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

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, Marc Cruts, Guy Froyen, Diether Lambrechts, Stéphane Plaisance, Christine Van Broeckhoven, Philip Van Damme, Herwig Van Marck, Nir Barzilai, Ariel Darvasi, Kenneth Offit, Susan Bressman, Laurie J. Ozelius, Inga Peter, Judy H. Cho, Harry Ostrer, Gil Atzmon, Lorraine N. Clark, Todd Lencz () and Itsik Pe’er ()
Additional contact information
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
Kinnari Upadhyay: Albert Einstein College of Medicine
Dan Ben-Avraham: Albert Einstein College of Medicine
Semanti Mukherjee: Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, 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
Joseph Vijai: Cancer Biology and Genetics Program, 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
Herwig Van Marck: VIB BioInformatics Training and Services facility, Rijvisschestraat 120
Nir Barzilai: 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
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
Gil Atzmon: Albert Einstein College of Medicine
Lorraine N. Clark: Columbia University Medical Center
Todd Lencz: Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System
Itsik Pe’er: Columbia University

Nature Communications, 2014, vol. 5, issue 1, 1-9

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms5835

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