Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture

Gaurav Bhatia, Arti Tandon, Nick Patterson, Melinda C. Aldrich, Christine B. Ambrosone, Christopher Amos, Elisa V. Bandera, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Cathryn H. Bock, Neil Caporaso, Graham Casey, Sandra L. Deming, W. Ryan Diver, Susan M. Gapstur, Elizabeth M. Gillanders, Curtis C. Harris, Brian E. Henderson, Sue A. Ingles & 29 others William Isaacs, Phillip L. De Jager, Esther M. John, Rick A Kittles, Emma Larkin, Lorna H. McNeill, Robert C. Millikan, Adam Murphy, Christine Neslund-Dudas, Sarah Nyante, Michael F. Press, Jorge L. Rodriguez-Gil, Benjamin A. Rybicki, Ann G. Schwartz, Lisa B. Signorello, Margaret Spitz, Sara S. Strom, Margaret A. Tucker, John K. Wiencke, John S. Witte, Xifeng Wu, Yuko Yamamura, Krista A. Zanetti, Wei Zheng, Regina G. Ziegler, Stephen J. Chanock, Christopher A. Haiman, David Reich, Alkes L. Price

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.

Original languageEnglish (US)
Pages (from-to)437-444
Number of pages8
JournalAmerican Journal of Human Genetics
Volume95
Issue number4
DOIs
StatePublished - 2014
Externally publishedYes

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African Americans
Genome
Gene Frequency
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)
  • Medicine(all)

Cite this

Bhatia, G., Tandon, A., Patterson, N., Aldrich, M. C., Ambrosone, C. B., Amos, C., ... Price, A. L. (2014). Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. American Journal of Human Genetics, 95(4), 437-444. https://doi.org/10.1016/j.ajhg.2014.08.011

Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. / Bhatia, Gaurav; Tandon, Arti; Patterson, Nick; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Bock, Cathryn H.; Caporaso, Neil; Casey, Graham; Deming, Sandra L.; Diver, W. Ryan; Gapstur, Susan M.; Gillanders, Elizabeth M.; Harris, Curtis C.; Henderson, Brian E.; Ingles, Sue A.; Isaacs, William; De Jager, Phillip L.; John, Esther M.; Kittles, Rick A; Larkin, Emma; McNeill, Lorna H.; Millikan, Robert C.; Murphy, Adam; Neslund-Dudas, Christine; Nyante, Sarah; Press, Michael F.; Rodriguez-Gil, Jorge L.; Rybicki, Benjamin A.; Schwartz, Ann G.; Signorello, Lisa B.; Spitz, Margaret; Strom, Sara S.; Tucker, Margaret A.; Wiencke, John K.; Witte, John S.; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A.; Zheng, Wei; Ziegler, Regina G.; Chanock, Stephen J.; Haiman, Christopher A.; Reich, David; Price, Alkes L.

In: American Journal of Human Genetics, Vol. 95, No. 4, 2014, p. 437-444.

Research output: Contribution to journalArticle

Bhatia, G, Tandon, A, Patterson, N, Aldrich, MC, Ambrosone, CB, Amos, C, Bandera, EV, Berndt, SI, Bernstein, L, Blot, WJ, Bock, CH, Caporaso, N, Casey, G, Deming, SL, Diver, WR, Gapstur, SM, Gillanders, EM, Harris, CC, Henderson, BE, Ingles, SA, Isaacs, W, De Jager, PL, John, EM, Kittles, RA, Larkin, E, McNeill, LH, Millikan, RC, Murphy, A, Neslund-Dudas, C, Nyante, S, Press, MF, Rodriguez-Gil, JL, Rybicki, BA, Schwartz, AG, Signorello, LB, Spitz, M, Strom, SS, Tucker, MA, Wiencke, JK, Witte, JS, Wu, X, Yamamura, Y, Zanetti, KA, Zheng, W, Ziegler, RG, Chanock, SJ, Haiman, CA, Reich, D & Price, AL 2014, 'Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture', American Journal of Human Genetics, vol. 95, no. 4, pp. 437-444. https://doi.org/10.1016/j.ajhg.2014.08.011
Bhatia, Gaurav ; Tandon, Arti ; Patterson, Nick ; Aldrich, Melinda C. ; Ambrosone, Christine B. ; Amos, Christopher ; Bandera, Elisa V. ; Berndt, Sonja I. ; Bernstein, Leslie ; Blot, William J. ; Bock, Cathryn H. ; Caporaso, Neil ; Casey, Graham ; Deming, Sandra L. ; Diver, W. Ryan ; Gapstur, Susan M. ; Gillanders, Elizabeth M. ; Harris, Curtis C. ; Henderson, Brian E. ; Ingles, Sue A. ; Isaacs, William ; De Jager, Phillip L. ; John, Esther M. ; Kittles, Rick A ; Larkin, Emma ; McNeill, Lorna H. ; Millikan, Robert C. ; Murphy, Adam ; Neslund-Dudas, Christine ; Nyante, Sarah ; Press, Michael F. ; Rodriguez-Gil, Jorge L. ; Rybicki, Benjamin A. ; Schwartz, Ann G. ; Signorello, Lisa B. ; Spitz, Margaret ; Strom, Sara S. ; Tucker, Margaret A. ; Wiencke, John K. ; Witte, John S. ; Wu, Xifeng ; Yamamura, Yuko ; Zanetti, Krista A. ; Zheng, Wei ; Ziegler, Regina G. ; Chanock, Stephen J. ; Haiman, Christopher A. ; Reich, David ; Price, Alkes L. / Genome-wide scan of 29,141 African Americans finds no evidence of directional selection since admixture. In: American Journal of Human Genetics. 2014 ; Vol. 95, No. 4. pp. 437-444.
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abstract = "The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study's conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.",
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AU - Tandon, Arti

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AU - Aldrich, Melinda C.

AU - Ambrosone, Christine B.

AU - Amos, Christopher

AU - Bandera, Elisa V.

AU - Berndt, Sonja I.

AU - Bernstein, Leslie

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AU - Caporaso, Neil

AU - Casey, Graham

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AU - Diver, W. Ryan

AU - Gapstur, Susan M.

AU - Gillanders, Elizabeth M.

AU - Harris, Curtis C.

AU - Henderson, Brian E.

AU - Ingles, Sue A.

AU - Isaacs, William

AU - De Jager, Phillip L.

AU - John, Esther M.

AU - Kittles, Rick A

AU - Larkin, Emma

AU - McNeill, Lorna H.

AU - Millikan, Robert C.

AU - Murphy, Adam

AU - Neslund-Dudas, Christine

AU - Nyante, Sarah

AU - Press, Michael F.

AU - Rodriguez-Gil, Jorge L.

AU - Rybicki, Benjamin A.

AU - Schwartz, Ann G.

AU - Signorello, Lisa B.

AU - Spitz, Margaret

AU - Strom, Sara S.

AU - Tucker, Margaret A.

AU - Wiencke, John K.

AU - Witte, John S.

AU - Wu, Xifeng

AU - Yamamura, Yuko

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AU - Zheng, Wei

AU - Ziegler, Regina G.

AU - Chanock, Stephen J.

AU - Haiman, Christopher A.

AU - Reich, David

AU - Price, Alkes L.

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