The landscape of recombination in African Americans

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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.

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Figure 1: Building an African-American genetic map.
Figure 2: Association of PRDM9 genetic variation with hotspot activity.
Figure 3: A sequence motif specifying the positions of African-enriched hotspots.

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Acknowledgements

We are grateful to the participants who donated DNA samples, to D. Altshuler, J. Buard, K. Bryc, J. Kovacs, B. de Massy, G. McVean, B. Pasaniuc and S. Sankararaman for conversations and critiques, and to A. Auton for facilitating analysis of the 1000 Genomes Project data. Analysis was supported by the Wellcome Trust and NIH grants HL084107 and GM091332. CARe was supported by a contract from the National Heart, Lung and Blood Institute (HHSN268200960009C) to create a phenotype and genotype database for dissemination to the biomedical research community. Eight parent studies contributed phenotypic data and DNA samples through the Broad Institute (N01-HC-65226): the Atherosclerosis Risk in Communities study (ARIC), the Cleveland Family Study (CFS), the Coronary Artery Risk Development in Young Adults study (CARDIA), the Jackson Heart Study (JHS), the Multi-Ethnic Study of Atherosclerosis (MESA) study, the Cardiovascular Health Study (CHS), the Framingham Heart Study (FHS) and the Sleep Heart Health Study (SHHS). Support for CARe also came from the individual research institutions, investigators, field staff and study participants. Individual funding information is available at http://public.nhlbi.nih.gov/GeneticsGenomics/home/care.aspx. All genome-wide genotyping of samples from the Children’s Hospital of Pennsylvania (CHOP) was supported by an Institutional Development Award to the Center for Applied Genomics from the Children’s Hospital of Philadelphia, a research award from the Landenberger Foundation and the Cotswold Foundation. We thank all study participants and the staff at the Center for Applied Genomics for performing the genotyping. The African American Breast Cancer Consortium (AABCC) was supported by a DoD Breast Cancer Research Program Era of Hope Scholar Award to C.A.H. and the Norris Foundation, and by grants to the component studies: MEC (CA63464, CA54281); CARE (HD33175); WCHS (CA100598, DAMD 170100334, Breast Cancer Research Foundation); SFBC (CA77305, DAMD 17966071); CBCS (CA58223, ES10126), PLCO (NCI Intramural Research Program); NHBS (CA100374); WFBC (R01-CA73629); and CPS-II (the American Cancer Society). The African American Prostate Cancer Consortium (AAPCC) was supported by grants CA63464, CA54281, CA1326792, CA148085 and HG004726, and by grants to the component studies: PLCO (NCI Intramural Research Program), LAAPC (Cancer Research Fund 99-00524V-10258), both MEC and LAAPC (PC35139, DP000807); MDA (CA68578, CA140388, ES007784, DAMD W81XWH0710645); GECAP (ES011126); CaP Genes (CA88164); IPCG (W81XWH0710122); DCPC (GM08016, DAMD W81XWH0710203, DAMD W81XWH0610066); and SCCS (CA092447, CA68485). The African American Lung Cancer Consortium (AALCC) was supported by grants CA060691, CA87895, PC35145 and CA22453, CA68578, CA140388, ES007784, ES06717, CA55769, CA127219, CA1116460S1, CA1116460, CA121197, CA141716, CA121197S2, CPRIT RP100443, CA148127, DAMD W81XWH0710645, University Cancer Foundation, Duncan Family institute, Center for Community, Implementation and Dissemination Research Core, and by grants to the component studies: PLCO and the Maryland Studies (NCI Intramural Research Program), LAAPC (Cancer Research Fund 99-00524V-10258), and both MEC and LAAPC (PC35139, DP000807).

Author information

D.R. and S.R.M. conceived the study. A.G.H., A.T., N.P., Y.S., N.R., C.D.P., G.K.C., K.W., S.G.B., D.R. and S.R.M. performed analyses. N.R. performed the experimental work (genotyping of polymorphisms at PRDM9). A.G.H., N.P., J.N.H., B.E.H., H.A.T. Jr, A.L.P., H.H., S.J.C., C.A.H., J.G.W., D.R. and S.R.M. coordinated the study. A.G.H., D.R. and S.R.M. wrote the paper. N.R., C.D.P., G.K.C., K.W., S.G.B., S.R., J.N.H., B.E.H., H.A.T. Jr, H.H., S.J.C., C.A.H., J.G.W., D.R. and all the alphabetically listed authors contributed to sample collection and generation of SNP array data. All authors contributed to revision and review of the manuscript.

Correspondence to David Reich.

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Competing interests

The authors declare no competing financial interests.

Additional information

Crossover rate estimates for the AA map can be found at http://www.well.ox.ac.uk/~anjali/AAmap/. We also provide estimates of uncertainty for the map based on samples from the MCMC. Association testing results for each SNP are available from the authors on request.

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Supplementary Information

The file contains Supplementary Notes 1-6, Supplementary Tables 1-2 and Supplementary Figures 1-11 with legends. (PDF 2875 kb)

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