ArticleNature communications2014
Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.
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Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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101citing papers in PubMed
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101 citing papers in PubMed.
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- Genomic reconstruction of the Pakistani Roma reveals dual South Asian ancestry, medieval bottlenecks, and the early dispersal routes of the Romani people.Human genomics · 2026Article
- The Use of Population Isolates to Identify Metabolic Syndrome's Genetic Aetiology.Molecular genetics & genomic medicine · 2026Review
- Genetic associations with longevity in a Calabrian cohort: an exploratory genome-wide study.GeroScience · 2026Article
- Integrated Stress Response Signatures Drive Monocyte Dysfunction in GBA1- and LRRK2-Linked Parkinson's Disease.Research square · 2026Article
- Genetics and context for precision health in Greater Boston.Nature communications · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.American journal of human genetics · 2025Article
- Integrated Stress Response Signatures Drive Monocyte Dysfunction inmedRxiv : the preprint server for health sciences · 2025Article
- Tracing human genetic histories and natural selection with precise local ancestry inference.Nature communications · 2025Article
- Multiple-testing corrections in selection scans using identity-by-descent segments.bioRxiv : the preprint server for biology · 2025Article
- Regionally enriched rare deleterious exonic variants in the UK and Ireland.Nature communications · 2024Article
- Heritability of complex traits in sub-populations experiencing bottlenecks and growth.Journal of human genetics · 2024Article
- Obesity risk in young adults from the Jerusalem Perinatal Study (JPS): the contribution of polygenic risk and early life exposure.International journal of obesity (2005) · 2024Article
- Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.iScience · 2024Article
- Genome wide association study and genomic risk prediction of age related macular degeneration in Israel.Scientific reports · 2024Article
- The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population.Bioinformatics (Oxford, England) · 2024Article
- Shortcomings of ethnicity-based carrier screening for conditions associated with Ashkenazi Jewish ancestry.Genetics in medicine open · 2024Article
- Fine-scale genetic structure and rare variant frequencies.PloS one · 2024Article
- Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel.Journal of medical genetics · 2023Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors.
Shai CarmiDepartment of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA.
Ken Y HuiDepartment of Internal Medicine, Genetics &Pediatrics, Yale School of Medicine, 300 Cedar Street, New Haven, Connecticut 06519, USA.
Ethan KochavDepartment of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA.
Xinmin LiuDepartment of Pathology and Cell Biology, Columbia University Medical Center, 1150 St Nicholas Avenue, New York, New York 10032, USA.
James XueDepartment of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA.
Fillan GradyDepartment of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA.
Saurav Guha1] Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York 11030, USA [2] Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore-Long Island Jewish Health System, Glen Oaks, New York 11004, USA [3] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York 10029, USA.
Kinnari UpadhyayDepartment of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Dan Ben-Avraham1] Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA [2] Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Semanti Mukherjee1] Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York 11030, USA [2] Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore-Long Island Jewish Health System, Glen Oaks, New York 11004, USA.
B Monica BowenDepartment of Internal Medicine, Genetics &Pediatrics, Yale School of Medicine, 300 Cedar Street, New Haven, Connecticut 06519, USA.
Tinu Thomas1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA [2] Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
Joseph Vijai1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA [2] Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
Marc CrutsVIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
Guy FroyenVIB Center for the Biology of Disease, KU Leuven, Herestraat 49, bus 602, 3000 Leuven, Belgium.
Diether LambrechtsVIB Vesalius Research Center, KU Leuven, Herestraat 49, bus 912, 3000 Leuven, Belgium.
Stéphane PlaisanceVIB BioInformatics Training and Services facility, Rijvisschestraat 120, 9052 Gent, Belgium.
Christine Van BroeckhovenVIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.
Philip Van Damme1] VIB Vesalius Research Center, KU Leuven, Herestraat 49, bus 912, 3000 Leuven, Belgium [2] Neurology Department, University Hospital Leuven, 3000 Leuven, Belgium.
Herwig Van MarckVIB BioInformatics Training and Services facility, Rijvisschestraat 120, 9052 Gent, Belgium.
Nir Barzilai1] Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA [2] Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Ariel DarvasiDepartment of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel.
Kenneth Offit1] Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA [2] Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.
Susan BressmanDepartment of Neurology, Beth Israel Medical Center, New York, New York 10003, USA.
Laurie J OzeliusDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York 10029, USA.
Inga PeterDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York 10029, USA.
Judy H ChoDepartment of Internal Medicine, Genetics &Pediatrics, Yale School of Medicine, 300 Cedar Street, New Haven, Connecticut 06519, USA.
Harry Ostrer1] Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA [2] Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Gil Atzmon1] Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA [2] Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.
Lorraine N Clark1] Department of Pathology and Cell Biology, Columbia University Medical Center, 1150 St Nicholas Avenue, New York, New York 10032, USA [2] Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 1150 St Nicholas Avenue, New York, New York 10032, USA.
Todd Lencz1] Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York 11030, USA [2] Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore-Long Island Jewish Health System, Glen Oaks, New York 11004, USA [3] Departments of Psychiatry and Molecular Medicine, Hofstra University School of Medicine, Hempstead, New York 11550, USA.
Itsik Pe'er1] Department of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA [2] Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA.
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Nicholas D Socci · 1985 to 2026
$347.4MMEDICAL SCIENTIST TRAINING PROGRAMT32GM007205 · NIGMS · YALE UNIVERSITY · PI KAZMIERCZAK, BARBARA I · 1985 to 2019
$42.9MNation Center: Multi-Scale Study- Cellular Networks(RMI)U54CA121852 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2005 to 2015
$37.4MCore-010UL1TR001073 · NCATS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI KELLER, MARLA J, SHAMOON, HARRY · 2013 to 2017
$21.3MInflammatory Bowel Disease Genetics Consortium Data Coordinating CenterU01DK062429 · NIDDK · YALE UNIVERSITY · PI CHO, JUDY H. · 2002 to 2016
$16.8MPrecision IBD via genetics and genomics: integrating International and multi-omic datasets, expanding studies in diverse populations, and defining mechanisms of unmet clinical needs in IBDU24DK062429 · NIDDK · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Ling-shiang Chuang, Ron Do · 2017 to 2026
$13.9MYale University Inflammatory Bowel Disease Genetics Research CenterU01DK062422 · NIDDK · YALE UNIVERSITY · PI Ling-shiang Chuang · 2002 to 2026
$10.8MROLE OF NUTRIENTS IN AGE-RELATED INSULIN RESISTANCEP01AG021654 · NIA · YESHIVA UNIVERSITY · PI BARZILAI, NIR J · 2003 to 2007
$10.6MSTATISTICS AND DATA MANAGEMENT COREP01AG027734 · NIA · ALBERT EINSTEIN COLLEGE OF MEDICINE · PI MORROW, BERNICE E · 2007 to 2012
$9.3MTraining in Aging ResearchT32AG023475 · NIA · ALBERT EINSTEIN COL OF MED YESHIVA UNIV · PI NIR J BARZILAI, DEREK Major HUFFMAN · 2004 to 2026
$8.6MNext Generation Sequencing for Disease Mapping in a Founder PopulationR01MH095458 · NIMH · FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH · PI DARVASI, ARIEL, LENCZ, TODD · 2013 to 2016
$3.8MCommon and Rare Genetic Factors in an Ethnically Homogeneous Schizophrenia CohortRC2MH089964 · NIMH · FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH · PI LENCZ, TODD · 2009 to 2010
$3.5MNCATS NIH HHS UL1 TR001073NCI NIH HHS CA121852NCI NIH HHS P30 CA008748NCI NIH HHS U54 CA121852NIA NIH HHS AG021654NIA NIH HHS AG027734NIA NIH HHS AG042188NIA NIH HHS P01 AG021654NIA NIH HHS P01 AG027734NIA NIH HHS R01 AG042188NIA NIH HHS T32 AG023475NIDDK NIH HHS DK062422NIDDK NIH HHS DK092235NIDDK NIH HHS DK098927NIDDK NIH HHS DK62429NIDDK NIH HHS F30 DK098927NIDDK NIH HHS R01 DK092235NIDDK NIH HHS U01 DK062422NIDDK NIH HHS U01 DK062429NIDDK NIH HHS U24 DK062429NIGMS NIH HHS GM007205NIGMS NIH HHS T32 GM007205NIMH NIH HHS MH084098NIMH NIH HHS MH089964NIMH NIH HHS MH095458NIMH NIH HHS R01 MH084098NIMH NIH HHS R01 MH095458NIMH NIH HHS RC2 MH089964NINDS NIH HHS NS050487NINDS NIH HHS NS060113NINDS NIH HHS R01 NS060113NINDS NIH HHS R21 NS050487
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.
Indexed as
Genetics, PopulationGenetic VariationAdultAgedAged, 80 and overFemaleGene FrequencyGenomeGenomicsHealthy VolunteersHumansJewsMaleMetagenomicsMiddle AgedPolymorphism, Single Nucleotide
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