Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “SNPs”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed2004

New SNPs in the coding and 5' flanking regions of porcine MYOD1 (MYF3) and MYF5 genes.

Myogenic factor 3 (myf - 3) and myogenic factor 5 (myf - 5) are the products of genes: MYOD1 (MYF3) and MYF5, respectively, which belong to the MyoD family. These transcription factors control the processes of myogenesis. The fragments of both the genes comprising exons and promoters were amplified and sequenced. In the 5'UTR region of gene MYOD1, the G302A transition was identified and it is not recognized by any restriction endonuclease. In the promoter region of gene MYF5 we identified three mutations at positions: A65C (PCR-RFLP/AciI); C580T (PCR-RFLP/FokI) and C613T (PCR-RFLP/HinPI). Mutations C580T and C613T were characteristic for Pietrain x (Polish Large White x Polish Landrace) crossbred pigs named Torhyb. The C2931T transition, which is not recognized by any restriction enzyme, was identified in exon 3 of gene MYF5. This mutation results in a change of the amino acid sequence (Leu-->Pro). The frequency of particular genotypes at the MYOD1 and MYF5 loci proved to be dependent on pig breed. However, Duroc pigs were monomorphic at all the SNPs presented in this study. These SNPs might be analyzed in a further study as probably influencing carcass meatiness.

5' Untranslated Regions↗
PubMed2000

Identification of seven novel SNPS (five nucleotide and two amino acid substitutions) in the connexin31 (GJB3) gene.

Connexin31 (GJB3) has been associated with hearing impairment and erythrokeratodermia variabilis. We have analyzed this gene in samples from patients with peripheral neuropathies, deafness and controls and have found several single nucleotide polymorphisms (SNPs). In the noncoding exon 1 of GJB3 two small deletions, 581del2 and 632del4 (GenBank accession number AF052692), were found at frequencies of 30% and 14%, respectively. In exon 2 we found two amino acid changes, R32W (1227C-T) and V200I (1731G-A), and three nucleotide variants not affecting the amino acid sequence, 1610G-A, 1700C-T and 1931C-T. Most of these changes were found at similar frequencies in patients with deafness, patients with peripheral neuropathies and control subjects. V200I, 1700C-T and 1610G-A were found associated in three unrelated patients with deafness and in a fourth patient with peripheral neuropathy, but were not detected in control subjects.

Amino Acid Substitution↗
PubMed2000

Zero-recombinant haplotyping: applications to fine mapping using SNPs.

As the number of single nucleotide polymorphisms (SNPs) available for genetic analysis increases, researchers will be saturating smaller and smaller regions of the genome with these biallelic markers in an effort to fine map complex diseases. An important tool in this fine-mapping effort is haplotyping. Algorithms are presented that find all possible haplotype configurations of the pedigree data under the assumption that there are no recombinants between the markers. These configurations can be used to estimate the haplotype frequencies, and identify the most common haplotypes in the data. These algorithms have been implemented into a software program (ZAPLO), and were tested on a published data set.

Algorithms↗
PubMed2005

Exclusion of non-synonymous SNPs and a polyglutamine tract in SMRT/N-CoR2 as common deleterious mutation for bipolar disorder in the Sagnenay-Lac-St-Jean population.

Bipolar disorder (BP) is a psychiatric illness with both genetic and environmental components occurring with a prevalence of slightly more than 1%. Our previous linkage and case/control studies have pointed to a susceptibility locus for BP in the 12q24.31 chromosomal region. Here, we investigated the possible involvement of the SMRT/N-CoR2 gene, which encodes for the nuclear receptor co-repressor 2. SMRT/N-CoR2 was retained as a candidate gene for BP because of its location within our candidate gene region and its interactions with thyroid hormone receptors. We screened SMRT/N-CoR2 for the presence of polymorphism/mutation in coding sequences and exon-intron junctions. Four non-synonymous SNPs and a polyglutamine tract (CAG repeat) in the coding exon 14 were analyzed in a case/control sample from the Saguenay-Lac-St-Jean (SLSJ) area of Quebec (213 cases and 214 controls). Our data indicated no significant allelic/genotypic association between any of the five mutations and bipolar phenotype when they were considered either individually or as haplotypes. Finally, the CAG repeat observed in SMRT/N-CoR2 did not demonstrate allelic instability and consequently it is unlikely that this polymorphism could be involved in the anticipation phenomenon reported for BP.

Alleles↗
PubMed2007

Evaluation of association of SNPs in the TNF alpha gene region with schizophrenia.

The association of the tumor necrosis factor alpha (TNFalpha) -G308A promoter polymorphism with schizophrenia has complemented clinical findings of increased levels of the TNFalpha cytokine in schizophrenic patients, with some support for a functional consequence of the variant. Our previous studies of genetic causes in schizophrenia supported findings of linkage to the major histocompatibility complex (MHC) region where the TNFalpha gene is located as well as association with the -G308A promoter polymorphism. While the common G-allele shows association in our sample, association with the A-allele has been reported by other groups. This suggests linkage disequilibrium (LD) rather than direct involvement in the disorder. In order to define LD of DNA variants with the disorder in this area, we analyzed 36 SNPs in a 165-kb region around this polymorphism. We detected nominally significant associations (P < 0.05) of three markers (including the -G308A promoter polymorphism) and multiple haplotypes with schizophrenia in our sample of 204 families (79 sib-pairs and 125 trios). The association is largely restricted to a 30 kb high LD region/block and should assist in the identification of a schizophrenia susceptibility gene within the block or elsewhere in the MHC.

Family↗
PubMed2005

Detection of genotyping errors and pseudo-SNPs via deviations from Hardy-Weinberg equilibrium.

Genotype error can greatly reduce the power of a genetic study. For family data, genotype error can be assessed by examining marker data for non-Mendelian inconsistencies, closely linked markers for double recombination events, and consistency of duplicate genotypes. For case-control data, duplicate samples are genotyped, and controls are tested for deviations from Hardy-Weinberg equilibrium (HWE). Duplicate samples can provide accurate estimates of genotyping error rates, unless systematic genotyping errors have occurred. Although genotyping errors can cause deviations from HWE, these deviations are usually small, and the power to detect them is low except for high rates of genotyping error and/or large sample sizes. An additional problem is that even when deviations from HWE are detected for marker loci, without additional experimentation it is not possible to unequivocally implicate genotyping error as the cause. The power and sample sizes necessary to detect deviations from HWE for single-nucleotide polymorphism (SNP) data are examined for a variety of genotyping error and pseudo-SNP models. For the majority of genotyping models examined, the power is poor to detect deviations from HWE. For example, for 1,000 controls, if an allele with a frequency of 0.1 fails to amplify for 28% of the heterozygous genotypes producing a sample error rate of 0.05, the power is 0.51 to detect a deviation from HWE at an alpha level of 0.05. On the other hand, the detection of deviations from HWE for pseudo-SNPs (paralogous and ectopic sequence variants) for the majority of models examined produces a power of >0.8 for sample sizes as small as 50 individuals.

Gene Frequency↗
PubMed2002

rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites.

Since the human genome was sequenced in draft, single nucleotide polymorphism (SNP) analysis has become one of the keynote fields of bioinformatics. We have developed an integrated database-tools system, rSNP_Guide (http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/), devoted to prediction of transcription factor (TF) binding sites, alterations of which could be associated with disease phenotype. By inputting data on alterations in DNA sequence and in DNA binding pattern of an unknown TF, rSNP_Guide searches for a known TF with alterations in the recognition score calculated on the basis of TF site's sequence and consistent with the input alterations in DNA binding to the unknown TF. Our system has been tested on many relationships between known TF sites and diseases, as well as on site-directed mutagenesis data. Experimental verification of rSNP_Guide system was made on functionally important SNPs in human TDO2and mouse K-ras genes. Additional examples of analysis are reported involving variants in the human gammaA-globin (HBG1), hsp70(HSPA1A), and Factor IX (F9) gene promoters.

Animals↗
PubMed2001

Haplotyping of wild type and I278T alleles of the human cystathionine beta-synthase gene based on a cluster of novel SNPs in IVS12.

Homocystinuria is most frequently due to deficiency of cystathionine beta-synthase (CBS). We identified IVS12 as a polymorphism hot spot of the human CBS gene and report five novel single nucleotide polymorphisms (SNPs): g.13514G>A, g.13617A>G, g.13715C>T, g.13800G>A, and g.13904C>T. Analyzing 50 control DNA samples of unaffected and unrelated subjects of German origin the observed frequencies of heterozygosity were 0.02, 0.36, 0.18, 0.36, and 0.36, respectively. These polymorphic markers were combined into four distinct IVS12-haplotypes A1, A2, B1, and B2, revealing frequencies of 0.75, 0.01, 0.15, and 0.09, respectively, with an observed overall frequency of heterozygosity at 0.38. This haplotype system and the SNP c.699 were employed in the analysis of ten alleles affected by the most prevalent CBS mutation, c.833T>C (exon 8; I278T). We found that the I278T alleles segregate with at least two distinct haplotypes characterized by upstream and downstream polymorphic sites instead of sharing a common ancestral haplotype. This was a remarkable finding even in patients with very similar ethnic background. The novel haplotype system may facilitate future studies on the evolution of the CBS gene and might be suited for genotyping of families affected by homocystinuria.

Alleles↗
PubMed2005

Corroboration of a familial chordoma locus on chromosome 7q and evidence of genetic heterogeneity using single nucleotide polymorphisms (SNPs).

Chordoma, a rare bone tumor originating from notochordal remnants, has a genetic predisposition in some families. Previously, we performed linkage analysis using microsatellite (STR) markers on 3 unrelated chordoma kindreds (16 patients with chordoma) and reported significant evidence for linkage to chromosome 7q33 (Z(max) = 4.78) with a minimal disease gene region of 11 cM. In our present study, we performed linkage analysis in these 3 families using chromosome 7 single nucleotide polymorphisms (SNPs). Parametric and nonparametric multipoint analyses showed significant linkage to 7q markers with p < 0.001 and Z(max) = 2.77, respectively. The minimal disease gene region was not reduced by combined SNP and STR haplotype analysis compared to the previous STR haplotype analysis alone. We genotyped members of a fourth chordoma family with SNP and STR markers for chromosome 7q and for 1p36, the location of a previously reported chordoma locus. Affected members of this family did not share a common haplotype on 7q, and the family did not show evidence of linkage to 1p36. Thus, we corroborated a chordoma locus on chromosome 7q in the 3 original families and demonstrated evidence for genetic heterogeneity in the fourth family. Our study also provided insights into some limitations and analytical complexities associated with using a dense SNP marker set in linkage analysis of complex pedigrees.

Adult↗
PubMed2005

Genome-wide association study to identify SNPs conferring risk of myocardial infarction and their functional analyses.

Myocardial infarction might result from the interactions of multiple genetic and environmental factors, none of which can cause disease solely by each of themselves. Although molecular biological studies revealed that a number of proteins are possibly involved in its pathogenesis, little, if any genetic findings have been reported so far. To reveal genetic backgrounds of myocardial infarction, we performed a large-scale, case-control association study using 92,788 gene-based single-nucleotide polymorphism (SNP) markers. We have identified functional SNPs within the lymphotoxin-alpha gene (LTA) located on chromosome 6p21 that conferred susceptibility to myocardial infarction. Furthermore, we could identify galectin-2 protein as a binding partner of LTA protein. The association study further revealed that a functional SNP in LGALS2 encoding galectin-2, which led to altered secretion of LTA, also indicated a risk of myocardial infarction. A combined strategy of genetic and molecularcellular biological approaches may be useful in clarifying pathogenesis of common diseases.

Case-Control Studies↗
PubMed2005

Temperature gradient capillary electrophoresis (TGCE)--a tool for the high-throughput discovery and mapping of SNPs and IDPs.

Temperature gradient capillary electrophoresis (TGCE) can be used to distinguish heteroduplex from homoduplex DNA molecules and can thus be applied to the detection of various types of DNA polymorphisms. Unlike most single nucleotide polymorphism (SNP) detection technologies, TGCE can be used even in the absence of prior knowledge of the sequences of the underlying polymorphisms. TGCE is both sensitive and reliable in detecting SNPs, small InDel (insertion/deletion) polymorphisms (IDPs) and simple sequence repeats, and using this technique it is possible to detect a single SNP in amplicons of over 800 bp and 1-bp IDPs in amplicons of approximately 500 bp. Genotyping data obtained via TGCE are consistent with data obtained via gel-based detection technologies. For genetic mapping experiments, TGCE has a number of advantages over alternative heteroduplex-detection technologies such as celery endonuclease (CELI) and denaturing high-performance liquid chromatography (dHPLC). Multiplexing can increase TGCE's throughput to 12 markers on 94 recombinant inbreds per day. Given its ability to efficiently and reliably detect a variety of subtle DNA polymorphisms that occur at high frequency in genes, TGCE shows great promise for discovering polymorphisms and conducting genetic mapping and genotyping experiments.

Chromosome Mapping↗
PubMed2005

Polymorphisms of IL-13 and IL-4-IL-13-SNPs in patients with penicillin allergies.

OBJECTIVE: Although IL-4 and IL-13 share many biologic activities, some are unique to IL-13. We genotype the IL-13 and IL-4-IL-13-SNPs genes for polymorphisms that could then be used to determine associations with IgE regulation as well as levels of IL-4 and IL-13. METHODS: Eight kinds of IgE specific to penicillins were determined with radioallergosorbent test (RAST) in the sera of 158 patients with penicillin allergies and 89 healthy subjects. Serum levels of IL-4 and IL-13 were measured by using enzyme-linked immunosorbent assay (ELISA). The genotyping of IL-13Arg130Gln, IL-4-IL-13-SNP3 and IL-4-IL13-SNP4 was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. RESULTS: Among patients with positive specific IgE, significant differences between the IL-4-IL-13-SNP3 and IL-4-IL-13-SNP4 genotypes were observed between patients with positive BPA and the control group (P<0.05, P<0.05). Additionally, we also found significant differences in the IL-4-IL-13-SNP4 genotype between positive and negative BPA-IgE patients (P<0.05). However, we found no significant differences in the prevalence of these polymorphisms between any of the symptomatic groups studied and the control group. Nor were there any significant differences between levels of IL-4 and IL-13 and any of genotypes. CONCLUSION: The data suggest that IL-4-IL-13-SNP genes between IL-4 and IL-13 play a role in regulation of specific IgE levels in patients with penicillin allergies.

Adult↗
PubMed2001

An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes.

This paper assesses the use of single nucleotide polymorphisms (SNPs) for forensic analysis. It demonstrates that relatively small arrays of approx. 50 loci are comparable to existing short tandem repeat (STR) multiplexes. A quantitative test, however, is a prerequisite for mixture interpretation. In addition, as the mixture proportion becomes low, it will be necessary to distinguish between the allele and background. Relatively small biallelic arrays are also suitable to distinguish between closely related individuals such as brothers.

Alleles↗
PubMed2004

Polymorphisms within a polymorphism: SNPs in and around a polymorphic Alu insertion in intron 44 of the human dystrophin gene.

A polymorphic Yb-type Alu insertion on Xp21.3 shows a genotypic gradient across worldwide populations. We used single strand conformational polymorphism (SSCP), denaturing high-pressure liquid chromatography (DHPLC), and sequencing to characterize the level of polymorphism within this region. Two novel polymorphic sites were found within the Alu insertion itself, and a further seven novel polymorphic sites in the 2-kb flanking region. Our results showed that while DHPLC was more sensitive than SSCP, the limitations of DHPLC included the lack of ability to distinguish between multiple alleles or safely identify mutations on a polymorphic background. We believe that this is the first report of polymorphic single nucleotide polymorphisms (SNPs) within a polymorphic Alu distribution and that together they promise to provide a useful marker for human population and evolutionary genetics.

Africa South of the Sahara↗
PubMed2004

Identification of 20 novel SNPs in the guanine nucleotide binding protein alpha 12 gene locus.

Heterotrimeric guanine nucleotide binding proteins (G proteins) regulate various signals from transmembrane receptors to intracellular effectors thereby mediating cell growth, differentiation, and apoptosis. We have been publishing a series of genetic variations detected in the genomic regions corresponding to the potential drug target genes. As an addition to genetic information reported earlier, we provide here 20 novel single nucleotide polymorphisms (SNPs) in the region corresponding to a gene encoding alpha subunits of G(12) protein, GNA12, in the Japanese population: 16 in introns, two in the coding region, and two in the 3' flanking region. We also identified 12 genetic variations of other types from this locus. The collection of genetic variations reported here will serve as a useful resource for analyzing potential associations between genotypes and susceptibility to common diseases as well as efficacy and/or adverse reactions to drugs.

Asian People↗
PubMed2000

Twenty single nucleotide polymorphisms (SNPs) and their allelic frequencies in four genes that are responsible for familial long QT syndrome in the Japanese population.

We report here 20 single nucleotide polymorphisms (SNPs), including 10 novel ones, and their allelic frequencies detected in four genes that are known to be responsible for familial long QT syndrome in the Japanese population; 7 polymorphisms are in the KCNQ1 gene, 6 in the KCNH2 gene, 5 in the SCN5A gene, and 2 in the KCNE1 gene. These data will be of use for genetic association studies of acquired cardiac arrhythmias.

Alleles↗
PubMed2001

Catalog of 46 single-nucleotide polymorphisms (SNPs) in the microsomal glutathione S-transferase 1 (MGST1) gene.

A major goal in our laboratory is to understand the role of common genetic variations among individual patients as regards susceptibility to common diseases and differences in therapeutic efficacy and/or side effects of drugs. As an addition to the high-density SNP (single-nucleotide polymorphism) maps of 12 glutathione S-transferase and related genes reported earlier, we provide here an SNP map of the microsomal glutathione S-transferase 1 (MGST1) gene. Among 48 healthy Japanese volunteers examined. we identified a total of 46 SNPs at this locus, 36 of which had not been reported before: 4 in the promoter region, 34 in introns, 3 in the 3' untranslated region, and 5 in the 3' flanking region. No SNP was found in 5'untranslated or coding regions. The ratio of transition to transversion was approximately 1.2:1. Among the 13 insertion-deletion polymorphisms was a 2-bp deletion in the coding region of MGST1 in DNA from one of the volunteers, which resulted in a frame-shift mutation. Since the gene product encoded by this mutant allele would lack the C-terminal half including the MAPEG (membrane-associated proteins in eicosanoid and glutathione metabolism) domain, MGST1 activity is likely to be reduced in the carrier's cells. The SNP map presented here adds to the archive of tools for studying complex genetic diseases, population migration patterns, and a variety of pharmacogenetic possibilities.

3' Untranslated Regions↗
PubMed2007

A study of how socioeconomic status moderates the relationship between SNPs encompassing BDNF and ADHD symptom counts in ADHD families.

Recent animal research suggests that brain-derived neurotrophic factor (BDNF), may mediate response to different environmental stimuli. In this paper, we evaluated the possible role of BDNF as a moderator of attention deficit hyperactivity disorder (ADHD) in the context of different socioeconomic classes. We genotyped ten single nucleotide polymorphisms (SNPs) in and around BDNF in 229 families and evaluate whether there are SNP-by-socioeconomic status (SES) interactions for attention deficit hyperactivity. We developed three quantitative phenotypes for ADHD from nine inattentive and nine hyperactive-impulsive symptoms that were used in SNP-by-SES interaction analyses using a new methodology implemented in the computer program PBAT. Findings were adjusted for multiple comparisons using the false discovery rate. We found multiple significant SNP-by-SES interactions using the inattentive symptom count. This study suggests that different SES classes may modify the effect of the functional variant(s) in and around BDNF to have an impact on the number of ADHD symptom counts that are observed. The two exons within BDNF represent potential functional variants that may be causing the observed associations.

Attention Deficit Disorder with Hyperactivity↗