期刊文献+
任意字段
题名或关键词
题名
关键词
文摘
作者
第一作者
机构
刊名
分类号
参考文献
作者简介
基金资助
栏目信息

随机SNP在全基因组关联研究人群分层分析中的应用

Analysis of population stratification using random SNPs in genome-wide association studies
下载PDF
导出
摘要 在复杂疾病的全基因组关联研究中,人群分层现象会增加结果的假阳性率,因此考虑人群遗传结构、控制人群分层是很有必要的。而在人群分层研究中,使用随机选择的SNP的效果还有待进一步探讨。文章利用HapMap Phase2人群中无关个体的Affymetrix SNP6.0芯片分型数据,在全基因组上随机均匀选择不同数量的SNP,同时利用f值和Fisher精确检验方法筛选祖先信息标记(Ancestry Informative markers,AIMs)。然后利用HapMap Phase3中的无关个体的数据,以F-statistics和STRUCTURE分析两种方法评估所选出的不同SNP组合对人群的区分效果。研究发现,随机均匀分布于全基因组的SNP可用于识别人群内部存在的遗传结构。文章进一步提示,在全基因组关联研究中,当没有针对特定人群的AIMs时,可在全基因组上随机选择3000以上均匀分布的SNP来控制人群分层。 Since population genetic STRUCTURE can increase false-positive rate in genome-wide association studies （GWAS） for complex diseases, the effect of population stratification should be taken into account in GWAS. However, the effect of randomly selected SNPs in population stratification analysis is underdetermined. In this study, based on the genotype data generated on Genome-Wide Human SNP Array 6.0 from unrelated individuals of HapMap Phase2, we randomly selected SNPs that were evenly distributed across the whole-genome, and acquired Ancestry Informative Markers （AIMs） by the method of f value and allelic Fisher exact test. F-statistics and STRUCTURE analysis based on the select different sets of SNPs were used to evaluate the effect of distinguishing the populations from HapMap Phase3. We found that randomly selected SNPs that were evenly distributed across the whole-genome were able to be used to identify the population structure. This study further indicated that more than 3 000 randomly selected SNPs that were evenly distributed across the whole-genome were substituted for AIMs in population stratification analysis, when there were no available AIMs for spe-cific populations.
作者 曹宗富 马传香 王雷 蔡斌
机构地区 生物芯片北京国家工程研究中心 博奥生物有限公司
出处 《遗传》 CAS CSCD 北大核心 2010年第9期921-928,共8页 Hereditas（Beijing)
基金 国家高技术研究发展计划项目(863计划)(编号:2009AA022708)资助
关键词 全基因组关联研究 人群分层 祖先信息标记 随机SNP AFFYMETRIX SNP 6.0芯片 genome-wide association study population stratification ancestry informative markers random SNP Af-fymetrix SNP 6.0 array
分类号 Q987 [生物学—遗传学]
  • 相关文献

参考文献21

  • 1Wang WY, Barratt BJ, Clayton DG, Todd JA. Ge-nome-wide association studies: theoretical and practical concerns. Nat Rev Genet, 2005, 6(2): 109-118.
  • 2Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet, 2006, 7(10): 781-791.
  • 3The Wellcome Trust Case Control Consortium. Ge-nome-wide association study of 14 000 cases of seven common diseases and 3 000 shared controls. Nature, 2007, 447(7145): 661-683.
  • 4Zhang XJ, Huang W, Yang S, Sun LD, Zhang FY, Zhu QX, Zhang FR, Zhang C, Du WH, Pu XM, Li H, Xiao FL, Wang ZX, Cui Y, Hao F, Zheng J, Yang XQ, Cheng H, He CD, Liu XM, Xu LM, Zheng HF, Zhang SM, Zhang JZ, Wang HY, Cheng YL, Ji BH, Fang QY, Li YZ, Zhou FS, Han JW, Quan C, Chen B, Liu JL, Lin D, Fan L, Zhang AP, Liu SX, Yang CJ, Wang PG, Zhou WM, Lin GS, Wu WD, Fan X, Gao M, Yang BQ, Lu WS, Zhang Z, Zhu KJ, Shen SK, Li M, Zhang XY, Cao TT, Ren W, Zhang X, He J, Tang XF, Lu S, Yang JQ, Zhang L, Wang DN, Yuan F, Yin XY, Huang HJ, Wang HF, Lin XY, Liu JJ. Psoriasis ge-nome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. Nat Genet, 2009, 41(2): 205-210.
  • 5Han JW, Zheng HF, Cui Y, Sun LD, Ye DQ, Hu Z, Xu JH, Cai ZM, Huang W, Zhao GP, Xie HF, Fang H, Lu QJ, Xu JH, Li XP, Pan YF, Deng DQ, Zeng FQ, Ye ZZ, Zhang XY, Wang QW, Hao F, Ma L, Zuo XB, Zhou FS, Du WH, Cheng YL, Yang JQ, Shen SK, Li J, Sheng YJ, Zuo XX, Zhu WF, Gao F, Zhang PL, Guo Q, Li B, Gao M, Xiao FL, Quan C, Zhang C, Zhang Z, Zhu KJ, Li Y, Hu DY, Lu WS, Huang JL, Liu SX, Li H, Ren YQ, Wang ZX, Yang CJ, Wang PG, Zhou WM, Lv YM, Zhang AP, Zhang SQ, Lin D, Li Y, Low HQ, Shen M, Zhai ZF, Wang Y, Zhang FY, Yang S, Liu JJ, Zhang XJ. Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus. Nat Genet, 2009, 41(11): 1234-1237.
  • 6Gudmundsson J, Sulem P, Manolescu A, Amundadottir LT, Gudbjartsson D, Helgason A, Rafnar T, Bergthorsson JT, Agnarsson BA, Baker A, Sigurdsson A, Benediktsdottir KR, Jakobsdottir M, Xu J, Blondal T, Kostic J, Sun J, Ghosh S, Stacey SN, Mouy M, Saemundsdottir J, Backman VM, Kristjansson K, Tres A, PartinAW, Albers- Akkers MT, Godino-Ivan Marcos J, Walsh PC, Swinkels DW, Navarrete S, Isaacs SD, Aben KK, Graif T, Cashy J, Ruiz-Echarri M, Wiley KE, Suarez BK, Witjes JA, Frigge M, Ober C, Jonsson E, Einarsson GV, Mayordomo JI, Kiemeney LA, Isaacs WB, Catalona WJ, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet, 2007, 39(5): 631-637.
  • 7Papassotiropoulos A, Stephan DA, Huentelman MJ, Ho-erndli FJ, Craig DW, Pearson JV, Huynh KD, Brunner F, Corneveaux J, Osborne D, Wollmer MA, Aerni A, Coluc-cia D, H?nggi J, Mondadori CR, Buchmann A, Reiman EM, Caselli RJ, Henke K, de Quervain DJ. Common Kibra alleles are associated with human memory performance. Science, 2006, 314(5798): 475-478.
  • 8Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S, Balkau B, Heude B, Charpentier G, Hudson TJ, Montpetit A, Pshez-hetsky AV, Prentki M, Posner BI, Balding DJ, Meyre D, Polychronakos C, Froguel P. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature, 2007, 445(7130): 881-885.
  • 9Bouatia-Naji N, Bonnefond A, Cavalcanti-Proen?a C, Spars? T, Holmkvist J, Marchand M, Delplanque J, Lob-bens S, Rocheleau G, Durand E, De Graeve F, Chèvre JC, Borch-Johnsen K, Hartikainen AL, Ruokonen A, Tichet J, Marre M, Weill J, Heude B, Tauber M, Lemaire K, Schuit F, Elliott P, J?rgensen T, Charpentier G, Hadjadj S, Cauchi S, Vaxillaire M, Sladek R, Visvikis-Siest S, Balkau B, Lévy-Marchal C, Pattou F, Meyre D, Blakemore AI, Jar-velin MR, Walley AJ, Hansen T, Dina C, Pedersen O, Froguel P. A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. Nat Genet, 2009, 41(1): 89-94.
  • 10Bouatia-Naji N, Rocheleau G, Van Lommel L, Lemaire K, Schuit F, Cavalcanti-Proen?a C, Marchand M, Hartikainen AL, Sovio U, De Graeve F, Rung J, Vaxillaire M, Tichet J, Marre M, Balkau B, Weill J, Elliott P, Jarvelin MR, Meyre D, Polychronakos C, Dina C, Sladek R, Froguel P. A polymor-phism within the G6PC2 gene is associated with fasting plasma glucose levels. Science, 2008, 320(5879): 1085-1088.
遗传
2010年 第9期

相关作者

内容加载中请稍等...

相关机构

内容加载中请稍等...

相关主题

内容加载中请稍等...

浏览历史

内容加载中请稍等...
;
使用帮助 返回顶部