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 Cai; Neil 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

doi:10.1038/nature10336

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 journal › Article

177 Scopus citations

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 language	English (US)
Pages (from-to)	170-175
Number of pages	6
Journal	Nature
Volume	476
Issue number	7359
DOIs	https://doi.org/10.1038/nature10336
State	Published - Aug 11 2011
Externally published	Yes

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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., ... 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 journal › Article

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, 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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title = "The landscape of recombination in African Americans",

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.",

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

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AU - Tandon, Arti

AU - Patterson, Nick

AU - Song, Yunli

AU - Rohland, Nadin

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.

AU - Bock, Cathryn H.

AU - Boerwinkle, Eric

AU - Cai, Qiuyin

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AU - Casey, Graham

AU - Cupples, L. Adrienne

AU - Deming, Sandra L.

AU - Diver, W. Ryan

AU - Divers, Jasmin

AU - Fornage, Myriam

AU - Gillanders, Elizabeth M.

AU - Glessner, Joseph

AU - Harris, Curtis C.

AU - Hu, Jennifer J.

AU - Ingles, Sue A.

AU - Isaacs, William

AU - John, Esther M.

AU - Kao, W. H.Linda

AU - Keating, Brendan

AU - Kittles, Rick A.

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AU - Larkin, Emma

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AU - Millikan, Robert C.

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AU - Neslund-Dudas, Christine

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AU - Psaty, Bruce M.

AU - Reiner, Alex P.

AU - Rich, Stephen S.

AU - Rodriguez-Gil, Jorge L.

AU - Rotter, Jerome I.

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

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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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N2 - 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.

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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10.1038/nature10336