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            UHT: Ultra-High Throughput SNP Genotyping for Pharmacogenomics and Drug Discovery

Bell, Peter A.; Chaturvedi, Surendrakumar; Gelfand, Craig A.; Huang, Ching Yu; Kochersperger, Michael; Kopla, Rafael; Modica, Frank S.; Pohl, Mark; Varde, Shobha; Zhao, Renbin; Zhao, Xianzheng; Boyce-Jacino, Michael T.; Yassen, Azzam

doi:10.2144/jun0205

Cited by 165 publications

(127 citation statements)

References 9 publications

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“…Because nearly all SNPs within the exon 4 LD block have minor allele frequencies Ͻ5% in the HapMap CHB databank, we additionally selected eight SNPs with known associations with type 2 diabetes (rs4506565, rs12243326, rs7895340, rs7904146, rs12255372, rs7079711, rs11196192, and rs11196213) within this region. Genotyping was performed using the GenomeLab SNPstream genotyping platform (Beckman Coulter) and its accompanying SNPstream software suite (30). Statistical analyses.…”

Section: Methodsmentioning

confidence: 99%

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

et al. 2007

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OBJECTIVE-Genetic polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene is one of the few validated genetic variants with large effects on the risk of type 2 diabetes in the populations of European ancestry. In this study, we aimed to explore the effect of the TCF7L2 polymorphisms in a Han Chinese population. RESEARCH DESIGN AND METHODS-We genotyped 20single nucleotide polymorphisms (SNPs) across the TCF7L2 gene in 1,520 unrelated subjects from a Han Chinese population in Taiwan. The associations of SNPs and haplotypes with type 2 diabetes and linkage disequilibrium (LD) structure of the TCF7L2 gene were analyzed. RESULTS-The previously reported SNPs rs7903146 T-and rs12255372 T-alleles of the TCF7L2 gene were rare and were not associated with type 2 diabetes in a Chinese population, which may attribute to the low frequencies of these two SNPs. SNP rs290487 located in an LD block close to the 3Ј end of the gene was associated with type 2 diabetes (allele-specific P ϭ 0.0021; permuted P ϭ 0.03). The odds ratio was 1.36 for the CT genotype (95% CI 1.08Ϫ1.71; P ϭ 0.0063) and 1.51 for the CC genotype (1.10 Ϫ2.07; P ϭ 0.0085) compared with the TT genotype, corresponding to a population attributable risk fraction of 18.7%. The haplotypes composed of rs290487 were also significantly associated with type 2 diabetes (global P ϭ 0.012).CONCLUSIONS-We identified a novel risk-conferring genetic variant of TCF7L2 for type 2 diabetes in a Chinese population. Our data suggested that the TCF7L2 genetic polymorphisms are major determinants for risk of type 2 diabetes in the Chinese population. Diabetes 56: [2631][2632][2633][2634][2635][2636][2637] 2007 T ype 2 diabetes is a highly inheritable metabolic disorder of polygenetic nature (1). Although theoretical analyses emphasized the power of genetic association study in common multifactorial diseases, the search for genes that increase the risk of type 2 diabetes has not been very successful so far. The genes implicated in type 2 diabetes confer only modest effects on the disease risk and in many cases have yielded inconsistent results in replication efforts (2). Only few associations, notably the Pro12Ala polymorphism in the peroxisome proliferator-activated receptor (PPARG) gene (3), the Glu23Lys polymorphism in the KCNJ11 gene (4), and the genetic variants of calpain-10 genes (5), have been convincingly replicated.Recently, researchers seeking the cause of a previously identified linkage signal on chromosome 10q found a strong association of a common microsatellite (DG10S478) of the transcription factor 7-like 2 gene (TCF7L2) with type 2 diabetes in an Icelandic sample, and the result was replicated in the samples from the U.S. and Denmark (6). DG10S478 is located within a well-defined linkage disequilibrium (LD) block of 92.1 kb that encompassed exon 4 and parts of two large flanking introns. Five single nucleotide polymorphisms (SNPs) (rs12255372, rs7903146, rs7901695, rs11196205, and rs7895340) within the LD block also showed similarly robust associations wit...

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Section: Methodsmentioning

confidence: 99%

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

et al. 2007

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“…Genotype identification was performed with the GenomeLab SNPstream (ultra-high throughput; UHT [22]) system, which uses multiplexed polymerase chain reaction (PCR) in conjunction with tag array single-base extension genotyping (Beckman Coulter, Fullerton, CA, USA). This system and its accompanying SNPstream software has been described by Demomme and Van Oene [23].…”

Section: Selection Of Polymorphisms and Genotypingmentioning

confidence: 99%

The effects of polymorphisms in methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), and methionine synthase reductase (MTRR) on the risk of cervical intraepithelial neoplasia and cervical cancer in Korean women

Tong

Lee

Song

et al. 2009

Cancer Causes Control

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The purpose of the study was to investigate the association between cervical cancer risk and single-nucleotide polymorphisms (SNPs) in three one-carbon metabolism genes, methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), and methionine synthase reductase (MTRR) in Korean women. Twelve SNPs were identified in MTHFR, MTR, and MTRR in the 927 casecontrol samples, which included 165 cervical intraepithelial neoplasia 1 (CIN1), 167 cervical intraepithelial neoplasia 2 and 3 (CIN2/3), 155 cervical cancer patients, and 440 normal controls. The frequencies of the genotypes and haplotypes were assessed in the controls, CINs, and cervical cancers. Individual carriers of the variant allele C of MTHFR A1298C (rs1801131) had a 0.64-fold [95% confidence interval (CI): 0.42-0.98] decreased risk for CIN2/3 compared with common homozygotes. However, no significant association was found between most other variants and cervical cancer risk. The results also identified an increased CIN1 risk in carriers with at least one copy of haplotype 3 in the MTHFR gene (odds ratio, 1.88; 95% CI: 1.03-3.42). In conclusion, there was no significant association between most SNPs in MTHFR, MTR, or MTRR and the risk of CIN and cervical cancer in Korean women. In addition, there was no significant association of MTHFR haplotypes with risk of CIN2/3 and cervical cancer.

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“…Large-scale genotyping process was performed at the SNP Core Facility of Semmelweis University using a GenomeLab SNPstream Genotyping System (Beckman Coulter, Fullerton, CA, USA). This automated ultrahigh-throughput genotyping system utilizes multiplexed PCR in conjunction with tagged-array, multiplexed, single-base primer extension technology (15). Briefly, the workflow steps were as follows: 1) A multiplex PCR was applied to amplify the selected genes.…”

Section: Genotypingmentioning

confidence: 99%

Single nucleotide polymorphisms in new candidate genes are associated with bone mineral density and fracture risk

Lazáry

Kósa

Tobiás

et al. 2008

European Journal of Endocrinology

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Objective: Osteoporosis (OP) is a multifactorial disease with high heritability but its exact genetic background is still poorly understood. We examined the effect of 24 single nucleotide polymorphisms (SNPs) located in five genes -alkaline phosphatase, matrix metalloproteinase-2, tissue inhibitor of metalloproteases-2 (TIMP2), fibroblast growth factor receptor-1 (FGFR1), and fatty acid-binding protein-3 (FABP3) -previously not associated with OP. Design: We performed a genotype-phenotype association study at a university hospital. Methods: A total of 360 Hungarian postmenopausal women were involved in the study. Bone mineral density (BMD) was determined at spine, hip, and distal radius. Genomic DNA was extracted from venous blood samples and a high-throughput genotyping method based on single-based primer extension was applied for allelic discrimination. Robust statistical tools were utilized for multiplex data analysis. Results: SNP rs6996321 in FGFR1 was significantly related to spine BMD (PZ0.002) and rs10914367 in FABP3 was associated with hip BMD (PZ0.028). Non-vertebral fracture risk was significantly increased in carriers of ' A' allele of rs9900972 in TIMP2 (odds ratioZ2.06, PZ0.0187). We could also identify validated gene-gene interactions significantly affecting BMD and fracture risk. Conclusions: We identified two previously unreported SNPs in FGFR1 and FABP3 associated with BMD and a third SNP in TIMP2 related to risk for non-vertebral osteoporotic fractures. This is the first report about the association between these allelic variants and the phenotypes of postmenopausal OP. Further studies need to clarify the role of these genes and their polymorphisms in the process of bone loss.

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SNPstream ^® UHT: Ultra-High Throughput SNP Genotyping for Pharmacogenomics and Drug Discovery

Cited by 165 publications

References 9 publications

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

The effects of polymorphisms in methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), and methionine synthase reductase (MTRR) on the risk of cervical intraepithelial neoplasia and cervical cancer in Korean women

Single nucleotide polymorphisms in new candidate genes are associated with bone mineral density and fracture risk

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SNPstream ® UHT: Ultra-High Throughput SNP Genotyping for Pharmacogenomics and Drug Discovery

Cited by 165 publications

References 9 publications

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

Association Study of the Genetic Polymorphisms of the Transcription Factor 7-Like 2 (TCF7L2) Gene and Type 2 Diabetes in the Chinese Population

The effects of polymorphisms in methylenetetrahydrofolate reductase (MTHFR), methionine synthase (MTR), and methionine synthase reductase (MTRR) on the risk of cervical intraepithelial neoplasia and cervical cancer in Korean women

Single nucleotide polymorphisms in new candidate genes are associated with bone mineral density and fracture risk

Contact Info

Product

Resources

About

SNPstream ^® UHT: Ultra-High Throughput SNP Genotyping for Pharmacogenomics and Drug Discovery