Human Population Genetic Structure and Inference of Group Membership Export

@article{Bamshad2003a, abstract = {A major goal of biomedical research is to develop the capability to provide highly personalized health care. To do so, it is necessary to understand the distribution of interindividual genetic variation at loci underlying physical characteristics, disease susceptibility, and response to treatment. Variation at these loci commonly exhibits geographic structuring and may contribute to phenotypic differences between groups. Thus, in some situations, it may be important to consider these groups separately. Membership in these groups is commonly inferred by use of a proxy such as place-of-origin or ethnic affiliation. These inferences are frequently weakened, however, by use of surrogates, such as skin color, for these proxies, the distribution of which bears little resemblance to the distribution of neutral genetic variation. Consequently, it has become increasingly controversial whether proxies are sufficient and accurate representations of groups inferred from neutral genetic variation. This raises three questions: how many data are required to identify population structure at a meaningful level of resolution, to what level can population structure be resolved, and do some proxies represent population structure accurately? We assayed 100 Alu insertion polymorphisms in a heterogeneous collection of sim565 individuals, sim200 of whom were also typed for 60 microsatellites. Stripped of identifying information, correct assignment to the continent of origin (Africa, Asia, or Europe) with a mean accuracy of at least 90\% required a minimum of 60 Alu markers or microsatellites and reached 99\%ndash100\% when ges100 loci were used. Less accurate assignment (87\%) to the appropriate genetic cluster was possible for a historically admixed sample from southern India. These results set a minimum for the number of markers that must be tested to make strong inferences about detecting population structure among Old World populations under ideal experimental conditions. We note that, whereas some proxies correspond crudely, if at all, to population structure, the heuristic value of others is much higher. This suggests that a more flexible framework is needed for making inferences about population structure and the utility of proxies.}, author = {Bamshad, Michael J. and Wooding, Stephen and Watkins, Scott W. and Ostler, Christopher T. and Batzer, Mark A. and Jorde, Lynn B.}, citeulike-article-id = {1775946}, citeulike-linkout-0 = {http://www.journals.uchicago.edu/cgi-bin/resolve?id=doi:10.1086/368061&erFrom=4458593044078582007Guest}, citeulike-linkout-1 = {http://dx.doi.org/10.1086/368061}, doi = {10.1086/368061}, journal = {American Journal of Human Genetics}, keywords = {alu, discriminant-function, pai, structure}, pages = {578--589}, posted-at = {2007-10-16 19:49:06}, priority = {2}, title = {Human Population Genetic Structure and Inference of Group Membership}, url = {http://dx.doi.org/10.1086/368061}, volume = {72}, year = {2003} }

TY - JOUR ID - Bamshad2003a L3 - citeulike-article-id:1775946 N2 - A major goal of biomedical research is to develop the capability to provide highly personalized health care. To do so, it is necessary to understand the distribution of interindividual genetic variation at loci underlying physical characteristics, disease susceptibility, and response to treatment. Variation at these loci commonly exhibits geographic structuring and may contribute to phenotypic differences between groups. Thus, in some situations, it may be important to consider these groups separately. Membership in these groups is commonly inferred by use of a proxy such as place-of-origin or ethnic affiliation. These inferences are frequently weakened, however, by use of surrogates, such as skin color, for these proxies, the distribution of which bears little resemblance to the distribution of neutral genetic variation. Consequently, it has become increasingly controversial whether proxies are sufficient and accurate representations of groups inferred from neutral genetic variation. This raises three questions: how many data are required to identify population structure at a meaningful level of resolution, to what level can population structure be resolved, and do some proxies represent population structure accurately? We assayed 100 Alu insertion polymorphisms in a heterogeneous collection of sim565 individuals, sim200 of whom were also typed for 60 microsatellites. Stripped of identifying information, correct assignment to the continent of origin (Africa, Asia, or Europe) with a mean accuracy of at least 90% required a minimum of 60 Alu markers or microsatellites and reached 99%ndash100% when ges100 loci were used. Less accurate assignment (87%) to the appropriate genetic cluster was possible for a historically admixed sample from southern India. These results set a minimum for the number of markers that must be tested to make strong inferences about detecting population structure among Old World populations under ideal experimental conditions. We note that, whereas some proxies correspond crudely, if at all, to population structure, the heuristic value of others is much higher. This suggests that a more flexible framework is needed for making inferences about population structure and the utility of proxies. JF - American Journal of Human Genetics EP - 589 TI - Human Population Genetic Structure and Inference of Group Membership VL - 72 SP - 578 KW - alu KW - discriminant-function KW - pai KW - structure AU - Bamshad, Michael AU - Wooding, Stephen AU - Watkins, Scott AU - Ostler, Christopher AU - Batzer, Mark AU - Jorde, Lynn PY - 2003/// UR - http://dx.doi.org/10.1086/368061 ER -