The landscape of recombination in African Americans

Anjali G. Hinch, Arti Tandon, Nick Patterson, Yunli Song, Nadin Rohland, Cameron D. Palmer, Gary K. Chen, Kai Wang, Sarah G. Buxbaum, Ermeg L. Akylbekova, Melinda C. Aldrich, Christine B. Ambrosone, Christopher Amos, Elisa V. Bandera, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Cathryn H. Bock, Eric Boerwinkle, Qiuyin CaiNeil Caporaso, Graham Casey, L. Adrienne Cupples, Sandra L. Deming, W. Ryan Diver, Jasmin Divers, Myriam Fornage, Elizabeth M. Gillanders, Joseph Glessner, Curtis C. Harris, Jennifer J. Hu, Sue A. Ingles, William Isaacs, Esther M. John, W. H Linda Kao, Brendan Keating, Rick A Kittles, Laurence N. Kolonel, Emma Larkin, Loic Le Marchand, Lorna H. McNeill, Robert C. Millikan, Adam Murphy, Solomon Musani, Christine Neslund-Dudas, Sarah Nyante, George J. Papanicolaou, Michael F. Press, Bruce M. Psaty, Alex P. Reiner, Stephen S. Rich, Jorge L. Rodriguez-Gil, Jerome I. Rotter, Benjamin A. Rybicki, Ann G. Schwartz, Lisa B. Signorello, Margaret Spitz, Sara S. Strom, Michael J. Thun, Margaret A. Tucker, Zhaoming Wang, John K. Wiencke, John S. Witte, Margaret Wrensch, Xifeng Wu, Yuko Yamamura, Krista A. Zanetti, Wei Zheng, Regina G. Ziegler, Xiaofeng Zhu, Susan Redline, Joel N. Hirschhorn, Brian E. Henderson, Herman A. Taylor, Alkes L. Price, Hakon Hakonarson, Stephen J. Chanock, Christopher A. Haiman, James G. Wilson, David Reich, Simon R. Myers

Research output: Contribution to journalArticle

173 Citations (Scopus)

Abstract

Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value < 10 -245). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.

Original languageEnglish (US)
Pages (from-to)170-175
Number of pages6
JournalNature
Volume476
Issue number7359
DOIs
StatePublished - Aug 11 2011
Externally publishedYes

Fingerprint

African Americans
Genetic Recombination
Alleles
Nucleotide Motifs
Molecular Evolution
Medical Genetics
Base Pairing
Genome
Mutation
Research
Population

ASJC Scopus subject areas

  • General

Cite this

Hinch, A. G., Tandon, A., Patterson, N., Song, Y., Rohland, N., Palmer, C. D., ... Myers, S. R. (2011). The landscape of recombination in African Americans. Nature, 476(7359), 170-175. https://doi.org/10.1038/nature10336

The landscape of recombination in African Americans. / Hinch, Anjali G.; Tandon, Arti; Patterson, Nick; Song, Yunli; Rohland, Nadin; Palmer, Cameron D.; Chen, Gary K.; Wang, Kai; Buxbaum, Sarah G.; Akylbekova, Ermeg L.; Aldrich, Melinda C.; Ambrosone, Christine B.; Amos, Christopher; Bandera, Elisa V.; Berndt, Sonja I.; Bernstein, Leslie; Blot, William J.; Bock, Cathryn H.; Boerwinkle, Eric; Cai, Qiuyin; Caporaso, Neil; Casey, Graham; Cupples, L. Adrienne; Deming, Sandra L.; Diver, W. Ryan; Divers, Jasmin; Fornage, Myriam; Gillanders, Elizabeth M.; Glessner, Joseph; Harris, Curtis C.; Hu, Jennifer J.; Ingles, Sue A.; Isaacs, William; John, Esther M.; Kao, W. H Linda; Keating, Brendan; Kittles, Rick A; Kolonel, Laurence N.; Larkin, Emma; Marchand, Loic Le; McNeill, Lorna H.; Millikan, Robert C.; Murphy, Adam; Musani, Solomon; Neslund-Dudas, Christine; Nyante, Sarah; Papanicolaou, George J.; Press, Michael F.; Psaty, Bruce M.; Reiner, Alex P.; Rich, Stephen S.; Rodriguez-Gil, Jorge L.; Rotter, Jerome I.; Rybicki, Benjamin A.; Schwartz, Ann G.; Signorello, Lisa B.; Spitz, Margaret; Strom, Sara S.; Thun, Michael J.; Tucker, Margaret A.; Wang, Zhaoming; Wiencke, John K.; Witte, John S.; Wrensch, Margaret; Wu, Xifeng; Yamamura, Yuko; Zanetti, Krista A.; Zheng, Wei; Ziegler, Regina G.; Zhu, Xiaofeng; Redline, Susan; Hirschhorn, Joel N.; Henderson, Brian E.; Taylor, Herman A.; Price, Alkes L.; Hakonarson, Hakon; Chanock, Stephen J.; Haiman, Christopher A.; Wilson, James G.; Reich, David; Myers, Simon R.

In: Nature, Vol. 476, No. 7359, 11.08.2011, p. 170-175.

Research output: Contribution to journalArticle

Hinch, AG, Tandon, A, Patterson, N, Song, Y, Rohland, N, Palmer, CD, Chen, GK, Wang, K, Buxbaum, SG, Akylbekova, EL, Aldrich, MC, Ambrosone, CB, Amos, C, Bandera, EV, Berndt, SI, Bernstein, L, Blot, WJ, Bock, CH, Boerwinkle, E, Cai, Q, Caporaso, N, Casey, G, Cupples, LA, Deming, SL, Diver, WR, Divers, J, Fornage, M, Gillanders, EM, Glessner, J, Harris, CC, Hu, JJ, Ingles, SA, Isaacs, W, John, EM, Kao, WHL, Keating, B, Kittles, RA, Kolonel, LN, Larkin, E, Marchand, LL, McNeill, LH, Millikan, RC, Murphy, A, Musani, S, Neslund-Dudas, C, Nyante, S, Papanicolaou, GJ, Press, MF, Psaty, BM, Reiner, AP, Rich, SS, Rodriguez-Gil, JL, Rotter, JI, Rybicki, BA, Schwartz, AG, Signorello, LB, Spitz, M, Strom, SS, Thun, MJ, Tucker, MA, Wang, Z, Wiencke, JK, Witte, JS, Wrensch, M, Wu, X, Yamamura, Y, Zanetti, KA, Zheng, W, Ziegler, RG, Zhu, X, Redline, S, Hirschhorn, JN, Henderson, BE, Taylor, HA, Price, AL, Hakonarson, H, Chanock, SJ, Haiman, CA, Wilson, JG, Reich, D & Myers, SR 2011, 'The landscape of recombination in African Americans', Nature, vol. 476, no. 7359, pp. 170-175. https://doi.org/10.1038/nature10336
Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD et al. The landscape of recombination in African Americans. Nature. 2011 Aug 11;476(7359):170-175. https://doi.org/10.1038/nature10336
Hinch, Anjali G. ; Tandon, Arti ; Patterson, Nick ; Song, Yunli ; Rohland, Nadin ; Palmer, Cameron D. ; Chen, Gary K. ; Wang, Kai ; Buxbaum, Sarah G. ; Akylbekova, Ermeg L. ; Aldrich, Melinda C. ; Ambrosone, Christine B. ; Amos, Christopher ; Bandera, Elisa V. ; Berndt, Sonja I. ; Bernstein, Leslie ; Blot, William J. ; Bock, Cathryn H. ; Boerwinkle, Eric ; Cai, Qiuyin ; Caporaso, Neil ; Casey, Graham ; Cupples, L. Adrienne ; Deming, Sandra L. ; Diver, W. Ryan ; Divers, Jasmin ; Fornage, Myriam ; Gillanders, Elizabeth M. ; Glessner, Joseph ; Harris, Curtis C. ; Hu, Jennifer J. ; Ingles, Sue A. ; Isaacs, William ; John, Esther M. ; Kao, W. H Linda ; Keating, Brendan ; Kittles, Rick A ; Kolonel, Laurence N. ; Larkin, Emma ; Marchand, Loic Le ; McNeill, Lorna H. ; Millikan, Robert C. ; Murphy, Adam ; Musani, Solomon ; Neslund-Dudas, Christine ; Nyante, Sarah ; Papanicolaou, George J. ; Press, Michael F. ; Psaty, Bruce M. ; Reiner, Alex P. ; Rich, Stephen S. ; Rodriguez-Gil, Jorge L. ; Rotter, Jerome I. ; Rybicki, Benjamin A. ; Schwartz, Ann G. ; Signorello, Lisa B. ; Spitz, Margaret ; Strom, Sara S. ; Thun, Michael J. ; Tucker, Margaret A. ; Wang, Zhaoming ; Wiencke, John K. ; Witte, John S. ; Wrensch, Margaret ; Wu, Xifeng ; Yamamura, Yuko ; Zanetti, Krista A. ; Zheng, Wei ; Ziegler, Regina G. ; Zhu, Xiaofeng ; Redline, Susan ; Hirschhorn, Joel N. ; Henderson, Brian E. ; Taylor, Herman A. ; Price, Alkes L. ; Hakonarson, Hakon ; Chanock, Stephen J. ; Haiman, Christopher A. ; Wilson, James G. ; Reich, David ; Myers, Simon R. / The landscape of recombination in African Americans. In: Nature. 2011 ; Vol. 476, No. 7359. pp. 170-175.
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AU - Patterson, Nick

AU - Song, Yunli

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AU - Palmer, Cameron D.

AU - Chen, Gary K.

AU - Wang, Kai

AU - Buxbaum, Sarah G.

AU - Akylbekova, Ermeg L.

AU - Aldrich, Melinda C.

AU - Ambrosone, Christine B.

AU - Amos, Christopher

AU - Bandera, Elisa V.

AU - Berndt, Sonja I.

AU - Bernstein, Leslie

AU - Blot, William J.

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AU - Diver, W. Ryan

AU - Divers, Jasmin

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AU - Gillanders, Elizabeth M.

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AU - Hu, Jennifer J.

AU - Ingles, Sue A.

AU - Isaacs, William

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AU - Keating, Brendan

AU - Kittles, Rick A

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AU - Rybicki, Benjamin A.

AU - Schwartz, Ann G.

AU - Signorello, Lisa B.

AU - Spitz, Margaret

AU - Strom, Sara S.

AU - Thun, Michael J.

AU - Tucker, Margaret A.

AU - Wang, Zhaoming

AU - Wiencke, John K.

AU - Witte, John S.

AU - Wrensch, Margaret

AU - Wu, Xifeng

AU - Yamamura, Yuko

AU - Zanetti, Krista A.

AU - Zheng, Wei

AU - Ziegler, Regina G.

AU - Zhu, Xiaofeng

AU - Redline, Susan

AU - Hirschhorn, Joel N.

AU - Henderson, Brian E.

AU - Taylor, Herman A.

AU - Price, Alkes L.

AU - Hakonarson, Hakon

AU - Chanock, Stephen J.

AU - Haiman, Christopher A.

AU - Wilson, James G.

AU - Reich, David

AU - Myers, Simon R.

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AB - Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value < 10 -245). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.

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