The landscape of recombination in African Americans.
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., Le Marchand L., 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.
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.