• 我要登录|
  • 免费注册
    |
  • 我的丁香通
    • 企业机构:
    • 成为企业机构
    • 个人用户:
    • 个人中心
  • 移动端
    移动端
丁香通 logo丁香实验_LOGO
搜实验

    大家都在搜

      大家都在搜

        0 人通过求购买到了急需的产品
        免费发布求购
        发布求购
        点赞
        收藏
        wx-share
        分享

        Overview of Admixture Mapping

        互联网

        1244
        • Abstract
        • Table of Contents
        • Figures
        • Literature Cited

        Abstract

         

        Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping has been applied most often to African Americans who trace ancestry to Europeans and West Africans. Recent developments in admixture mapping include improvements in methods to take advantage of higher densities of genetic variants, as well as extensions to admixed populations with three or more ancestral populations, such as Latino Americans. In this unit, the author outlines the key concepts of admixture mapping. The author describes several approaches for inferring local ancestry and provides strategies for performing admixture mapping depending on the study design. Finally, the author compares and contrasts linkage analysis, association analysis, and admixture mapping, with an emphasis on integrating admixture mapping and association testing. Curr. Protoc. Hum. Genet. 76:1.23.1?1.23.8. © 2013 by John Wiley & Sons, Inc.

        Keywords: admixture; admixture mapping; ancestry

             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Table of Contents

        • Introduction
        • Key Concepts
        • Strategic Approaches
        • Commentary
        • Conclusions
        • Acknowledgments
        • Literature Cited
        • Figures
             
         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Materials

         
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library

        Figures

        •   Figure 1.23.1 The admixture process. After two generations of interbreeding between previously isolated parental populations, chromosomes in admixed individuals are mosaics of ancestry.
          View Image
        •   Figure 1.23.2 Marker density to detect all ancestry switches. The number of ancestry switches detected as a function of marker density for an individual with the median number ( n = 191, solid line) or most extreme numbers ( n = 35 or 737, dashed lines) of ancestry switches among 1976 African Americans (Adeyemo et al., ). For admixed African Americans, high‐throughput genotyping of approximately 1 million markers using commercially available microarrays is more than sufficient to extract all of the information on local ancestry.
          View Image
        •   Figure 1.23.3 Detecting excess ancestry at a disease locus. The black line represents local ancestry among controls and the red line represents local ancestry among cases. Excess local ancestry in cases but not in controls suggests the presence of a disease locus.
          View Image

        Videos

        Literature Cited

        Literature Cited
           Adeyemo, A., Gerry, N., Chen, G., Herbert, A., Doumatey, A., Huang, H., Zhou, J., Lashley, K., Chen, Y., Christman, M., and Rotimi, C. 2009. A genome‐wide association study of hypertension and blood pressure in African Americans. PLoS Genet. 5:e100564.
           Baran, Y., Pasaniuc, B., Sankararaman, S., Torgerson, D.G., Gignoux, C., Eng, C., Rodriguez‐Cintron, W., Chapela, R., Ford, J.G., Avila, P.C., Rodriguez‐Santana, J., Burchard, E.G., and Halperin, E. 2012. Fast and accurate inference of local ancestry in Latino populations. Bioinformatics 28:1359‐1367.
           Henn, B.M., Botigué, L.R., Gravel, S., Wang, W., Brisbin, A., Byrnes, J.K., Fadhlaoui‐Zid, K., Zalloua, P.A., Moreno‐Estrada, A., Bertranpetit, J., Bustamante, C.D., and Comas, D. 2012. Genomic ancestry of North Africans supports back‐to‐Africa migrations. PLoS Genet. 8:e1002397.
           Hinch, A.G., Tandon, A., Patterson, N., Song, Y., Rohland, N., Palmer, C.D., Chen, G.K., Wang, K., Buxbaum, S.G., Akylbekova, E.L., Aldrich, M.C., Ambrosone, C.B., Amos, C., Bandera, E.V., Berndt, S.I., Bernstein, L., Blot, W.J., Bock, C.H., Boerwinkle, E., Cai, Q., Caporaso, N., Casey, G., Cupples, L.A., Deming, S.L., Diver, W.R., Divers, J., Fornage, M., Gillanders, E.M., Glessner, J., Harris, C.C., Hu, J.J., Ingles, S.A., Isaacs, W., John, E.M., Kao, W.H.L., Keating, B., Kittles, R.A., Kolonel, L.N., Larkin, E., Le Marchand, L., McNeill, L.H., Millikan, R.C., Murphy, A., Musani, S., Neslund‐Dudas, C., Nyante, S., Papanicolaou, G.J., Press, M.F., Psaty, B.M., Reiner, A.P., Rich, S.S., Rodriguez‐Gil, J.L., Rotter, J.I., Rybicki, B.A., Schwartz, A.G., Signorello, L.B., Spitz, M., Strom, S.S., Thun, M.J., Tucker, M.A., Wang, Z., Wiencke, J.K., Witte, J.S., Wrensch, M., Wu, X., Yamamura, Y., Zanetti, K.A., Zheng, W., Ziegler, R.G., Zhu, X., Redline, S., Hirschhorn, J.N., Henderson, B.E., Taylor, H.A. Jr., Price, A.L., Hakonarson, H., Chanock, S.J., Haiman, C.A., Wilson, J.G., Reich, D. and Myers, S. 2011. The landscape of recombination in African Americans. Nature 476:170‐175.
           Hoggart, C.J., Shriver, M.D., Kittles, R.A., Clayton, D.G., and McKeigue, P.M. 2004. Design and analysis of admixture mapping studies. Am. J. Hum. Genet. 74:965‐978.
           Montana, G. and Pritchard, J.K. 2004. Statistical tests for admixture mapping with case‐control and cases‐only data. Am. J. Hum. Genet. 75:771‐789.
           Pasaniuc, B., Zaitlen, N., Lettre, G., Chen, G.K., Tandon, A., Kao, W.H.L., Ruczinski, I., Fornage, M., Siscovick, D.S., Zhu, X., Larkin, E., Lange, L.A., Cupples, L.A., Yang, Q., Akylbekova, E.L., Musani, S.K., Divers, J., Mychaleckyj, J., Li, M., Papanicolaou, G.J., Millikan, R.C., Ambrosone, C.B., John, E.M., Bernstein, L., Zheng, W., Hu, J.J., Ziegler, R.G., Nyante, S.J., Bandera, E.V., Ingles, S.A., Press, M.F., Chanock, S.J., Deming, S.L., Rodriguez‐Gil, J.L., Palmer, C.D., Buxbaum, S., Ekunwe, L., Hirschhorn, J.N., Henderson, B.E., Myers, S., Haiman, C.A., Reich, D., Patterson, N., Wilson, J.G., and Price, A.L. 2011. Enhanced statistical tests for GWAS in admixed populations: Assessment using African Americans from CARe and a Breast Cancer Consortium. PLoS Genet. 7:e1001371.
           Patterson, N., Hattangadi, N., Lane, B., Lohmueller, K.E., Hafler, D.A., Oksenberg, J.R., Hauser, S.L., Smith, M.W., O'Brien, S.J., Altshuler, D., Daly, M.J., and Reich, D. 2004. Methods for high‐density admixture mapping of disease genes. Am. J. Hum. Genet. 74:979‐1000.
           Price, A.L., Tandon, A., Patterson, N., Barnes, K.C., Rafaels, N., Ruczinski, I., Beaty, T.H., Mathias, R., Reich, D., and Myers, S. 2009. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5:e100519.
           Qin, H., Morris, N., Kang, S.J., Li, M., Tayo, B., Lyon, H., Hirschhorn, J., Cooper, R.S., and Zhu, X. 2010. Interrogating local population structure for fine mapping in genome‐wide association studies. Bioinformatics 26:2961‐2968.
           Redden, D.T., Divers, J., Vaughan, L.K., Tiwari, H.K., Beasley, T.M., Fernández, J.R., Kimberly, R.P., Feng, R., Padilla, M.A., Liu, N., Miller, M.B., and Allison, D.B. 2006. Regional admixture mapping and structured association testing: Conceptual unification and an extensible general linear model. PLoS Genet. 2:e137.
           Rife, D.C. 1954. Populations of hybrid origin as source material for the detection of linkage. Am. J. Hum. Genet. 6:26‐33.
           Rosenberg, N.A., Li, L.M., Ward, R., and Pritchard, J.K. 2003. Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 73:1402‐1422.
           Sankararaman, S., Sridhar, S., Kimmel, G., and Halperin, E. 2008. Estimating local ancestry in admixed populations. Am. J. Hum. Genet. 82:290‐303.
           Sha, Q., Zhang, X., Zhu, X., and Zhang, S. 2006. Analytical correction for multiple testing in admixture mapping. Hum. Hered. 62:55‐63.
           Shriner, D., Adeyemo, A., Ramos, E., Chen, G., and Rotimi, C.N. 2011a. Mapping of disease‐associated variants in admixed populations. Genome Biol. 12:223.
           Shriner, D., Adeyemo, A., and Rotimi, C.N. 2011b. Joint ancestry and association testing in admixed individuals. PLoS Comput. Biol. 7:e1002325.
           Smith, M.W., Patterson, N., Lautenberger, J.A., Truelove, A.L., McDonald, G.J., Waliszewska, A., Kessing, B.D., Malasky, M.J., Scafe, C., Le, E., De Jager, P.L., Mignault, A.A., Yi, Z., De Thé, G., Essex, M., Sankalé, J.L., Moore, J.H., Poku, K., Phair, J.P., Goedert, J.J., Vlahov, D., Williams, S.M., Tishkoff, S.A., Winkler, C.A., De La Vega, F.M., Woodage, T., Sninsky, J.J., Hafler, D.A., Altshuler, D., Gilbert, D.A., O'Brien, S.J., and Reich, D. 2004. A high‐density admixture map for disease gene discovery in African Americans. Am. J. Hum. Genet. 74:1001‐1013.
           Tang, H., Siegmund, D.O., Johnson, N.A., Romieu, I., and London, S.J. 2010. Joint testing of genotype and ancestry association in admixed families. Genet. Epidemiol. 34:783‐791.
           Winkler, C.A., Nelson, G.W., and Smith, M.W. 2010. Admixture mapping comes of age. Annu. Rev. Genomics Hum. Genet. 11:65‐89.
        GO TO THE FULL PROTOCOL:
        PDF or HTML at Wiley Online Library
         
        ad image
        提问
        扫一扫
        丁香实验小程序二维码
        实验小助手
        丁香实验公众号二维码
        扫码领资料
        反馈
        TOP
        打开小程序