Integrating common and rare genetic variation in diverse human populations (original) (raw)

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Acknowledgements

We dedicate this work to Leena Peltonen for her vital leadership role in this study, and in memory of a valued friend and colleague. We thank E. Boerwinkle and R. Durbin for critical reading of the manuscript. We thank the USA National Institutes of Health, the National Human Genome Research Institute, the National Institute on Deafness and Other Communication Disorders and the Wellcome Trust for supporting the majority of this work. Funding was also provided by the Louis-Jeantet Foundation and the NCCR ‘Frontiers in Genetics’ (Swiss National Science Foundation). We thank the people from the following communities who were generous in donating their blood samples to be studied in this project: the Yoruba in Ibadan, Nigeria; the Maasai in Kinyawa, Kenya; the Luhya in Webuye, Kenya; the Han Chinese in Beijing, China; the Japanese in Tokyo, Japan; the Chinese in metropolitan Denver, Colorado; the Gujarati Indians in Houston, Texas; the Toscani in Italia; the community of African ancestry in the southwestern USA; and the community of Mexican ancestry in Los Angeles, California. We also thank the people in the Utah Centre d’Etude du Polymorphisme Humain community who allowed the samples they donated earlier to be used for the project. The authors acknowledge use of DNA from the 1958 British birth cohort collection, funded by the UK Medical Research Council grant G0000934 and the Wellcome Trust grant 068545/Z/02. The Illumina 550K genotype data for the 1958 British birth cohort samples were made available by the Sanger Institute. For the 1958 British birth cohort Affymetrix 500K genotype data, we thank the Wellcome Trust Case Control Consortium (http://www.wtccc.org.uk), which was funded by Wellcome Trust award 076113.

Author information

Author notes

  1. Leena Peltonen, Leena Peltonen and Leena Peltonen: ‡Deceased.

Authors and Affiliations

  1. Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02138, USA.,
    David M. Altshuler, David M. Altshuler, Stephen F. Schaffner, David M. Altshuler, Paul I. W. de Bakker (Co-leader), Stacey B. Gabriel, Xiaoming Jia, Melissa Parkin (Co-leader), Joshua M. Korn, Steven A. McCarroll (Co-leader), James Nemesh, Samuela Pollack, Wendy Brodeur, Huy Nguyen, Stephen F. Schaffner (Leader), Samuela Pollack, Stephen F. Schaffner (Co-leader) & Ilya Shlyakhter
  2. Department of Molecular and Human Genetics, Baylor College of Medicine, Human Genome Sequencing Center, One Baylor Plaza, Houston, Texas 77030, USA.,
    Richard A. Gibbs, Richard A. Gibbs, Fuli Yu, Penelope E. Bonnen, Richard A. Gibbs, Fuli Yu (Leader), Kyle Chang, Alicia Hawes, Lora R. Lewis, Yanru Ren, David Wheeler, Richard A. Gibbs, Donna Marie Muzny, Penelope E. Bonnen, Richard A. Gibbs, Claudia Gonzaga-Jauregui & Fuli Yu (Leader)
  3. Department of Genetic Medicine and Development, University of Geneva, Medical School, Faculty of Medicine, Geneva 1211, Switzerland.,
    Emmanouil Dermitzakis, Emmanouil Dermitzakis, Emmanouil Dermitzakis & Stephen B. Montgomery
  4. Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,
    Paul I. W. de Bakker (Co-leader)
  5. Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1HH, UK.,
    Panos Deloukas (Co-leader), Rhian Gwilliam, Sarah Hunt, Michael Inouye (Co-leader), Aarno Palotie, Pamela Whittaker, Chris Barnes, Matthew Hurles (Co-leader), Kati Kristiansson, Nicole Soranzo, Verneri Anttila, Qingrun Zhang, Mohammed J. R. Ghori, Ralph McGinnis (Co-leader), William McLaren & Fumihiko Takeuchi
  6. Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Haartmaninkatu 8, 00290 Helsinki, Finland.,
    Aarno Palotie & Verneri Anttila
  7. Department of Medical Genetics, University of Helsinki and University Central Hospital, Haartmaninkatu 8, 00290 Helsinki, Finland.,
    Aarno Palotie & Verneri Anttila
  8. Department of Pathology, Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts 02115, USA.,
    Katayoon Darvishi & Charles Lee
  9. Department of Biological Statistics and Computational Biology, Cornell University, 102A Weill Hall, Ithaca, New York 14853, USA.,
    Alon Keinan (Leader) & Alon Keinan
  10. Departments of Epidemiology and Biostatistics, Harvard School of Public Health, 665 Huntington Avenue, Building 2 Room 211, Boston, Massachusetts 02115, USA.,
    Alkes L. Price, Alkes L. Price & Alkes L. Price (Co-leader)
  11. Massachusetts General Hospital, Center for Human Genetic Research, Simches Research Center, 185 Cambridge Street, Boston, Massachusetts 02114, USA.,
    Mark J. Daly
  12. Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.,
    Stephen Leslie, Gil McVean & Loukas Moutsianas
  13. Department of Organismic and Evolutionary Biology, Harvard University, Center for Systems Biology, 52 Oxford Street, Room 469, Cambridge, Massachusetts 02215, USA.,
    Sharon R. Grossman, Elizabeth B. Hostetter & Pardis C. Sabeti (Leader)
  14. Department of Epidemiology and Preventative Medicine, University of Maryland School of Medicine, N406 Institute of Human Virology, 725 West Lombard Street, Baltimore, Maryland 21201, USA.,
    Clement A. Adebamowo
  15. Department of Anthropology, University of Oklahoma, 455 West Lindsey Room 505C, Norman, Oklahoma 73019, USA.,
    Morris W. Foster
  16. Department of Anthropology, University of California, San Francisco, History and Social Medicine, 3333 California Street Suite 485, San Francisco, 94143-0850, California, USA
    Deborah R. Gordon
  17. The Australian National University, John Curtin School of Medical Research, Garran Road, Building 131, Canberra, ACT2603, Australia.,
    Julio Licinio
  18. Institute for Oncological Study and Prevention, 50139, Florence, Italy
    Maria Cristina Manca
  19. Department of Bioethics, Case Western Reserve University, School of Medicine TA200, 10900 Euclid Avenue, Cleveland, Ohio 44106-4976, USA.,
    Patricia A. Marshall
  20. Health Sciences University of Hokkaido, 1757 Kanazawa, Tobetsu-cho, Ishikari-gun, Hokkaido 061-0293, Japan.,
    Ichiro Matsuda
  21. Department of Population and Family Health, Moi University, PO Box 4606, Eldoret 30100, Kenya.,
    Duncan Ngare
  22. National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane Suite 3039, Bethesda, Maryland 20892, USA.,
    Vivian Ota Wang
  23. Department of Anthropology, University of Houston at Clear Lake, 2700 Bay Area Boulevard, PO Box 295, Houston, Texas 77058-1098, USA.,
    Deepa Reddy
  24. National Human Genome Research Institute, Center for Research on Genomics and Global Health, 12 South Drive, MSC 5635, Building 12A, Room 4047, Bethesda, Maryland 20892-5635, USA.,
    Charles N. Rotimi
  25. Duke University, Institute for Genome Sciences and Policy, 450 Research Drive, PO Box 91009, LSRC B-Wing, Room 320B, Durham, North Carolina 27708, USA.,
    Charmaine D. Royal
  26. Department of Bioethics, The Cleveland Clinic, 9500 Euclid Avenue JJ60, Cleveland, Ohio 44124, USA.,
    Richard R. Sharp
  27. Beijing Institute of Genomics, Chinese Academy of Science, Beijing Airport Industrial Zone B-6, Beijing 101300, China.,
    Changqing Zeng
  28. National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane Suite 4076, Bethesda, Maryland 20892, USA ,
    Lisa D. Brooks & Jean E. McEwen

Consortia

The International HapMap 3 Consortium

Corresponding authors

Correspondence toDavid M. Altshuler, Richard A. Gibbs, David M. Altshuler, Richard A. Gibbs, David M. Altshuler, Richard A. Gibbs, Richard A. Gibbs or Richard A. Gibbs.

Ethics declarations

Competing interests

The author declare no competing financial interests.

Additional information

The HapMap 3/ENCODE 3 data set has been deposited at http://www.hapmap.org. The sequence traces of ENCODE 3 can be accessed at http://www.ncbi.nlm.nih.gov/Traces/trace.cgi by submitting the query:species_code5“HOMO SAPIENS” and CENTER_NAME 5 “BCM” and CENTER_PROJECT 5 “RHIAY”.

A list of participants and their affiliations appears at the end of the paper

Supplementary information

Supplementary Information

This file contains Supplementary Information comprising Introduction, Large Scale Genotyping, Rare Allele Calling Bias, Deep PCR Sequencing, Copy Number Polymorphism (CNP) Analysis, Population Analyses, Recurrent SNPs and Haplotype sharing (see Contents page for full details). It also includes Supplementary Tables 1-11, Supplementary Figures 1-9 with legends and additional references. (PDF 1111 kb)

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The International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations.Nature 467, 52–58 (2010). https://doi.org/10.1038/nature09298

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