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Am J Hum Genet. 2014 Oct 2;95(4):437-44. doi: 10.1016/j.ajhg.2014.08.011. Epub 2014 Sep 18.

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

Author information

1
Division of Health, Science, and Technology, the Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. Electronic address: gbhatia@mit.edu.
2
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
3
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.
4
Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Nashville, TN 37203, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Department of Thoracic Surgery, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
5
Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.
6
Section of Biostatistics and Epidemiology, Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03766, USA.
7
Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.
8
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA.
9
Division of Cancer Etiology, Department of Population Sciences, Beckman Research Institute, City of Hope, CA 91010, USA.
10
Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Nashville, TN 37203, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; International Epidemiology Institute, Rockville, MD 20850, USA.
11
Karmanos Cancer Institute and Department of Oncology, Wayne State University of Medicine, Detroit, MI 48201, USA.
12
Departments of Preventive Medicine and Pathology, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA.
13
Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Nashville, TN 37203, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
14
Epidemiology Research Program, American Cancer Society, Atlanta, GA 30303, USA.
15
Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD 20892, USA.
16
Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
17
James Buchanan Brady Urological Institute, Johns Hopkins Hospital and Medical Institutions, Baltimore, MD 21287, USA.
18
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.
19
Cancer Prevention Institute of California, Fremont, CA 94538, USA; Stanford Cancer Center, Stanford Medicine, Stanford, CA 94305, USA.
20
Department of Medicine, University of Illinois at Chicago, Chicago, IL 60607, USA.
21
Division of Allergy, Pulmonary, and Critical Care, Department of Medicine, Vanderbilt University Medical Center, 6100 Medical Center East, Nashville, TN 37232-8300, USA.
22
Department of Health Disparities Research, Cancer Prevention and Population Sciences, the University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Center for Community Implementation and Dissemination Research, Duncan Family Institute, the University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
23
Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
24
Department of Urology, Northwestern University, Chicago, IL 60611, USA.
25
Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI 48202, USA.
26
Sylvester Comprehensive Cancer Center and Department of Epidemiology and Public Health, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
27
Department of Epidemiology, the University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
28
University of California, San Francisco, San Francisco, CA 94158, USA.
29
Departments of Epidemiology and Biostatistics and Urology, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94158, USA.
30
Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD 20892, USA; Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
31
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA; Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

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.

PMID:
25242497
PMCID:
PMC4185117
DOI:
10.1016/j.ajhg.2014.08.011
[Indexed for MEDLINE]
Free PMC Article

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