In this article the relational ethics approach is further explored in the context of genetic counseling to enhance our understanding of how the counselor-client relationship is contextually developed and maintained. Qualitative interviews were conducted with six adult clients undergoing genetic counseling for predictive testing. Engagement, dialogue and presence were revealed as relevant to genetic counselor-client relationships. A relational ethics approach in genetic counseling challenges the concept of nondirectiveness and may enhance the outcome of counseling for both counselor and client. |
2,339,147 | The diagnostic significance of the detection of cytokeratin 19 mRNA by quantitative RT-PCR in benign and malignant pleural effusions. | To evaluate the diagnostic significance of detecting cytokeratin 19 (CK19) mRNA by quantitative reverse transcription polymerase chain reaction (RT-PCR) in benign and malignant pleural effusions.</AbstractText>CK19 mRNA was examined by quantitative RT-PCR and CK19 was detected by Enzyme-linked immunoadsorbent assay (ELISA) in 32 patients with malignant pleural effusions and 35 patients with benign pleural effusions.</AbstractText>On the threshold of 200 copies/microl, the positive rate of CK19 mRNA in patients with malignant pleural effusions was 62.5%. The positive rates of CK19 mRNA and CK19 in the malignant pleural effusions were significantly higher than those in the benign group (P<0.01). Furthermore, the positive rate of CK19 mRNA was higher than that of CK19 in the malignant group (P<0.05).</AbstractText>Detection of CK19 mRNA can be a promising diagnostic marker in differential diagnosis of benign and malignant pleural effusions.</AbstractText> |
2,339,148 | [The supply of breast/ovarian cancer genetic susceptibility tests in France]. | One example of the recent advances of scientific research on the human genome is the identification of two susceptibility genes to breast/ovarian cancer, BRCA1 and BRCA2, making possible the introduction in medical practices of genetic testing to detect patients with an increased risk of developing such cancers. In this context of diffusion, two surveys were carried out to appraise the activity profiles in 1998 and in 2001 of all the different participants in those new medical practices in France, physicians in charge of genetic counselling, medical centres where consultations take place and laboratories. Results show that over the period 1998-2001, few changes occurred, mainly the reduction of the average waiting time to get the result of a genetic test, the increase in the annual number of BRCA2 families identified to a level similar to the one of BRCA1 and the automation of the biological analyses without noting a considerable increase in the annual output of laboratories till 2001 however. This surprising moderate evolution must be connected to the existence of some particular external factors making the framework of the development of these new medical and biological practices and their future really uncertain. The diffusion of BRCA1/2 genetic testing has been carried out facing the traditional difficulties of any innovating activities, but also the uncertainties related to intellectual property rights on genes and the reimbursement of genetic counselling and biological testing. These uncertainties have certainly restrained the pace of change as many actors in this field have opted for a wait and see strategy bearing in mind the possible future constraints imposed to their future activity, especially if European patents on the BRCA1/2 genes are finally granted by the European patent office (EPO). |
2,339,149 | Genetic practice, education, and research: an overview for advanced practice nurses. | <AbstractText Label="PURPOSE/OBJECTIVES" NlmCategory="OBJECTIVE">The purpose of this article is to describe how the new genomic era will affect advanced practice registered nurses (APRNs) patient care, education, and research.</AbstractText><AbstractText Label="BACKGROUND/RATIONALE" NlmCategory="BACKGROUND">Given the exponential growth of genetic information and that 9 of the top 10 leading causes of mortality have genetic components (www.cdc.gov), it is imperative to educate advanced practice nurses about this salient topic.</AbstractText>Because few APRNs in practice or academia have had formal education on genetics, the first step of nursings' own gene discovery is recognizing that there is an ongoing need to understand state of the science genetic information to gain clinical and educational utility.</AbstractText>By recognizing APRNs need to know genetics, APRNs will clamor within their workplace for continuing education about this dynamic information. It is critical knowledge for APRNs to classify risk based on family history, target individualized patient prevention and education, modify pharmacologic interventions, and refer when genetic testing is necessary.</AbstractText><AbstractText Label="INTERPRETATION/CONCLUSION" NlmCategory="CONCLUSIONS">This article stresses the timely relevance of applying genetics and genomics to practice, teaching, and research.</AbstractText>APRNs need to maintain a place at the genetic table with all healthcare providers by developing strategies to expand this nursing knowledge to their practice, teaching, and research. Nurses need to be cognizant of the keen genetic value of family histories, how risk classification will individualize prevention recommendations, and the exciting role of pharmacogenetics, given many APRNs' prescriptive authority. Our core professional belief that each human is highly unique has probably never been more accurate than with the future in genetic and genomic nursing.</AbstractText> |
2,339,150 | [A family of acute intermittent porphyria]. | A 62-year-old man who had twice received laparotomies for abdominal pain of unknown origin was admitted to our hospital with acute abdominal pain. His family history of acute intermittent porphyria (AIP) suggested that it arose from acute porphyria. We treated the patient with 5% glucose solution by i.v. drip infusion and his abdominal pain improved rapidly. Diagnosis of AIP was established by the demonstration of reduced erythrocyte porphobilinogen deaminase (PBGD) activity and a point mutation (CAG --> CGG) in a splicing site in intron 10/exon 11 in the PBGD gene by DNA analysis. For screening of AIP carriers in his family, we measured erythrocyte PBGD activity. Four of his seven children were successfully diagnosed as AIP carriers. This is the ninth AIP family report, in which a mutation in the PBGD gene was revealed by DNA analysis. |
2,339,151 | Macrophage-specific overexpression of human matrix metalloproteinase-12 in transgenic rabbits. | Increased matrix metalloproteinase-12 (MMP-12) has been implicated in atherosclerosis and many other inflammatory processes. To define MMP-12 functions in vivo, we generated transgenic rabbits that expressed human (h) MMP-12 gene under the control of a macrophage-specific promoter, the human scavenger receptor promoter. Two transgenic founder rabbits were found to have hMMP-12 transgene integration by Southern blot analysis. hMMP-12 mRNA was expressed in peritoneal and alveolar macrophages, and in tissues enriched in macrophages in transgenic rabbits. High levels of hMMP-12 protein were detected in the conditioned media of cultured peritoneal and alveolar macrophages from transgenic rabbits. Zymography showed that hMMP-12 secreted from macrophages possessed enzymatic activity toward beta-casein. To evaluate the expression of hMMP-12 in inflammatory sites, we used carrageenan-induced granulomas as an in vivo model for tissue macrophages and foam cells. Granuloma size in transgenic rabbits was significantly increased compared to that in control rabbits, and histological examination revealed that granulomas of transgenic rabbits were enriched in macrophages associated with increased hMMP-12 expression. We believe that this transgenic rabbit model with increased expression of hMMP-12 may become a useful model for further mechanistic studies of MMP-12 in inflammatory diseases and cancer invasion; it is also an ideal model for testing the in vivo action of MMP-12 inhibitors. |
2,339,152 | Genetic aspects of Alzheimer's disease, Pick's disease, and other dementias. | Although genetic testing is available for some degenerative diseases, in most types of dementia, both genetic and environmental factors are involved. Overall, dementing diseases can be either sporadic or inherited, and in general, the earlier the onset, the more likely a disease is to be inherited. Before genetic testing is performed, the ethical issues, such as the effect the tests might have on asymptomatic children, should be considered. The ethical use of DNA samples in research is another genetic testing issue to be considered. |
2,339,153 | Identifying patterns of DNA for tumor diagnosis using capillary electrophoresis-amplified fragment length polymorphism (CE-AFLP) screening. | Amplified Fragment Length Polymorphism (AFLP) screening is a genome-wide genotyping strategy that has been widely used in plants and bacteria, but little has been reported concerning its use in humans. We investigated if the AFLP procedure could be coupled with high-throughput capillary electrophoresis (CE) for use in tumor diagnosis and classification. Using CE-AFLP, a series of molecular 'fingerprints' were generated for a set of gastric tumor and normal genomic DNA samples. The CE-AFLP procedure was qualitatively and quantitatively robust, and a variety of clustering tools were used to identify a specific DNA marker 'pattern' of 20 features that classified the tumor and normal samples to reasonable degrees of accuracy (Sensitivity 95%, Specificity 80%). The CE-AFLP-based approach also correctly classified 16 tumor samples, which in a previous study had exhibited no detectable genomic aberrations by comparative genome hybridization (CGH). This is the first reported application of CE-AFLP screening in tumor diagnosis. As the procedure is relatively inexpensive and requires minimal prior sequence knowledge and biological material, we suggest that CE-AFLP-based protocols may represent a promising new approach for DNA-based cancer screening and diagnosis. |
2,339,154 | Genotypic and phenotypic biomarker profiles for individual risk assessment and cancer detection (lessons from bladder cancer risk assessment in symptomatic patients and workers exposed to benzidine). | There is a need for improved methods for detecting individuals at risk for cancer to target subsets of patients for more intensive individual screening and targeted cancer therapy and chemoprevention. One approach for accomplishing this objective is to detect premalignant molecular fingerprints in an organ at risk for cancer or to define biomarkers reflective of treatment selection and response. Bladder cancer is an excellent model for testing this approach; however, comprehending the strategy for biomarker selection and analysis is more complicated than is generally appreciated. The objective of this article is to provide a succinct overview of our experience with the selection of biomarkers for bladder cancer detection, first in symptomatic patients and then in high-risk cohorts of workers at risk for bladder cancer. Biomarker selection depends on multiple parameters, each of which must be optimized to enhance the utility of a biomarker for clinical application. Many markers that initially show promise fail in the clinical arena for a variety of reasons. Important parameters include when a biomarker is expressed in carcinogenesis (i.e., early vs. late), the sample type, and the method of analysis. These all contribute to the sensitivity, specificity, and ultimate clinical utility of a biomarker. New technologies/ support the notion that all diseases start in the cell, and Seymore West indicated the cell, under appropriate conditions, can function as a microcuvette for biophysical cytochemical analysis. Spectroscopy provides an accurate and sensitive method for quantitative single-cell proteomics. Improved and more stable fluorescence probes will enhance the utility of cellular chemistry, as will a rationale approach for biomarker selection based on the concepts of field cancerization, complemented by improved quantitative analysis of protein markers at the single-cell level. Our laboratory has developed a platform for single-cell proteomic analysis that can be applied to multiple basic science and clinical problems. Single-cell proteomics also facilitates the study of genetic instability and epigenetic signaling (stromal-epithelial interactions) in relation to cancer therapy and diagnosis. Because most cancers arise through multiple signaling pathways and are heterogeneous, the identification of appropriate biomarker profiles provides a number of strategic advantages over a single biomarker. Complex networks of signaling pathways lead to increased cell proliferation, decreased cell adhesion, cellular differentiation, genetic instability, and other functions associated with the malignant phenotype. The purpose of this presentation is to illustrate the fundamental concepts for selection and profile analysis of high-level phenotypic biomarkers developed for bladder cancer risk assessment, screening, and early bladder cancer detection. |
2,339,155 | Alternatives to growth hormone stimulation testing in children. | Despite more than 40 years of pediatric growth hormone (GH) replacement, we are still limited in our ability to make a definitive diagnosis of GH deficiency (GHD) in children. Historically, GH stimulation tests (GHSTs) have been used to discriminate between GHD and idiopathic short stature. Over the years, increases in the peak diagnostic GH cutoffs and the proliferation of GH assays have fundamentally changed the nature of the GHST. In our opinion, today's GHSTs lack reproducibility and accuracy, are expensive, and can be dangerous. Moreover, newer diagnostic tools, such as high-resolution neuroimaging, measurements of serum insulin-like growth factor 1 and insulin-like growth factor-binding protein 3, and an increasing number of genetic tests, have emerged. We believe that it is no longer appropriate to use GHSTs to diagnose childhood GHD. Instead, diagnosis should be based on a combination of auxological, biochemical, neuroradiological and genetic considerations. Here, we examine the alternatives to the GHST that are currently available and literature that supports their use. We believe that these alternative methods should replace the GHST. |
2,339,156 | Oculomotor control in asymptomatic and recently diagnosed individuals with the genetic marker for Huntington's disease. | We compared oculomotor control among individuals in the early stages of Huntington's disease (HD), with that of individuals who are presymptomatic HD gene carriers (PSGC) and nongene carriers (NGC). The oculomotor testing paradigm included both traditional tests and a novel experimental procedure to assess visual scanning. Traditional tests elicited saccades, pursuit and optokinetic nystagmus (OKN). HD patients demonstrated marked delay in the initiation of volitional saccades (anti-saccade and memory-guided saccades), a reduced number of correct volitional saccades, reduced velocity of saccades, and a decreased OKN gain. We also studied visual scanning while the participants completed the Digit Symbol Subscale of the Wechsler Adult Intelligence Survey-Revised (WAIS-R). The HD participants demonstrated an abnormal gaze strategy, which may be associated with attention and/or planning deficits. Differences between the PSGC and NGC groups were only observed for two measures: PSGC had a decreased number of memory-guided saccades and a subtle delay in the initiation of volitional saccades. Our results suggest that oculomotor measures are a sensitive biomarker in the early stage of HD and demonstrate that the combination of more traditional oculomotor tests with visual scanning tests is useful in the evaluation of visual performance. |
2,339,157 | Informativeness of linkage analysis for genetic diagnosis of haemophilia A in India. | The objective of this study was to assess the frequency of factor VIII (FVIII) gene intron 1 and intron 22 inversions and the informativeness of polymorphic markers for the genetic diagnosis of patients with haemophilia A (HA). Fifty unrelated patients with HA were first assessed for the intron 1 and intron 22 inversion mutations. Inversion-negative families were then screened for the bi-allelic intragenic markers--intron 7 G-->A polymorphism, HindIII site in intron 19 and XbaI site in intron 22 and the multiallelic dinucleotide CA repeat alleles in introns 13 and 22. The extragenic, multiallelic VNTR DXS52 (st14) was also analysed. Intron 22 inversion mutation was found in 38% (n = 19) of all patients and 46% of those with severe HA. Intron 1 inversion was found in one (2%) patient. Of the 30 inversion-negative families, XbaI site polymorphism was the single most informative marker (70%, n = 21/30) followed by HindIII (60%, n = 18/30), intron 13 CA repeats (56.66%, n = 17/30), intron 22 CA repeats (50%, n = 15/30), DXS52 VNTR (23.33%, n = 7/30) and intron 7 G-->A polymorphism (6.66%, n = 2/30). The combined use of these markers was informative in 92% (n = 46/50) of HA families. Based on the informativeness of these markers a comprehensive algorithm has been proposed for genetic diagnosis of HA in India. |
2,339,158 | A novel missense mutation A1081P in the cystic fibrosis transmembrane conductance regulator (CFTR) gene identified in a Laotian patient with congenital bilateral absence of the vas deferens. | Cystic fibrosis is the most common autosomal disorder in the Caucasion population. However, the disease is rare in Asia and little is known about the spectrum of CF transmembrane conductance regulator, CFTR, mutations in this population. We studied a 39-year-old Loatian patient with congenital bilateral absence of the vas deferens and identified a novel missense mutation in exon 17b (3373G>C). Identification of novel mutations in this Asian population is of particular interest when designing a genetic testing strategy in Asian countries and also in other countries where immigration from Asia is common. |
2,339,159 | Isolation from cochlea of a novel human intronless gene with predominant fetal expression. | We have cloned a novel human gene, designated PFET1 (predominantly fetal expressed T1 domain) (HUGO-approved symbol KCTD12 or C13orf2), by subtractive hybridization and differential screening of human fetal cochlear cDNA clones. Also, we have identified the mouse homolog, designated Pfet1. PFET1/Pfet1 encode a single transcript of approximately 6 kb in human, and three transcripts of approximately 4, 4.5, and 6 kb in mouse with a 70% GC-rich open reading frame (ORF) consisting of 978 bp in human and 984 bp in mouse. Both genes have unusually long 3' untranslated (3' UTR) regions (4996 bp in human PFET1, 3700 bp in mouse Pfet1) containing 12 and 5 putative polyadenylation consensus sequences, respectively. Pfetin, the protein encoded by PFET1/Pfet1, is predicted to have 325 amino acids in human and 327 amino acids in mouse and to contain a voltage-gated potassium (K+) channel tetramerization (T1) domain. Otherwise, to date these genes have no significant homology to any known gene. PFET1 maps to the long arm of human chromosome 13, in band q21 as shown by FISH analysis and STS mapping. Pfet1 maps to mouse chromosome 14 near the markers D14Mit8, D14Mit93, and D14Mit145.1. The human 6 kb transcript is present in a variety of fetal organs, with highest expression levels in the cochlea and brain and, in stark contrast, is detected only at extremely low levels in adult organs, such as brain and lung. Immunohistochemistry with a polyclonal antibody raised against a synthetic peptide to PFET1 sequence (pfetin) reveals immunostaining in a variety of cell types in human, monkey, mouse, and guinea pig cochleas and the vestibular system, including type I vestibular hair cells. |
2,339,160 | [Genetics in movement disorders--dystonia, tremor and chorea]. | Several dystonias, Huntington's disease, essential tremor and various rare conditions are among the hereditary movement disorders, disorders with considerable genetic and clinical heterogeneity. It may be hoped that better understanding of the genetics and pathogenetic mechanisms involved will improve management.</AbstractText>This review is based on personal experience and recent literature.</AbstractText>At least 13 types of dystonias are genetically defined. DYT 1 seems to be the most important, and is easily tested. The Huntington gene is readily available for symptomatic as well as presymptomatic testing. Presymptomatic testing gives rise to ethical concerns and require thorough genetic counselling. Also essential tremor seems to show an autosomal dominant inheritance, but the responsible gene(s) has not been identified.</AbstractText>As for other movement disorders, involvement of different genes may give similar phenotypes and defects in a single gene give rise to various different phenotypes.</AbstractText> |
2,339,161 | A novel mutation in IFN-gamma receptor 2 with dominant negative activity: biological consequences of homozygous and heterozygous states. | We identified two siblings homozygous for a single base pair deletion in the IFN-gammaR2 transmembrane domain (791delG) who presented with multifocal Mycobacterium abscessus osteomyelitis (patient 1) and disseminated CMV and Mycobacterium avium complex infection (patient 2), respectively. Although the patients showed no IFN-gammaR activity, their healthy heterozygous parents showed only partial IFN-gammaR activity. An HLA-identical bone marrow transplant from the mother led patient 1 to complete hemopoietic reconstitution, but only partial IFN-gammaR function. We cloned and expressed fluorescent fusion proteins of the wild-type IFN-gammaR2, an IFN-gammaR2 mutant previously described to produce a complete autosomal recessive deficiency (278del2), and of 791delG to determine whether the intermediate phenotype in the 791delG heterozygous state was caused by haploinsufficiency or a dominant negative effect. When cotransfected together with the wild-type vector into IFN-gammaR2-deficient fibroblasts, the fusion protein with 791delG inhibited IFN-gammaR function by 48.7 +/- 5%, whereas fusion proteins with 278del2 had no inhibitory effect. Confocal microscopy of 791delG fusion proteins showed aberrant diffuse intracellular accumulation without plasma membrane localization. The fusion protein created by 791delG did not complete Golgi processing, and was neither expressed on the plasma membrane, nor shed extracellularly. The mutant construct 791delG exerts dominant negative effects on IFN-gamma signaling without cell surface display, suggesting that it is acting on pathways other than those involved in cell surface recognition of ligand. |
2,339,162 | Current advances in the human lupus genetics. | Genetic predisposition has been firmly established as a key element in susceptibility to systemic lupus erythematosus (SLE). During the past three decades, association studies have assessed many genes for potential roles in predisposing to SLE. These studies have identified a few risk factors including hereditary deficiency of complement components, major histocompatibility complex class II alleles, and allelic variants for the Fc portion of IgG (FCGR) genes. In recent years, a few groups have completed linkage analyses in data sets from families containing multiple members affected with SLE. Results from these initial genome scans are encouraging; approximately eight chromosomal regions have been identified exhibiting evidence for significant linkage to SLE and have been confirmed using independent cohorts (1q23, 1q25-31, 1q41-42, 2q35-37, 4p16-15.2, 6p11-21, 12q24, and 16q12), suggesting the high likelihood of the presence of one or multiple SLE susceptibility genes at each locus. Another approach of linkage analyses conditioned on pedigrees where one affected member manifesting a particular clinical condition has also identified many chromosomal regions linked to SLE. Within several established susceptibility loci, evidence for association of positional candidate genes is emerging. Within 2q35-37, an intronic single nucleotide polymorphism (SNP) of the positional candidate gene program cell death 1 gene has been associated with SLE susceptibility. The SLE-associated SNP affects a transcription factor, RUNX1, binding site. Recently, SNPs of novel positional candidate genes that influence RUNX1 binding motifs have also been associated with other autoimmune diseases, suggesting the possibility of a common theme shared among susceptibility genes for autoimmune diseases. In the coming years, susceptibility genes responsible for the observed linkage will be identified, and will lead to further delineating genetic pathways involved in susceptibility to SLE. |
2,339,163 | Cost analysis of DNA-based testing in a large Canadian family with multiple endocrine neoplasia type 2. | One of the major goals of genetic testing is the reduction of morbidity and mortality. Given the appropriate circumstances, this can result in reduction in health care costs. Such savings can be demonstrated most effectively in large families with mutations in well characterized, dominantly acting genes. In our large family, a point mutation TGC>CGC in exon 10 of the RET proto-oncogene, which results in a missense mutation (Cys620Arg), was identified in two individuals. The proband has medullary thyroid carcinoma (MTC), as did her deceased mother. One son has MTC and Hirschsprung's disease. The proband's mother had nine siblings; the proband has three siblings, another son, and 69 maternal cousins. Genetic testing has been performed on the closest relatives and has identified four individuals with, and 54 individuals without, a familial RET mutation. Significant cost savings have been realized in both genetic testing and clinical surveillance. In this family, for every at-risk individual identified as a true-negative, the minimum yearly savings in clinical surveillance is 508 dollars per person. As demonstrated by this case, economic costs of genetic diagnostics should take into account the potential saved monies in tests, both molecular and clinical. |
2,339,164 | Genetic discrimination: the clinician perspective. | Clinicians attending continuing education sessions in California were surveyed about their beliefs and attitudes regarding genetic discrimination and their knowledge of protective legislation. Two hundred seventy-one surveys were collected from physicians (n = 191) and nurses (n = 80). Most respondents lacked information or were misinformed about the existence of protective legislation (58.3%) or published cases of insurance discrimination (85.2%); 52.4% believed that mutation carriers have difficulty obtaining health insurance; 13% would not encourage genetic testing, despite a family history of cancer. Clinician concerns about potential genetic discrimination, and lack of information regarding protective legislation, may influence access to care. |
2,339,165 | Will the new cytogenetics replace the old cytogenetics? | With the advent of array-based comparative genomic hybridization technology, the analog cytogenetic analysis that has been used for the past 100 years could be replaced by the quantitative, microarray-based molecular analysis. Major advantages of the new array-based cytogenetic technologies are the high resolution and the high throughput. This technology is the first to offer an autonomous whole-chromosome analysis in one hybridization reaction for the detection of submicroscopic gains/losses. However, as with any new technology, it needs to be validated with regard to its performance in various applications (e.g. clinical genetic testing and cancer applications), comparative cost, and the data interpretation. |
2,339,166 | Prevalence of drug resistance and newly recognised treatment-related substitutions in the HIV-1 reverse transcriptase and protease genes from HIV-positive patients naïve for anti-retrovirals. | The aim of this study was to assess the prevalence of genetic changes in either the HIV reverse transcriptase (RT) or protease (Pro) genes in a cohort of patients naïve for anti-retroviral therapy. Of 61 patients, 43 (70.5%) were infected with HIV strains harbouring at least one resistance-related mutation, with 41 (67.2%) harbouring newly recognised treatment-related mutations. Among the 61 patients, the prevalence of specific mutations in the RT gene was as follows: 39A, 1.6%; 43E, 1.6%; and 228H, 1.6%. The prevalence of specific mutations in the Pro gene was as follows: 11I, 1.6%; 13V, 26.2%; 35D, 19.6%; 45R, 1.6%; 58E, 1.6%; 62V, 31%; 72V, 11.4%; 72M, 6.5%; 72T, 3.2%; 75I, 1.6%; and 89M, 13%. A higher prevalence of newly recognised mutations was found in strains from patients infected through sexual practices (30/36 = 83.4% vs. 11/25 = 44%; p 0.0023; OR 10.91; 95% CI 3.14-40.39). These findings support the use of resistance testing in patients naïve for anti-retroviral therapy, and suggest that the possible impact of newly recognised treatment-related mutations on clinical outcome requires further investigation. |
2,339,167 | An analysis of reference laboratory (send out) testing: an 8-year experience in a large academic medical center.<Pagination><StartPage>216</StartPage><EndPage>219</EndPage><MedlinePgn>216-9</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Utilization of outside reference laboratories for selected laboratory testing is common in the United States. However, relatively little data exist in the literature describing the scope and impact of these services. In this study, we reviewed use of reference laboratory testing at the Massachusetts General Hospital, a large urban academic medical center in Boston, Massachusetts.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">A retrospective review of hospital and laboratory administrative records over an 8-year period from fiscal years (FY) 1995-2002.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Over the 8 years studied, reference laboratory expenses increased 4.2-fold and totaled 12.4% of the total laboratory budget in FY 2002. Total reference laboratory test volume increased 4-fold to 68,328 tests in FY 2002 but represented only 1.06% of the total test volume in the hospital. The menu of reference laboratory tests comprised 946 tests (65.7% of the hospital test menu) compared to 494 (34.3%) of tests performed in house. The average unit cost of reference laboratory tests was essentially unchanged but was approximately 13 times greater than the average unit cost in the hospital laboratory. Much of the growth in reference laboratory cost can be attributed to the addition of new molecular, genetic, and microbiological assays. Four of the top 10 tests with the highest total cost in 2002 were molecular diagnostic tests that were recently added to the test menu.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Reference laboratory testing comprises a major component of hospital clinical laboratory services. Although send out tests represent a small percentage of the total test volume, these services account for the majority of the hospital laboratory test menu and a disproportionate percentage of laboratory costs.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>MacMillan</LastName><ForeName>Donna</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lewandrowski</LastName><ForeName>Elizabeth</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Lewandrowski</LastName><ForeName>Kent</ForeName><Initials>K</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Clin Leadersh Manag Rev</MedlineTA><NlmUniqueID>100900959</NlmUniqueID><ISSNLinking>1527-3954</ISSNLinking></MedlineJournalInfo><MeshHeadingList><MeshHeading><DescriptorName UI="D000046" MajorTopicYN="N">Academic Medical Centers</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D001900" MajorTopicYN="N">Boston</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003659" MajorTopicYN="N">Decision Making, Organizational</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017721" MajorTopicYN="N">Hospital Costs</DescriptorName><QualifierName UI="Q000706" MajorTopicYN="N">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007755" MajorTopicYN="N">Laboratories, Hospital</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName><QualifierName UI="Q000706" MajorTopicYN="Y">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015205" MajorTopicYN="N">Northwestern United States</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020416" MajorTopicYN="N">Outsourced Services</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName><QualifierName UI="Q000706" MajorTopicYN="Y">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010337" MajorTopicYN="N">Pathology Department, Hospital</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName><QualifierName UI="Q000706" MajorTopicYN="Y">statistics & numerical data</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014600" MajorTopicYN="Y">Utilization Review</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>9</Month><Day>10</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>12</Month><Day>31</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2004</Year><Month>9</Month><Day>10</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15354811</ArticleId></ArticleIdList></PubmedData></PubmedArticle><PubmedArticle><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15354386</PMID><DateCompleted><Year>2004</Year><Month>10</Month><Day>05</Day></DateCompleted><DateRevised><Year>2019</Year><Month>10</Month><Day>26</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0303-6995</ISSN><JournalIssue CitedMedium="Print"><Issue>68</Issue><PubDate><Year>2004</Year></PubDate></JournalIssue><Title>Journal of neural transmission. Supplementum</Title><ISOAbbreviation>J Neural Transm Suppl</ISOAbbreviation></Journal>Screening for mutations in synaptotagmin XI in Parkinson's disease. | Parkinson's disease (PD) is characterized by selective degeneration of neurons in the substantia nigra and subsequent dysfunction of dopaminergic neurotransmission. Genes identified in familial forms of PD encode proteins that are linked to the ubiquitin-proteasome system indicating the pathogenic relevance of disturbed protein degradation in PD. Some of them, i.e. alpha-synuclein, parkin and synphilin-1, have been implicated in presynaptic neurotransmission based on their localization in synaptic vesicles. Synaptotagmin XI is linked to the pathogenesis of PD based on its identification as a substrate of the ubiquitin-E3-ligase parkin. Moreover synaptotagmin XI is involved in the maintainance of synaptic function and represents a component of Lewy bodies (LB) in brains of PD patients. Therefore, we performed a detailed mutation analysis of the synaptotagmin XI gene in a large sample of 393 familial and sporadic PD patients. We did not find any disease causing mutations arguing against a major role of mutations in the synaptotagmin XI gene in the pathogenesis of PD. |
2,339,168 | Molecular screening for diseases frequent in Ashkenazi Jews: lessons learned from more than 100,000 tests performed in a commercial laboratory. | To determine the frequency of carriers of Ashkenazi Jewish (AJ) genetic diseases in the US population and compare these numbers with previously published frequencies reported in smaller more isolated cohorts.</AbstractText>A database containing more than 100,000 genotyping assays was queried. Assays for 10 separate AJ genetic diseases where comparisons were made with published data.</AbstractText>As expected, we observed lower carrier frequencies in a general, US population than those reported in literature. In 2427 patients tested for a panel of 8 AJ diseases, 20 (1:121) were carriers of two diseases and 331 (1:7) were carriers of a single disease. Fifty-three of 7184 (1:306) individuals tested for Gaucher disease had 2 Gaucher Disease mutations indicating a potentially affected phenotype.</AbstractText>As the number of AJ diseases increases, progressively more individuals will be identified as carriers of at least one disease.</AbstractText> |
2,339,169 | Preconception and prenatal cystic fibrosis carrier screening of African Americans reveals unanticipated frequencies for specific mutations. | It is recommended that cystic fibrosis (CF) carrier screening be made available to African Americans who are either pregnant or planning a pregnancy. We analyzed the carrier and mutant allele frequencies for African Americans undergoing CF carrier screening in our laboratories.</AbstractText>Between December 2001 and September 2003, we performed carrier screening for 2189 African Americans, testing for at least the 25 recommended mutations.</AbstractText>A total of 33 CF carriers were identified. The most common mutations detected were deltaF508, G622D, R117H/7T, and G551D. The G622D allele frequency among African Americans was 0.18%. We did not detect any 3120 + 1G --> A carriers, although 4 were expected (P < 0.05).</AbstractText>When considering only the 25 recommended CF mutations, 1 in 75 African Americans screened in our laboratories were carriers (within the expected range, given a 69% mutation detection rate). The addition of 2 mutations, G622D and Q98R (incidentally identified while screening for ACOG/ACMG mutations), increased the observed carrier frequency to 1 in 66, which is not significantly different from the known African American carrier frequency of 1 in 65. The frequencies of several specific mutations detected were unanticipated, as was the absence of 3120 + 1G --> A carriers. Further studies on African American patients with classic CF are needed to examine the incidence of CF mutations that are not part of the current panel, such as G622D.</AbstractText> |
2,339,170 | Cystic fibrosis screening: lessons learned from the first 320,000 patients. | To examine the data from > 335,000 Cystic fibrosis (CF) tests to detect unsuspected findings and obtain clinical data when indicated to optimize genetic counseling.</AbstractText>A proprietary database containing 335,204 consecutive CF DNA tests and 445 CF prenatal diagnostic tests was queried. Clinical information was obtained for prenatal and selected nonprenatal cases by telephone contact with physician offices.</AbstractText>The mutation 1078delT was found in much lower frequency than expected with rates of only 1:55,867 tests and 0.06% of CF mutations. This level is below the threshold set by the American College of Medical Genetics. Homozygosity was observed for 2789+5G>A in a 29-year-old women and compound heterozygosity with delta F408 in a 40-year-old woman with isolated chronic sinusitis. Many patients elected prenatal diagnosis when not at a 1:4 risk due to echogenic bowel or IVS-8 5T issues.</AbstractText>With the exception of 1078delT, all CF mutations in the ACMG panel were detected with a frequency of > 0.1% of CF chromosomes. When ACMG guidelines are strictly adhered to, population-based CF carrier screening will accurately identify couples at risk for having children with CF.</AbstractText> |
2,339,171 | In a Vietnamese population, MSX1 variants contribute to cleft lip and palate. | To identify causes of nonsyndromic cleft lip and palate in a Vietnamese population.</AbstractText>In this study, 175 families with at least one case of cleft lip and/or palate were studied using the candidate genes TGFA, MSX1, and TGFB3.</AbstractText>Transmission distortion for alleles of MSX1 were demonstrated for the whole population and two missense mutations were identified, including one (P147Q) that is found in approximately 2% of the population. The P147Q appears to arise from a founder individual based on shared haplotypes in unrelated families.</AbstractText>MSX1 contributes to nonsyndromic clefting in a Vietnamese population, and consistent with other studies, identifiable mutations in this gene cause about 2% of cases of nonsyndromic clefting.</AbstractText> |
2,339,172 | Preimplantation HLA typing and stem cell transplantation: report of International Meeting, Cyprus, 27-8 March, 2004. | There has been progress in the application of stem cell transplantation for the treatment of an increasing number of severe congenital and acquired bone marrow disorders that are currently restricted by the availability of human leukocyte antigen(HLA)-matched related donors. Preimplantation HLA typing has recently been introduced to improve the access to stem cell therapy for inherited bone marrow failures, and its possible use for the treatment of common sporadic malignant and non-malignant bone marrow disorders has also been explored. This paper describes the current experience of preimplantation HLA typing, reviewed by the International Meeting on the subject, which includes preimplantation HLA typing in 147 cycles, 109 of which were carried out as part of preimplantation genetic diagnosis (PGD) for Fanconi anaemia, thalassaemia, Wiscott-Aldrich syndrome, hyperimmunoglobulin M syndrome, hypohidrotic ectodermal dysplasia with immune deficiency, and X-linked adrenoleukodystrophy, and 38 for the sole purpose of HLA typing for leukaemias and aplastic and Diamond-Blackfan anaemias. The applied method resulted in the accurate pre-selection and transfer of HLA-matched embryos, yielding 25 clinical pregnancies and the birth of 14 HLA-matched children to the siblings who required stem cell transplantation. |
2,339,173 | A new model of glaucoma filtering surgery in the rat. | The most common reason for long-term failure of glaucoma filtering surgery (GFS) is scarring of the external filtering "bleb" tissues. The identification of the factors that mediate this process, as well as the development and initial testing of new therapies to limit scarring is enhanced by the use of appropriate animal models. The standard animal model for studying GFS is the rabbit but newer investigative tools that examine changes induced in biologic systems at a genetic level have made development of a rat model desirable.</AbstractText>Glaucoma filtering surgery was performed on 20 Sprague-Dawley rats by introducing a 30-gauge silicone cannula through a penetrating scleral tunnel, under a limbal-based conjunctival flap and suturing the conjunctiva closed. Identical GFS was performed on 3 additional rats, which underwent histologic evaluation at days 2, 5, and 11, following surgery.Fistulizing surgery was also performed on 6 Sprague-Dawley rats, for comparison, by creating a full-thickness needle sclerostomy under a limbal-based conjunctival flap and suturing the conjunctiva closed.</AbstractText>Following the cannula GFS, well-elevated filtering blebs formed and these gradually failed over the course of 8 to 13 days. Needle tract sclerostomy filtering blebs formed at the site of the fistulizing surgery but rapidly failed over the course of 2 to 3 days.</AbstractText>Cannulated filtering surgery in the rat provides a longer lasting and more predictable model than needle tract sclerostomy for studying wound healing following GFS and may facilitate the study of induced changes at the gene level.</AbstractText> |
2,339,174 | Sequencing of canine 5-hydroxytriptamine receptor (5-HTR) 1B, 2A, 2C genes and identification of polymorphisms in the 5-HTR1B gene. | Polymorphisms of human genes encoding 5-hydroxytriptamine (serotonin) receptors (5-HTRs) are thought to be associated with psychiatric disorders and behavioral traits. In the present study, we searched for corresponding polymorphisms in the dog and compared allelic frequencies for the canine 5-HTR1B, 5-HTR2A, and 5-HTR2C genes among five canine breeds. The canine genes consisted of the following: 5-HTR1B, 1170 bp; 5-HTR2A, 1413 bp; and 5-HTR2C, 1377 bp. All of these genes were highly homologous with the human genes. We found six single nucleotide polymorphisms (SNPs) in the 5-HTR1B gene (G57A, A157C, G246A, C660G, T955C, and G1146C). Genotyping of the respective SNPs revealed that there were inter-breed variations in the genotypes and allelic frequencies for four out of the six identified SNPs, suggesting that further analyses of the polymorphisms of the 5-HTR1B gene would be useful in order to gain an understanding of the genetic background underlying the diversified behavioral traits among canine species. |
2,339,175 | Role of INSL3 and LGR8 in cryptorchidism and testicular functions. | Cryptorchidism is the most frequent congenital anomaly of the urogenital tract in human males. INSL3 and LGR8/GREAT proteins seem to act as ligand and receptor respectively, and to have a role in gubernaculum development involved in testicular descent. Mutations in the INSL3 gene or LGR8/GREAT were found to be associated with cryptorchidism in humans. In a cohort of 135 ex-cryptorchid patients and 100 controls, mutations were sought in INSL3 and LGR8/GREAT genes by sequencing. Six patients were found with mutations in the INSL3 gene and four patients with LGR8/GREAT mutation (10/135, 7.4%). The 10 patients show different phenotypes, ranging from normozoospermia to complete azoospermia, and from bilateral cryptorchidism to retractile testes. Furthermore, the endocrine function of the testis appeared normal in all subjects. These findings demonstrate that INSL3-LGR8/GREAT mutations are frequently associated with human cryptorchidism, and that the only clinical consequence of alterations of the INSL3-LGR8/GREAT system seems to be failure of the testis to descend normally in the scrotum during embryonic development, without affecting the spermatogenic and endocrine components of the testis itself. The first analysis in humans of INSL3 was then performed using a novel radioimmunoassay kit to measure INSL3 concentrations in serum of adults. The results show that INSL3 circulates in adult men, it is a male-specific hormone, and it is of almost exclusively testicular origin. The role of this hormonal system in adulthood is, however, to date unknown. |
2,339,176 | Genetic basis of blood group diversity. | In the last 18 years the genes that encode all but one of the 29 blood group systems present on red blood cells (RBCs) have been identified. This body of knowledge has permitted the application of molecular techniques to characterize the common blood group antigens and to elucidate the background for some of the variant phenotypes. Just as the RBC was used as a model for the biochemical characterization of cell membranes, so the genes encoding blood groups provide a readily accessible model for the study of gene expression and diversity. The application of genotyping techniques to identify fetuses at risk of haemolytic disease of the newborn is now the standard of care, and the expansion of nucleic acid testing platforms to include both disease testing and blood typing in the blood centre is on the horizon. This review summarizes the molecular basis of blood groups and illustrates the mechanisms that generate diversity through specific examples. |
2,339,177 | Cost-effectiveness of thiopurine methyltransferase genotype screening in patients about to commence azathioprine therapy for treatment of inflammatory bowel disease. | Azathioprine is a useful agent in the management of inflammatory bowel disease. Its use is limited by its side-effect profile. Marrow toxicity occurs in approximately 3.2% of patients and is known to be associated with diminished thiopurine methyltransferase enzyme activity resulting from genetic polymorphisms.</AbstractText>To evaluate the cost-effectiveness of screening for thiopurine methyltransferase gene polymorphisms prior to initiation of azathioprine therapy.</AbstractText>Analysis of the literature was undertaken to calculate the expected frequency of leucopenia and its relationship with thiopurine methyltransferase polymorphisms in a model of theoretical inflammatory bowel disease patients. Decision analysis was then applied to assess the cost of a pre-treatment genotyping strategy, taking account of direct costs and cost per life-year saved.</AbstractText>In 1000 inflammatory bowel disease patients treated with azathioprine, 32 will develop myelosuppression and one will die because of this. Of those who develop myelosuppression during azathioprine therapy, 32% are attributable to lower thiopurine methyltransferase activity. Pre-treatment genotyping costs pound 347 per life-year saved for a 30 year old and pound 817 per life-year saved for a 60 year old. This compares favourably with other health care technologies.</AbstractText>The use of pre-treatment screening for thiopurine methyltransferase polymorphisms in inflammatory bowel disease patients commencing azathioprine therapy represents good value for money.</AbstractText> |
2,339,178 | [Predictive value of human genotoxicological biomarkers in the primary prevention of chronic non-infectious diseases]. | The main goal of biomarker research in the frame of primary prevention of chronic diseases is the prevention of appearance of clinical symptoms by an early recognition of the process leading to the symptoms. By the use of well-established biomarkers one can detect such tendencies finally leading to the manifestation of the disease far before the progress turns irreversible. As several parameters play role in such processes, the estimation of biological changes with the help of biomarkers is a precise and relatively simple means of the prevention. Indications of intervention in order to prevent the manifestation of a disease are rather determined by the nature but not the number of alterations. The use of genetic screening and monitoring by adequate biomarkers provide us with a new opportunity to measure such qualitative changes rather than the quantitative ones, ensuring a great improvement to the previous methods. The use of qualitative parameters as a routine method instead of the classic quantitative measures might represent a challenge for current prevention policies in Europe to approach health problems and safety at work. When the biomarkers give positive results that means a high probability to be at risk but not yet the manifestation of a certain illness. This stage may be relevant to the early onset of certain pathological processes, but it does not necessarily turn to a performed disease. In consequence a so-called positive result might cause unnecessary disturbances for the probands leading to ethical issues of risk communication. The monitoring system, however, should find acceptable communication strategies for the high-risk conditions detected by the well-established biomarkers. |
2,339,179 | Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA. | Single-nucleotide polymorphisms (SNPs) are considered useful polymorphic markers for genetic studies of polygenic traits. A new practical approach to high-throughput genotyping of SNPs in a large number of individuals is needed in association study and other studies on relationships between genes and diseases. We have developed an accurate and high-throughput method for determining the allele frequencies by pooling the DNA samples and applying a DNA microarray hybridization analysis. In this method, the combination of the microarray, DNA pooling, probe pair hybridization, and fluorescent ratio analysis solves the dual problems of parallel multiple sample analysis, and parallel multiplex SNP genotyping for association study. Multiple DNA samples are immobilized on a slide and a single hybridization is performed with a pool of allele-specific oligonucleotide probes. The results of this study show that hybridization of microarray from pooled DNA samples can accurately obtain estimates of absolute allele frequencies in a sample pool. This method can also be used to identify differences in allele frequencies in distinct populations. It is amenable to automation and is suitable for immediate utilization for high-throughput genotyping of SNP. |
2,339,180 | Clinical features of A3243G mitochondrial tRNA mutation. | Mitochondrial cytopathy is a heterogeneous group of disorders with a wide range of clinical features. To evaluate the incidence and clinical heterogeneity of A3243G mitochondrial tRNA mutation in the Korean population, we evaluated patients who were clinically suggestive of having mitochondrial encephalomyopathy. Eighty-five patients were included in this study. All showed clinical features of mitochondrial encephalomyopathy and had three or more of the following clinical manifestations: (1) psychomotor regression, (2) hyperlacticacidemia, (3) recurrent stoke-like episodes, (4) idiopathic cardiomyopathy, (5) sensoryneural hearing loss, (6) diabetes mellitus, (7) myopathy, (8) renal disease and (9) relatives with known mitochondrial disease. The patients were clinically classified as MELAS, MERRF, Leigh syndrome, Kearns-Sayre syndrome, chronic progressive external ophthalmoplegia and uncertain. Of the 85 patients, 19 had the A3243G mutation (22.3%). Thirty-one patients showed typical clinical characteristics of MELAS. Fourteen of those 31 patients had A3243G mutation (45.1%). Four patients harboring A3243G mutations showed atypical and heterogeneous clinical features, unlike MELAS. This study revealed the frequent occurrence of A3243G mutation in Korean patients with mitochondrial disorders and their clinical features can be heterogeneous. It will be helpful to screen the presence of A3243G mutation for the genetic diagnosis of mitochondrial encephalomyopathy in Korea. |
2,339,181 | Genotoxicity testing of a fenugreek extract. | Fenugreek seeds have been used in traditional medicines as a remedy for diabetes. Rich in protein, fenugreek seeds contain the unique major free amino acid 4-hydroxyisoleucine (4-OH-Ile), which has been characterized as one of the active ingredients for blood glucose control. Current use of fenugreek in foodstuff has been limited to its role as a flavoring agent, and not as an ingredient to help mitigate the blood glucose response for people with diabetes. As part of a safety evaluation of novel ingredients for use in blood glucose control, the potential genotoxicity of a fenugreek seed extract (THL), containing a minimum of 40% 4-OH-ILE, was evaluated using the standard battery of tests (reverse mutation assay; mouse lymphoma forward mutation assay; mouse micronucleus assay) recommended by US Food and Drug Administration (FDA) for food ingredients. THL was determined not to be genotoxic under the conditions of the tested genetic toxicity battery. The negative assay results provide support that addition of THL to foodstuffs formulated for people with diabetes is expected to be safe. A wide safety margin is established, as anticipated doses are small compared to the doses administered in the assays. |
2,339,182 | Minor histocompatibility antigen HA-1 and HPA-5 polymorphisms in HLA-identical related bone marrow transplantation. | The minor histocompatibility antigens (mHags), HA-1 and HPA-5, are immunogenic alloantigens shown to be responsible for graft-versus-host disease (GVHD) in HLA-identical bone marrow transplantation. Both antigens have two known alleles each, resulting in a single amino acid polymorphism. The HA-1H allele encodes histidine, whereas the HA-1R allele encodes arginine. The HPA-5b (Br(a)) allele encodes lysine, whereas the HPA-5a (Br(b)) encodes glutamic acid. In this study, 49 bone marrow transplant recipients and their genetically related HLA-identical donors were evaluated for the presence of HA-1, whereas 39 recipients, different from the abovementioned ones, and their HLA-identical siblings were analyzed for the presence of HPA-5. The frequencies of the two alleles of HA-1 in the recipient population were HA-1R = 0.663 and HA-1H = 0.336. In the donor population, the respective frequencies were 0.704 and 0.296. Seven donors (14.5%) were mismatched with the recipients for HA-1H. In contrast, the frequencies of the two alleles of HPA-5 in the recipient population were HPA-5a = 0.859 and HPA-5b = 0.141; whereas, among donors, they were 0.820 and 0.180, respectively. Five donors (12.8%) were found to be mismatched with their recipients for HPA-5. These results provide insight into the polymorphism of mH antigens based on the study of their frequencies in bone marrow transplant recipients and their genetically HLA-identical siblings, an endeavor that is essential to investigate the presence of HA-1 and HPA-5 mHags. |
2,339,183 | The effects of BRCA1 missense variants V1804D and M1628T on transcriptional activity. | Many families with multiple cases of ovarian cancer, breast cancer, or both segregate inherited mutations in one allele of the tumor suppressor gene BRCA1. Genetic testing is used to assess cancer risk; however, testing can detect missense DNA alterations, called unclassified variants, of unknown functional and biological significance with uncertain risk implications. Some missense variants at the transcriptional activation domain of BRCA1 of cancer patients inactivate transcriptional activity of BRCA1, providing evidence that they are deleterious. We identified the variants V1804D and M1628T at the transcriptional activation domain of BRCA1 of two ovarian cancer patients without a family history of ovarian or breast cancer. To test if these residues are critical for transcriptional activation, we created V1804D and M1628T independently in BRCA1 cDNA via site-directed mutagenesis in a mammalian expression vector, pcDNA3.1. Wild-type, mutant, and empty vector constructs were tested in human kidney 293 cells using a p53-responsive luciferase reporter. M1628T had the same transcriptional activity as wild-type BRCA1 but V1804D and the empty vector control showed a 60% reduction. This indicates that V1804D is deleterious but M1628T is not. |
2,339,184 | Molecular cytogenetic parameters in fibroblasts of ataxia telangiectasia carrier. | Ataxia telangiectasia (AT) is a pleiotropic and rare (1:40,000 to 1:100,000) recessive disease. Laboratory investigations have failed to detect any consistent anomaly in cells from AT heterozygotes. To estimate random aneuploidy, we applied a fluorescence in situ hybridization technique with alpha-satellite probes for chromosomes 8 and 9 and replication pattern for RB-1, HER-2/neu, and the imprinted SNRPN loci on primary AT carrier fibroblasts. Higher random aneuploidy was not found in the carrier fibroblasts compared to control amniocytic cells. The asynchrony pattern was higher in the AT carrier cells with the RB-1 locus (P=0.057) and significantly higher with the HER-2/neu locus (P < 0.001) compared to control cells. As for the imprinted locus SNRPN, there was a significantly lower asynchrony rate in the AT carriers (P < 10(-5)) compared to the control group. Molecular cytogenetic parameters of random aneuploidy and replication pattern may reflect predisposition for the development of cancer. It is possible that in some AT carriers the genetic instability phenomena associated with the abnormal replication pattern may represent their potential for developing malignancies. |
2,339,185 | Handling multiple testing while interpreting microarrays with the Gene Ontology Database. | The development of software tools that analyze microarray data in the context of genetic knowledgebases is being pursued by multiple research groups using different methods. A common problem for many of these tools is how to correct for multiple statistical testing since simple corrections are overly conservative and more sophisticated corrections are currently impractical. A careful study of the nature of the distribution one would expect by chance, such as by a simulation study, may be able to guide the development of an appropriate correction that is not overly time consuming computationally.</AbstractText>We present the results from a preliminary study of the distribution one would expect for analyzing sets of genes extracted from Drosophila, S. cerevisiae, Wormbase, and Gramene databases using the Gene Ontology Database.</AbstractText>We found that the estimated distribution is not regular and is not predictable outside of a particular set of genes. Permutation-based simulations may be necessary to determine the confidence in results of such analyses.</AbstractText> |
2,339,186 | [Importance of family examination in juvenile X-linked retinoschisis]. | Congenital (juvenile) retinoschisis belongs to the group of hereditary vitreoretinopathies. This disorder is inherited in an X-linked recessive pattern and its onset usually occurs in 5- to 10-year-old boys. Presenting clinical signs include decreased visual acuity due to maculopathy.</AbstractText>The authors present a case of a 17-year-old boy with decreased visual acuity, hypermetropia, and bilateral retinoschisis with maculopathy upon fundus examination. In view of a 50% risk of the disorder occurring in the brothers of the affected male, they underwent full ophthalmological and electrophysiological examinations (until then asymptomatic). In one of them decreased visual acuity, mixed astigmatism, and maculopathy were present, without any changes of the peripheral retina. In the youngest brother decreased visual acuity, hypermetropia, and maculopathy were diagnosed.</AbstractText>Genetic counseling and ophthalmological examination of family members at risk facilitated early recognition of the pathological changes in the siblings. Genetic counseling with pedigree analysis and genetic analysis, if possible, should be offered to all affected patients and family members.</AbstractText> |
2,339,187 | Utility of Interphase FISH Panels for Routine Clinical Cytogenetic Evaluation of Chronic Lymphocytic Leukemia and Multiple Myeloma. | Specific genetic abnormalities are of prognostic significance for patients with chronic lymphocytic leukemia (CLL) and multiple myeloma (MM); however, routine cytogenetic analysis usually provides normal results. We utilized two probe panels for interphase fluorescence in situ hybridization (FISH) studies to enhance the ability to detect genetic abnormalities in samples that were referred for routine cytogenetic studies for possible diagnoses of CLL or MM. The CLL panel consisted of probes for 11q22.3 (ATM gene), 13q14 (D13S319), the centromere of chromosome 12 (D12Z3) and 17p13.1 (P53 gene). The MM panel included probes for 14q32 (IgH gene) and/or t(11:14)(q13;q32) (BCL1/IgH), 13q14 (D13S319) and 17p13.1 (P53 gene). FISH detected clonal aberrations not identified by conventional cytogenetics in an additional 8 of 23 (35%) samples referred for possible CLL and 7 of 42 (17%) samples with possible MM. The prognostic significance of the aberrations identified ranged from favorable, to intermediate, to poor. Our studies indicate that many samples referred for routine cytogenetics testing for CLL and MM yield normal results for both conventional and FISH testing, likely due to lack of definitive diagnosis in a percentage of cases. However, FISH is more sensitive for the detection of clinically significant chromosome abnormalities and should be the testing methodology of choice for these disorders. |
2,339,188 | Hypermutable Haemophilus influenzae with mutations in mutS are found in cystic fibrosis sputum. | Hypermutable bacterial pathogens exist at surprisingly high prevalence and benefit bacterial populations by promoting adaptation to selective environments, including resistance to antibiotics. Five hundred Haemophilus influenzae isolates were screened for an increased frequency of mutation to resistance to rifampicin, nalidixic acid and spectinomycin: of the 14 hypermutable isolates identified, 12 were isolated from cystic fibrosis (CF) sputum. Analysis by enterobacterial repetitive intergenic consensus (ERIC)-PCR and ribotyping identified eight distinct genetic fingerprints. The hypermutable phenotype of seven of the eight unique isolates was associated with polymorphisms in conserved sites of mutS. Four of the mutant mutS alleles were cloned and failed to complement the mutator phenotype of a mutS : : TSTE mutant of H. influenzae strain Rd KW20. Antibiotic susceptibility testing of the hypermutators identified one beta-lactamase-negative ampicillin-resistant (BLNAR) isolate with two isolates producing beta-lactamase. Six isolates from the same patient with CF, with the same genetic fingerprint, were clonal by multilocus sequence typing (MLST). In this clone, there was an evolution to higher MIC values for the antibiotics administered to the patient during the period in which the strains were isolated. Hypermutable H. influenzae with mutations in mutS are prevalent, particularly in the CF lung environment, and may be selected for and maintained by antibiotic pressure. |
2,339,189 | Diagnosis of lysosomal storage disorders: current techniques and future directions. | Lysosomal storage disorders represent a group of over 45 distinct genetic diseases. The broad spectrum of clinical presentation of this group of disorders has led to the development of diagnostic protocols to facilitate their rapid and accurate diagnosis. However, with the development of new therapies, testing for many of these disorders now extends beyond diagnosis of affected individuals. The efficacy of many current and proposed therapies will rely heavily upon early detection and treatment prior to the onset of irreversible pathology. Newborn screening holds the promise of early detection. However, presymptomatic diagnosis raises a number of issues relating to patient management and treatment. Methods for prognoses and monitoring therapy in asymptomatic individuals will be required. |
2,339,190 | Exploring the genetic basis of disease using RNA interference. | Cancer and autoimmunity are polygenic diseases. In order to better understand the mechanisms of disease development and progression it is essential to uncover which genes are involved. Much has been learned from population studies in human patients by searching for polymorphic genetic loci associated with disease. In addition, animal models of tumor development, as well as models for various autoimmune conditions such as multiple sclerosis and Type I diabetes, have helped determine genetic loci that contribute to disease susceptibility. However, characterization of the exact genes involved is often difficult and requires lengthy and technically demanding genetic manipulations. The generation of knockout animals is the method of choice to probe single genes. However, this is not possible in all species or even in all inbred strains within a species. The recent discovery of a new post-transcriptional gene silencing pathway termed RNA interference, which is mediated by short fragments of double-stranded RNA (short-interfering RNA), has opened up new avenues for genetic manipulation of experimental animals. This review will consider how silencing genes by RNA interference within the context of experimental disease models promises to become a powerful new tool for the genetic analysis of cancer and autoimmunity. Advances in RNA interference technology now permit the relatively rapid generation of transgenic animals in a wide range of species with complex genetic backgrounds that were previously inaccessible to genetic manipulation. This novel approach should help refine the characterization of disease-associated genes, either by silencing specific candidates or even by screening a larger number of genes in vivo within a comparatively short time frame. |
2,339,191 | Hyperphenylalaninemia in a premature infant with heterozygosity for phenylketonuria. | Hyperphenylalaninemia in preterm neonates with heterozygosity for phenylketonuria has previously not been described. We report on a very low birth weight infant, born at a gestational age of 27+5 weeks with a birth weight of 1080 g. Due to a positive family history prenatal diagnosis for phenylketonuria was performed, revealing heterozygosity for classic phenylketonuria. Yet the girl showed hyperphenylalaninemia with a maximum serum phenylalanine concentration of 515 micromol/l on the eighth day of life. Phenylalanine-restrictive parenteral and enteral nutrition was kept from the eighth until the 41st day of life. At term serum phenylalanine concentrations had normalized. We hypothesize that heterozygosity for phenylketonuria may be a risk factor for hyperphenylalaninemia in preterm born infants. Prematurity and the resulting immaturity of liver function with the genetically determined reduced activity of phenylalanine hydroxylase might have caused hyperphenylalaninemia in this girl. |
2,339,192 | [Families at risk of colon cancer I. Familial adenomatous polyposis]. | Familial adenomatous polyposis (FAP) is a well-defined autosomal dominant inherited disease characterised by a diffuse polyposis of the colon and rectum leading to inevitable colorectal cancer by 50 years. The purpose of this review is to summarize the current knowledge regarding this entity with the focus on recent knowledge on genetic testing, surveillance guidelines and therapy of FAP. Available medical databases were searched from 1998 to May 2003 using keywords "familial adenomatous polyposis", followed by further search for particular issues. Additional articles were identified through the reference sections of retrieved articles and from personal archives of authors. Approximately 300 papers on FAP are published yearly. There has been a large progress in our understanding of the genetics of FAP leading to the development of genetic counselling, reliable genetic tests and screening strategies. There is accumulating evidence about genotype-phenotype associations with direct clinical implications. Our knowledge about the extracolonic manifestations is also expanding resulting in new surveillance and treatment strategies for FAP patients after proctocolectomy. Although still representing a serious burden for affected patients and their families, the research of last decades together with national registers improved the life expectancy and the quality of life of FAP patients dramatically. Further research in the area of molecular genetics, genetic testing and emerging gene therapy for FAP patients is to be expected in the near future. |
2,339,193 | Ataxia-telangiectasia mutated gene controls insulin-like growth factor I receptor gene expression in a deoxyribonucleic acid damage response pathway via mechanisms involving zinc-finger transcription factors Sp1 and WT1. | The IGF-I receptor (IGF-IR) has a central role in cell cycle progression as well as in the establishment of the transformed phenotype. Increased expression of the IGF-IR gene, in addition, is correlated with acquisition of radioresistance for cell killing. The ataxia-telangiectasia mutated (ATM) gene product has a pivotal role in coordinating the cellular response to DNA damage. The present study was aimed at testing the hypothesis that the ability of ATM to coordinate the DNA damage response that will lead to cell survival or, alternatively, to apoptosis depends, to a significant extent, on its capacity to control IGF-IR gene expression. The potential involvement of ATM in regulation of IGF-IR expression and function was investigated in isogenic cells with and without ATM function [AT22IJE-T/pEBS7 (ATM -/-) and ATM-corrected AT22IJE-T/YZ5 (ATM +/+) cells and 293 human embryonic kidney cells transfected with small interfering RNAs targeted to ATM]. In addition, the effect of ATM on IGF-IR expression was assessed in nonisogenic cells with ATM function (HFF + human telomerase reverse transcriptase) and without ATM function (GM5823 + human telomerase reverse transcriptase). Results obtained showed that IGF-IR gene expression and IGF-IR promoter activity were largely reduced in ATM -/- cells. Addition of the radiomimetic agent neocarzinostatin for 4 h, however, induced a significant increase in IGF-IR levels in cells without ATM function. In addition, IGF-I-induced IGF-IR and insulin receptor substrate-1 phosphorylation were greatly impaired in ATM-deficient cells. Furthermore, we identified zinc-finger transcription factors Sp1 and WT1 as potential mediators of the effect of ATM on IGF-IR gene expression. The present data suggests that the IGF-IR gene is a novel downstream target in an ATM-mediated DNA damage response pathway. Deregulated expression of the IGF-IR gene after ionizing radiation may be linked to genomic instability and enhanced transforming capacity. |
2,339,194 | Neuroscience research on the addictions: a prospectus for future ethical and policy analysis. | The increasing evidence that many addictive phenomena have a genetic and neurobiological basis promises improvements in societal responses to addiction that raise important ethical and social policy issues. One of the major potential benefits of such research is improved treatment of drug addiction, but in order to do the research required to realize this promise, it will be necessary to address ethical doubts raised about the capacity of addicted persons to give free and informed consent to participate in studies that involve the administration of drugs of dependence. Neuroscience research on addiction promises to transform the long running debate between moral and medical models of addiction by providing a detailed causal explanation of addiction in terms of brain processes. We must avoid causal models of addiction being misinterpreted as supporting simple-minded social policies, e.g., that we identify the minority of the community that is genetically and biologically vulnerable to addiction and hence can neglect social policy options for reducing addiction, including drug control policies. Causal accounts of addiction supplied by neuroscience and genetic research may also be seen to warrant the use of pharmacotherapies and drug vaccines under legal coercion. Neuroscientists also need to anticipate the ethical issues that may arise if the knowledge that they produce delivers interventions that enhance human cognitive and other capacities. Advances in neuroimaging that enable us to identify "addicts" or predict future risk of addiction will raise concerns about invasion of privacy, third-party use of neuroimaging data, the powers of courts to coerce defendants to undergo such tests, and consumer protection against the overinterpretation of test results. Given the strong public and media interest in the results of their research, neuroscientists and geneticists have a moral obligation, and a professional interest, to minimize popular misunderstandings of their work in the media that may rebound to its detriment. |
2,339,195 | Certificates of confidentiality in research: rationale and usage. | Certificates of confidentiality (COCs) are a tool to protect researchers from being compelled to release identifying information about their subjects. Whereas institutional review board (IRB) review and informed consent procedures are mandatory tools to protect human subjects, COCs are voluntary. There are limited data about who procures COCs and why, and whether they are useful. Three Institutes of the National Institutes of Health (NIH) provided data on 114 research projects that had received COCs. Eighty-three researchers had procured a single COC and 11 researchers had procured 31 COCs. One hundred and four (91%) of the COCs were obtained by researchers at academic sites, and 17 institutions collectively accounted for 82 COCs. The most commonly cited sources of information about COCs came from colleagues (n = 18, 35%) and previous experience (n = 17, 33%). The most common reasons for procuring a COC were that the research involved genetics (n = 28, 54%), the research could lead to social stigmatization or discrimination (n = 22, 42%), or the research could damage an individual's financial standing, employability, or reputation (n = 21, 40%). These findings show that COCs are often congregated within institutions and by particular individuals. This may be because others are unaware of COCs or because others do not believe they are necessary or useful. |
2,339,196 | Human subject protections in genetic research. | The Certificate of Confidentiality (COC) is a voluntary tool to protect researchers from being compelled to release identifying information about their subjects. Institutional review board (IRB) review and informed consent (IC) procedures are mandatory tools to protect human subjects. Although many studies reveal poor documentation of IRB and IC procurement, most published research undergoes IRB review and has appropriate IC procedures. There are no empirical data about the use of COCs. We examined the procurement and documentation of all these human subject protections in the genetics literature. A total of 112 (55%) articles documented IRB review, 108 (53%) document IC, and 82 (41%) documented both. None documented the procurement of a COC. Returned surveys provided additional information that confirmed that at least 74% (n = 150) of research had received appropriate IRB review, at least 71% (n = 143) had procured IC, and at least 10% (n = 21) had obtained a COC. An additional 22 respondents had procured COCs for other research, whereas 17 respondents were unaware of them and their purpose. In this era of public scrutiny of medical research, we recommend greater familiarity with and documentation of all human subject protections. |
2,339,197 | Patterns of chromosomal translocations identified by a birth defects registry, Hawaii, 1986-2000. | Using a birth defects registry, this investigation examined the distribution of translocations by type of translocation, chromosomes involved in the translocation, pregnancy outcome, method of diagnosis, inheritance, and diagnosis of major structural birth defects. A total of 121 cases were identified through a statewide population-based birth defects registry. The translocations were reciprocal in 89 (73.6%) cases, Robertsonian in 32 (26.4%) cases, balanced in 86 (71.1%) cases, and unbalanced in 35 (28.9%) cases. Live births accounted for 76 (88.4%) of balanced translocations and 22 (62.9%) of unbalanced translocations. Diagnosis was made by amniocentesis or chorionic villus sampling in 72 (83.7%) of balanced translocations and 11 (31.4%) of unbalanced translocations. Of cases of known inheritance, the translocation was of maternal origin in 38 (46.3%) cases, paternal origin in 25 (30.5%) cases, and de novo in 19 (23.2%) cases. Major structural birth defects were diagnosed in 17 (19.8%) of balanced translocations and 20 (57.1%) of unbalanced translocations. Translocations were more likely to be reciprocal, balanced, and of maternal origin. Infants and fetuses with unbalanced translocations were less likely to be live births and diagnosed by amniocentesis or chorionic villus sampling and more likely to be diagnosed with major structural birth defects. |
2,339,198 | Comprehensive analysis of genetic polymorphisms in the interleukin-10 promoter: implications for immune regulation in specific ethnic populations. | The association of interleukin-10 (IL-10) promoter single-nucleotide polymorphisms (SNPs) as risk factors for certain inflammatory diseases, viral infections, cancers, and transplant rejection have been the subject of recent studies. The SNPs -1082 G --> A, -819 C --> T, and -592 C --> A, which have been associated with differential IL-10 production, are strongly linked with ethnicity. In this study, we determined the ethnic distribution of IL-10 promoter SNPs and their haplotype rates among Hispanics, African Americans, and Caucasians from Texas and Ashkenazi Jews from New York. Significant differences in prevalence rates of IL-10 SNPs (and their haplotype distribution) were found. African Americans and Hispanics have a lower rate of putative high-producer SNPs and a higher rate of low IL-10 producers when compared to Caucasians or Ashkenazi Jews. No statistically significant differences in allelic frequencies and haplotype rates were observed between Caucasians and Ashkenazi Jews. This study provides critical new information on the ethnic distribution of IL-10 promoter SNPs in a regional U. S. population and is the first to analyze the rate of SNPs in an unstudied ethnic population, Ashkenazi Jews. Knowledge of IL-10 promoter polymorphisms may prove useful in prediction of immunization responses, disease severity, and in the intelligent design of customized immunotherapy. |
2,339,199 | PCR-RFLP genotyping assay for a lactase persistence polymorphism upstream of the lactase-phlorizin hydrolase gene. | The majority of the world's human population experiences a decline of lactase gene expression during maturation, so-called lactase nonpersistence. Thus, adults with lactase nonpersistence are susceptible to developing symptoms of lactose intolerance. By contrast, lactase persistence is an autosomal dominant heritable condition that results in a high level of lactase gene expression throughout adulthood and sustained lactose tolerance. Lactase persistence has recently been correlated with a single nucleotide genetic variant (a C --> T mutation) located 13,910 bases upstream from the lactase structural gene. We aimed to develop a restriction fragment length polymorphism (RFLP) method of detecting the C/T variants as a means of identifying individuals genetically inclined toward lactase persistence or nonpersistence. Genomic DNA in a 210-bp region surrounding the -13,910-bp variant site was PCR amplified with unique primers designed to avoid or mutate adjacent restriction sites. The amplified DNA was digested with a restriction enzyme, CviJI, that recognizes the base pair sequence generated by the lactase nonpersistence variant. Restriction digest gel analysis yielded DNA fragments of the expected diagnostic molecular weight sizes for individuals that were homozygote or heterozygote for the lactase persistence and nonpersistence variants. The genotypes predicted by the RFLP-based method were confirmed by DNA sequence analysis. The RFLP-based method provides a quick and noninvasive means of molecular detection of the presence or absence of the lactase persistence variant. |
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