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Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples
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نویسنده
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chiang c.w.k. ,gajdos z.k.z. ,korn j.m. ,kuruvilla f.g. ,butler j.l. ,hackett r. ,guiducci c. ,nguyen t.t. ,wilks r. ,forrester t. ,haiman c.a. ,henderson k.d. ,le marchand l. ,henderson b.e. ,palmert m.r. ,mckenzie c.a. ,lyon h.n. ,cooper r.s. ,zhu x. ,hirschhorn j.n.
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منبع
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plos genetics - 2010 - دوره : 6 - شماره : 3
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چکیده
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As we move forward from the current generation of genome-wide association (gwa) studies,additional cohorts of different ancestries will be studied to increase power,fine map association signals,and generalize association results to additional populations. knowledge of genetic ancestry as well as population substructure will become increasingly important for gwa studies in populations of unknown ancestry. here we propose genotyping pooled dna samples using genome-wide snp arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (aims) in populations of unknown origin. we constructed dna pools from african american,native hawaiian,latina,and jamaican samples and genotyped them using the affymetrix 6.0 array. aided by individual genotype data from the african american cohort,we established quality control filters to remove poorly performing snps and estimated allele frequencies for the remaining snps in each panel. we then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the international hapmap consortium as reference panels,and identified aims unique to each population. in this study,we demonstrated that genotyping pooled dna samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known aims. furthermore,through validation by individual genotyping,we demonstrated that pooling is quite effective for identifying snps with large allele frequency differences (i.e.,aims) and that these aims are able to differentiate two closely related populations (hapmap jpt and chb). © 2010 chiang et al.
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آدرس
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department of genetics,harvard medical school,boston,ma,united states,program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States, department of genetics,harvard medical school,boston,ma,united states,program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States, program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,center for human genetic research,massachusetts general hospital,boston,ma,united states,department of molecular biology,massachusetts general hospital,boston,ma, United States, program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,center for human genetic research,massachusetts general hospital,boston,ma,united states,department of molecular biology,massachusetts general hospital,boston,ma, United States, program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States, program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma, United States, program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma, United States, program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States, epidemiology research unit,tropical medicine research institute,university of the west indies,kingston, Jamaica, tropical metabolism research unit,tropical medicine research institute,university of the west indies,kingston, Jamaica, department of preventive medicine,keck school of medicine,university of southern california,los angeles,ca, United States, department of population sciences,division of cancer etiology,city of hope national medical center,duarte,ca, United States, epidemiology program,cancer research center of hawaii,university of hawaii,honolulu,hi, United States, department of preventive medicine,keck school of medicine,university of southern california,los angeles,ca, United States, division of endocrinology,hospital for sick children,toronto,on,canada,department of pediatrics,university of toronto,toronto,on, Canada, tropical metabolism research unit,tropical medicine research institute,university of the west indies,kingston, Jamaica, program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States, department of preventive medicine and epidemiology,stritch school of medicine,loyola university chicago,maywood,il, United States, department of biostatistics and epidemiology,case western reserve university,cleveland,oh, United States, department of genetics,harvard medical school,boston,ma,united states,program in medical and population genetics,broad institute of harvard and massachusetts institute of technology,cambridge,ma,united states,program in genomics,divisions of genetics and endocrinology,children's hospital,boston,ma, United States
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Authors
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