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Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins

Author

Listed:
  • Shai Carmi

    (Columbia University)

  • Ken Y. Hui

    (Genetics & Pediatrics, Yale School of Medicine)

  • Ethan Kochav

    (Columbia University)

  • Xinmin Liu

    (Columbia University Medical Center)

  • James Xue

    (Columbia University)

  • Fillan Grady

    (Columbia University)

  • Saurav Guha

    (Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System
    Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore–Long Island Jewish Health System
    Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place)

  • Kinnari Upadhyay

    (Albert Einstein College of Medicine)

  • Dan Ben-Avraham

    (Albert Einstein College of Medicine
    Albert Einstein College of Medicine)

  • Semanti Mukherjee

    (Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System
    Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore–Long Island Jewish Health System)

  • B. Monica Bowen

    (Genetics & Pediatrics, Yale School of Medicine)

  • Tinu Thomas

    (Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center
    Clinical Genetics Service, Memorial Sloan Kettering Cancer Center)

  • Joseph Vijai

    (Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center
    Clinical Genetics Service, Memorial Sloan Kettering Cancer Center)

  • Marc Cruts

    (University of Antwerp, Universiteitsplein 1)

  • Guy Froyen

    (VIB Center for the Biology of Disease, KU Leuven, Herestraat 49, bus 602)

  • Diether Lambrechts

    (VIB Vesalius Research Center, KU Leuven, Herestraat 49, bus 912)

  • Stéphane Plaisance

    (VIB BioInformatics Training and Services facility, Rijvisschestraat 120)

  • Christine Van Broeckhoven

    (University of Antwerp, Universiteitsplein 1)

  • Philip Van Damme

    (VIB Vesalius Research Center, KU Leuven, Herestraat 49, bus 912
    University Hospital Leuven)

  • Herwig Van Marck

    (VIB BioInformatics Training and Services facility, Rijvisschestraat 120)

  • Nir Barzilai

    (Albert Einstein College of Medicine
    Albert Einstein College of Medicine)

  • Ariel Darvasi

    (The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram)

  • Kenneth Offit

    (Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center
    Clinical Genetics Service, Memorial Sloan Kettering Cancer Center)

  • Susan Bressman

    (Beth Israel Medical Center)

  • Laurie J. Ozelius

    (Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place)

  • Inga Peter

    (Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place)

  • Judy H. Cho

    (Genetics & Pediatrics, Yale School of Medicine)

  • Harry Ostrer

    (Albert Einstein College of Medicine
    Albert Einstein College of Medicine)

  • Gil Atzmon

    (Albert Einstein College of Medicine
    Albert Einstein College of Medicine)

  • Lorraine N. Clark

    (Columbia University Medical Center
    Taub Institute for Research of Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, 1150 St Nicholas Avenue)

  • Todd Lencz

    (Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System
    Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore–Long Island Jewish Health System
    Hofstra University School of Medicine)

  • Itsik Pe’er

    (Columbia University
    Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue)

Abstract

The Ashkenazi Jewish (AJ) population is a genetic isolate close to European and Middle Eastern groups, with genetic diversity patterns conducive to disease mapping. Here we report high-depth sequencing of 128 complete genomes of AJ controls. Compared with European samples, our AJ panel has 47% more novel variants per genome and is eightfold more effective at filtering benign variants out of AJ clinical genomes. Our panel improves imputation accuracy for AJ SNP arrays by 28%, and covers at least one haplotype in ≈67% of any AJ genome with long, identical-by-descent segments. Reconstruction of recent AJ history from such segments confirms a recent bottleneck of merely ≈350 individuals. Modelling of ancient histories for AJ and European populations using their joint allele frequency spectrum determines AJ to be an even admixture of European and likely Middle Eastern origins. We date the split between the two ancestral populations to ≈12–25 Kyr, suggesting a predominantly Near Eastern source for the repopulation of Europe after the Last Glacial Maximum.

Suggested Citation

  • Shai Carmi & Ken Y. Hui & Ethan Kochav & Xinmin Liu & James Xue & Fillan Grady & Saurav Guha & Kinnari Upadhyay & Dan Ben-Avraham & Semanti Mukherjee & B. Monica Bowen & Tinu Thomas & Joseph Vijai & M, 2014. "Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms5835
    DOI: 10.1038/ncomms5835
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    Cited by:

    1. Alexandra M. Cheney & Stephanann M. Costello & Nicholas V. Pinkham & Annie Waldum & Susan C. Broadaway & Maria Cotrina-Vidal & Marc Mergy & Brian Tripet & Douglas J. Kominsky & Heather M. Grifka-Walk , 2023. "Gut microbiome dysbiosis drives metabolic dysfunction in Familial dysautonomia," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Orshay Gabay & Yoav Shoshan & Eli Kopel & Udi Ben-Zvi & Tomer D. Mann & Noam Bressler & Roni Cohen‐Fultheim & Amos A. Schaffer & Shalom Hillel Roth & Ziv Tzur & Erez Y. Levanon & Eli Eisenberg, 2022. "Landscape of adenosine-to-inosine RNA recoding across human tissues," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Mihail Halachev & Viktoria-Eleni Gountouna & Alison Meynert & Gannie Tzoneva & Alan R. Shuldiner & Colin A. Semple & James F. Wilson, 2024. "Regionally enriched rare deleterious exonic variants in the UK and Ireland," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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