Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples

被引：15

作者：

Hong, H. ^{[1
]}

Shi, L. ^{[1
]}

Su, Z. ^{[1
]}

Ge, W. ^{[1
]}

Jones, W. D. ^{[2
]}

Czika, W. ^{[3
]}

Miclaus, K. ^{[3
]}

Lambert, C. G. ^{[4
]}

Vega, S. C. ^{[5
]}

Zhang, J. ^{[6
]}

Ning, B. ^{[7
]}

Liu, J. ^{[7
]}

Green, B. ^{[7
]}

Xu, L. ^{[1
]}

Fang, H. ^{[8
]}

Perkins, R. ^{[1
]}

Lin, S. M. ^{[9
]}

Jafari, N. ^{[10
]}

Park, K. ^{[11
]}

Ahn, T. ^{[11
]}

Chierici, M. ^{[12
]}

Furlanello, C. ^{[12
]}

Zhang, L. ^{[13
]}

Wolfinger, R. D. ^{[3
]}

Goodsaid, F. ^{[13
]}

Tong, W. ^{[1
]}

机构：

[1] US FDA, Div Syst Toxicol, Natl Ctr Toxicol Res, Jefferson, AR 72079 USA

[2] Express Anal, Suite, NC USA

[3] SAS Inst, Cary, NC USA

[4] Golden Helix, Bozeman, MT USA

[5] Microsoft Corp, Hlth Solut Grp, Seattle, WA USA

[6] Syst Analyt, Waltham, MA USA

[7] US FDA, Div Personalized Nutr & Med, Natl Ctr Toxicol Res, Jefferson, AR USA

[8] US FDA, Z Tech Corp, Natl Ctr Toxicol Res, Jefferson, AR USA

[9] Northwestern Univ, Biomed Informat Ctr, Chicago, IL 60611 USA

[10] Northwestern Univ, Ctr Genet Med, Chicago, IL 60611 USA

[11] Samsung Adv Inst Technol, Yongin, Gyeonggi Do, South Korea

[12] Fondaz Bruno Kessler, Trento, Italy

[13] US FDA, Off Clin Pharmacol, Ctr Drug Evaluat & Res, Silver Spring, MD USA

来源：

PHARMACOGENOMICS JOURNAL | 2010年 / 10卷 / 04期

关键词：

repeatability; association; genotype; calling algorithm; intensity; copy number; POPULATION STRATIFICATION; BREAST-CANCER; SUSCEPTIBILITY VARIANT; MACULAR DEGENERATION; COLORECTAL-CANCER; CROHN-DISEASE; RISK LOCUS; SNPS; SCAN; GENE;

D O I：

10.1038/tpj.2010.24

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

The discordance in results of independent genome-wide association studies (GWAS) indicates the potential for Type I and Type II errors. We assessed the repeatibility of current Affymetrix technologies that support GWAS. Reasonable reproducibility was observed for both raw intensity and the genotypes/copy number variants. We also assessed consistencies between different SNP arrays and between genotype calling algorithms. We observed that the inconsistency in genotypes was generally small at the specimen level. To further examine whether the differences from genotyping and genotype calling are possible sources of variation in GWAS results, an association analysis was applied to compare the associated SNPs. We observed that the inconsistency in genotypes not only propagated to the association analysis, but was amplified in the associated SNPs. Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results. The Pharmacogenomics Journal (2010) 10, 364-374; doi: 10.1038/tpj.2010.24; published online 6 April 2010

引用

页码：364 / 374

页数：11

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