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Results for “single nucleotide polymorphisms”

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PubMed2006

Single nucleotide polymorphisms for integrative mapping in the Turkey (Meleagris gallopavo).

When multiple genetic maps exist for a species, integration of these maps requires a set of common markers be genotyped across the individual mapping populations. In the turkey, three genetic maps based on separate mapping populations are available. In this study, SNP-based markers were developed for integrating the cDNA/RFLP-based map (1) with microsatellite markers of the second-generation turkey genome map (2). Forty-eight primer sets were designed and tested and 33 (69%) correctly amplified turkey genomic DNA by PCR. Putative SNPs were detected in 20 (61%) of the amplified gene fragments, and 10 SNP markers were subsequently genotyped by PCR/RFLP for segregation analysis. Eight SNP markers were incorporated into the turkey genetic map.

Animals↗
PubMed2002

Single nucleotide polymorphism seeking long term association with complex disease.

Successful investigation of common diseases requires advances in our understanding of the organization of the genome. Linkage disequilibrium provides a theoretical basis for performing candidate gene or whole-genome association studies to analyze complex disease. However, to constructively interrogate SNPs for these studies, technologies with sufficient throughput and sensitivity are required. A plethora of suitable and reliable methods have been developed, each of which has its own unique advantage. The characteristics of the most promising genotyping and polymorphism scanning technologies are presented. These technologies are examined both in the context of complex disease investigation and in their capacity to face the unique physical and molecular challenges (allele amplification, loss of heterozygosity and stromal contamination) of solid tumor research.

Biotechnology↗
PubMed2002

A cautionary note: false homozygosity for BRCA2 6174delT mutation resulting from a single nucleotide polymorphism masking the wt allele.

Sequencing an amplification product of the terminal segment of BRCA2 exon 11 showed apparent homozygosity for the 6174delT mutation in two healthy sisters. Subsequent sequencing of an alternate overlapping amplicon revealed the presence of the 5972C >T polymorphism, which is within the standard upstream amplification primer. This mismatch was responsible for the failure to amplify the normal (5972T) allele in both sisters who were heterozygous for the 6174delT mutation. Though the unexpected finding of apparent homozygosity for the 6174delT mutation prompted re-evaluation of the assay, the potential for false negative results due to masking of a mutation-bearing allele by such a circumstance should be a cautionary note for the testing and also in the interpretation of the results published under such assay conditions.

DNA Primers↗
PubMed2005

Single nucleotide polymorphism: a new risk factor for endometrial cancer?

Continuous identification of common polymorphisms in various genes helps us to understand the possible association between endometrial cancer risk and the germline polymorphism. Estrogen receptor genes and the group of genes associated with the metabolism of estrogen have been investigated well. Second, the polymorphism in the p53 gene and the genes involved in its downstream pathway were correlated to a risk of developing endometrial cancer. Finally, the polymorphism in the genes involved in cellular proliferation and differentiation, regulating cell cycles, and DNA-damage repair were studied. In this way, recent research has begun to identify common genetic polymorphisms that augment the effects of risk-factor exposure, such as genes that affect the metabolism of hormones or are involved in cellular anti-tumor activities. The accumulation of data through these approaches would make genetic testing for the risk of development of endometrial cancer possible in the near future.

Endometrial Neoplasms↗
PubMed2006

A single nucleotide polymorphism genotyping method using phosphate-affinity polyacrylamide gel electrophoresis.

To date, various methods have been developed to facilitate the genotyping of a single nucleotide polymorphism (SNP) for aiding in the diagnosis and treatment of inherited diseases. The most commonly used method for SNP genotyping is an allele-specific hybridization procedure using an expensive fluorochrome-labeled oligonucleotide probe and a specialized fluorescence analyzer. Here, we introduce a simple and reliable genotyping method using a 1:1 mixture of 5'-phosphate-labeled and nonlabeled allele-specific polymerase chain reaction (PCR) primers. The method is based on the difference in mobility of the phosphorylated and nonphosphorylated PCR products (in the same number of basepairs) on phosphate-affinity polyacrylamide gel electrophoresis. The phosphate-affinity site is a polyacrylamide-bound dinuclear zinc(II) complex, which preferentially captures the 5'-phosphate-labeled allele-specific product compared with the corresponding nonlabeled product. The obtained DNA migration bands can be visualized by ethidium bromide staining. We demonstrate the genotyping of a SNP reported in a human cardiac sodium channel gene, SCN5A, using this novel procedure.

Electrophoresis, Polyacrylamide Gel↗
PubMed2003

Single nucleotide polymorphism study of IDDM 17 in a Bedouin Arab family.

Type 1 diabetes is an autoimmune disease caused by a combination of genetic and environmental factors. On the basis of a genomic search for linkage in a Bedouin Arab family with 19 members with type 1 diabetes, we previously mapped the IDDM 17 locus to the chromosome 10q25.1 region. The result from a recent genome scan showed suggestive evidence of linkage of IDDM 17 in a subset of Caucasian families in which all affected individuals have DR3, indicating that the IDDM 17 locus might have a measurable effect in Caucasian populations from the United Kingdom and the United States. High-resolution SNP typing provides strong evidence of linkage disequilibrium to the IDDM 17 locus.

Arabs↗
PubMed2004

[Study on significance of single nucleotide polymorphisms in the redox domain of aprimidinic/apurinic endonuclease/redox factor-1 gene in Chinese sporadic colorectal cancer].

OBJECTIVE: To investigate the relationship between the single nucleotide polymorphisms(SNPs) in the redox domain of aprimidinic/apurinic endonuclease/redox factor-1(APEX) gene and the development of sporadic colorectal cancer. METHODS: One hundred and fifty cases of sporadic colorectal cancers and 143 peripheral blood samples from healthy population were screened for genetic polymorphisms or mutations in the redox domain by denaturing gradient gel electrophoresis followed by DNA sequencing. RESULTS: There were two SNPs identified in the redox domain of APEX gene, namely, 453G to T and 1247A to G. The gene frequencies of 453T and 1247G were 1.3% and 5.7%, respectively, in patient group, while 1.05% and 4.55%, respectively, in healthy population. The genotype distribution at the two sites in healthy population was consistent with Hardy-Weinberg equilibrium. There was no difference in gene frequencies at the two sites between cancer patients and healthy population. CONCLUSION: The polymorphisms in the redox domain of APEX gene are irrelevant to the development of sporadic colorectal cancer, but their distribution may vary greatly among tribes.

Aged↗
PubMed2005

No evidence for association between 1858 C/T single-nucleotide polymorphism of PTPN22 gene and primary Sjögren's syndrome.

One-third of first-degree relatives of patients with primary Sjögren's syndrome (pSS) suffer from other autoimmune diseases, including type I diabetes, systemic lupus erythematosus and autoimmune thyroiditis. Recently, 1858 C/T polymorphism of PTPN22 gene was reported to predispose to these autoimmune diseases. We decided to investigate whether PTPN22 gene polymorphism was also involved in the genetic predisposition to pSS in a case-control study, including 183 patients with pSS and 172 healthy controls. No significant differences in allele (T allele frequency: 7.7% in patients with pSS vs 7.8% in controls, P=0.9) and genotype frequencies of PTPN22 polymorphism were detected between patients with pSS and controls. PTPN 22 gene polymorphism was not associated with a specific pattern of autoantibody secretion either. Thus, 1858 C/T polymorphism of PTPN22 gene is not involved in genetic predisposition to pSS.

Autoantibodies↗
PubMed2004

Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data.

Most of the available SNP data have eluded valid population genetic analysis because most population genetical methods do not correctly accommodate the special discovery process used to identify SNPs. Most of the available SNP data have allele frequency distributions that are biased by the ascertainment protocol. We here show how this problem can be corrected by obtaining maximum-likelihood estimates of the true allele frequency distribution. In simple cases, the ML estimate of the true allele frequency distribution can be obtained analytically, but in other cases computational methods based on numerical optimization or the EM algorithm must be used. We illustrate the new correction method by analyzing some previously published SNP data from the SNP Consortium. Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project.

Alleles↗
PubMed2002

Single-nucleotide polymorphism in the E-cadherin gene promoter modifies the risk of prostate cancer.

E-cadherin plays a major role in intercellular adhesion, cell polarity and tissue architecture. We determined the relative risk of PCa associated with a previously reported C/A SNP at -160 bp relative to the transcription-start site of the E-cadherin gene promoter. Eighty-two PCa patients and 188 controls were genotyped. Genotype and allele frequencies differed significantly among cases and controls. A-allele carriers had a higher relative risk of PCa (OR = 3.6, 95% CI 2.0-6.4) compared to C-only carriers. AC and AA genotypes had an increased risk of PCa (OR = 3.8, 95% CI 2.1-6.8 and OR = 1.7, 95% CI 0.4-6.6, respectively) compared to CC genotypes.

Aged↗
PubMed2005

[Analysis of two single nucleotide polymorphisms in von Hippel-Lindau gene and detection of loss of heterozygosity in Chinese sporadic renal cell carcinoma].

OBJECTIVE: To exam two single nucleotide polymorphism(SNP) in VHL gene and intragenic loss of heterozygosity (LOH) of VHL gene in 79 Chinese sporadic renal cell carcinomas(RCCs), and to analyze the relationships between VHL LOH and clinicopathological parameters. METHODS: The authors extracted tumor and normal tissue DNA and detected two genotypes of intragenic SNP sites, rs779805 in the 5'terminal and rs 1642742 in the 3'terminal of VHL gene by polymerase chain reaction-restriction frament length polymorphism, then analyzed VHL LOH by comparing tumor tissue versus normal tissue in heterozygosities. Subsequently the relationships between VHL LOH and clinicopathological parameters of RCCs were analyzed. RESULTS: The computed heritage parameters of two SNPs, included genotype frequency, allele frequency, heterozygosity, and polymorphism information content. Twenty-nine heterozygosities were detected in 79 RCCs. LOH was found in 41.4%(12/29) of RCCs. No significant relationships between VHL LOH and age, sex, tumor stage, pathological grade were found. CONCLUSION: LOH of VHL gene is an important genetic event in Chinese sporadic renal carcinoma, and the LOH frequency is 41.4%. VHL LOH has no influence on stage and grade of RCC.

Adult↗
PubMed2004

Single nucleotide polymorphism for animal fibre identification.

Animal fibres are highly valuable industrial products often adulterated during marketing. Currently, there is no precise method available to identify and differentiate the fibres. In this study, a PCR-RFLP technique was exploited to differentiate cashmere and wool fibres derived from goat and sheep, respectively. The presence of DNA in animal hair shafts has enabled the isolation of DNA from scoured cashmere and wool fibres. The mitochondrial cytochrome b sequences of both species were amplified by PCR using primers designed from conserved regions. The polymorphism observed between the two species was detected by restricting the amplified product by endonucleases viz., BamH1 and Ssp1. The RFLP profile clearly distinguishes the cashmere and wool fibres and this technique can also be exploited to test adulteration in animal fibres qualitatively.

Animals↗
PubMed2006

Role of single nucleotide polymorphisms and haplotypes in BRCA1 in breast cancer: Czech case-control study.

We aimed at determining whether any association exists between six single nucleotide polymorphisms in breast cancer associated gene (BRCA1) and the risk of breast cancer. We constructed haplotypes and analyzed their importance as well. Clinico-pathological characteristics of breast cancer patients were included in the study to evaluate the prognostic impact of BRCA1 polymorphisms and haplotypes. Polymerase chain reaction-restriction fragment length polymorphism-based genotyping assays were used to determine the frequency of polymorphisms in codons 356, 871, 1038, 1183, 1436, and 1613 of BRCA1 in a group of 306 incident breast cancer patients and 313 unaffected controls of Czech origin. Statistical analyses revealed that the BRCA1 Arg356 allele may play a protective role in breast cancer (age-adjusted OR = 0.61, CI = 0.39-0.94, p = 0.026). We also observed a significant correlation between polymorphism Gln356Arg and stage (p = 0.026) in premenopausal cases suggesting that carriers of the wild Gln356Gln allele are at significantly higher risk of advanced disease. The most common haplotypes of BRCA1 did not play a significant role in breast cancer either as risk factors or as prognostic factors. The study on rare BRCA1 haplotypes however should be repeated using larger groups. In conclusion, the BRCA1-Gln356 allele presents risk factor in the onset and progression of breast cancer in Czech population and its use as a possible screening tool should be considered.

Adult↗
PubMed2001

Polysubstance abuse-vulnerability genes: genome scans for association, using 1,004 subjects and 1,494 single-nucleotide polymorphisms.

Strong genetic contributions to drug abuse vulnerability are well documented, but few chromosomal locations for human drug-abuse vulnerability alleles have been confirmed. We now identify chromosomal markers whose alleles distinguish drug abusers from control individuals in each of two samples, on the basis of pooled-sample microarray and association analyses. Reproducibly positive chromosomal regions defined by these markers in conjunction with previous results were especially unlikely to have been identified by chance. Positive markers identify the alcohol dehydrogenase (ADH) locus, flank the brain-derived neurotropic factor (BDNF) locus, and mark seven other regions previously linked to vulnerability to nicotine or alcohol abuse. These data support polygenic contributions of common allelic variants to polysubstance abuse vulnerability.

Adult↗
PubMed2003

Association of transforming growth factor beta-1 single nucleotide polymorphisms with radiation-induced damage to normal tissues in breast cancer patients.

PURPOSE: To investigate whether transforming growth factor beta-1 (TGFbeta1) single nucleotide polymorphisms were associated with the susceptibility of breast cancer patients to severe radiation-induced normal tissue damage. MATERIALS AND METHODS: PCR-RFLP assays were performed for TGFbeta1 gene polymorphisms on DNA obtained from 103 breast cancer patients who received radiotherapy. The G-800A, C-509T, T+869C and G+915C polymorphic sites were examined, and genotype and allele frequencies of two subgroups of patients were calculated and compared. RESULTS: The less prevalent -509T and +869C alleles were significantly associated with a subgroup of patients who developed severe radiation-induced normal tissue fibrosis (n=15) when compared with those who did not (n=88) (odds ratio=3.4, p=0.0036, and 2.37, p=0.035, respectively). Furthermore, patients with the -509TT or +869CC genotypes were between seven and 15 times more likely to develop severe fibrosis. CONCLUSIONS: These findings imply a role for the -509T and +869C alleles in the pathobiological mechanisms underlying susceptibility to radiation-induced fibrosis. Their predictive value would be limited to patients who are -509TT or +869CC, but if "fibrosis-associated" polymorphic sites in other genes could be identified, it may be possible to detect fibrosis prone individuals before radiotherapy with greater certainty.

Alleles↗
PubMed2005

Single nucleotide polymorphism detection in promoter III of the acetyl-CoA carboxylase-alpha gene in sheep.

Three novel SNPs were identified in the locus OAR292286, encoding the DNA sequence of promoter III of the ovine acetyl-CoA carboxylase-alpha gene, in Italian sheep of four breeds: Gentile di Puglia (25 individuals) and Sopravissana (31) which are triple-purpose local endangered breeds, Comisana (25) which is a local non-selected, non-endangered dairy breed and Sarda (15) which is a popular selected high yielding dairy breed. Variant alleles are: G/T at 1330 bp, C/G at 1338 bp and C/T at 1430 bp. Frequencies of the variant alleles were calculated and chi-squared analysis of the differences in allele frequency between breed pairs was performed. Allele frequencies of the Sarda breed differ significantly from the other considered breeds.

Acetyl-CoA Carboxylase↗
PubMed2007

Predicting single nucleotide polymorphisms (SNP) from DNA sequence by support vector machine.

Recently, SNP has gained substantial attention as genetic markers and is recognized as a key element in the development of personalized medicine. Computational prediction of SNP can be used as a guide for SNP discovery to reduce the cost and time needed for the development of personalized medicine. We have developed a method for SNP prediction based on support vector machines (SVMs) using different features extracted from the SNP data. Prediction rates of 60.9% was achieved by sequence feature, 59.1% by free-energy feature, 58.1% by GC content feature, 58.0% by melting temperature feature, 56.2% by enthalpy feature, 55.1% by entropy feature and 54.3% by the gene, exon and intron feature. We introduced a new feature, the SNP distribution score that achieved a prediction rate of 77.3%. Thus, the proposed SNP prediction algorithm can be used to in SNP discovery.

Algorithms↗
PubMed2006

The association of single nucleotide polymorphisms in the MMP-9 genes with susceptibility to acute primary angle closure glaucoma in Taiwanese patients.

PURPOSE: To study the relationships between single nucleotide polymorphisms (SNPs) of extracellular matrix, matrix metalloproteases (MMPs), tissue inhibitors of MMPs, and other glaucoma-associated genes and acute primary angle closure glaucoma (PACG). METHODS: We extracted DNA samples from 78 adult patients with acute PACG and 86 control subjects to study the relationships between these specific genes and acute PACG. Genotyping was performed for 35 genes by the GenomeLab SNPstream genotyping system after PCR amplification of chromosomal DNA. The association between these genetic polymorphisms and risk of primary PACG was estimated by chi2 and logistic regression. RESULTS: The genotyping success rate was 99%. Genotyping for the MMP9 site (rs2664538) was significantly different between the two groups (p=0.000001) and the odds ratio was 2.586 (95% CI: 1.715-3.898, p<0.00001). However, there were no associations of SNPs to other genes in patients with acute PACG. CONCLUSIONS: Our results reveal that SNP rs2664538, which is located at the MMP9 gene, is likely to be associated with acute PACG.

Acute Disease↗