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Генетика евреев. 2014 год. Хазарии не было

Источник: http://www.nature.com/ncomms/2014/140909/ncomms5835/full/ncomms5835.html
PDF http://www.nature.com/ncomms/2014/140909/ncomms5835/extref/ncomms5835-s1.pdf

Published



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

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.

Моделирование древних историй для AJ и европейских странах с использованием их спектра частот совместного аллель определяет AJ быть даже примесь европейских и, вероятно, ближнего и Среднего Востока происхождения . Мы датировать раскол между двумя родовыми населения к ≈12-25 КИР , что предполагает преимущественно ближневосточная источник для репопуляции Европы после последнего ледникового максимума .

Accession codes: Whole-genome sequence data have been deposited at the European Genome-phenome Archive, which is hosted by the EBI, under accession code EGAS00001000664.

How to cite this article: Carmi, S. et al. Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins. Nat. Commun. 5:4835 doi: 10.1038/ncomms5835 (2014).

Affiliations

  1. Department of Computer Science, Columbia University, 500 W 120th Street, New York, New York 10027, USA


    • Shai Carmi,

    • Ethan Kochav,

    • James Xue,

    • Fillan Grady &

    • Itsik Pe’er


  2. Department of Internal Medicine, Genetics & Pediatrics, Yale School of Medicine, 300 Cedar Street, New Haven, Connecticut 06519, USA


    • Ken Y. Hui,

    • B. Monica Bowen &

    • Judy H. Cho


  3. Department of Pathology and Cell Biology, Columbia University Medical Center, 1150 St Nicholas Avenue, New York, New York 10032, USA


    • Xinmin Liu &

    • Lorraine N. Clark


  4. Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York 11030, USA


    • Saurav Guha,

    • Semanti Mukherjee &

    • Todd Lencz


  5. 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


    • Saurav Guha,

    • Semanti Mukherjee &

    • Todd Lencz


  6. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, New York 10029, USA


    • Saurav Guha,

    • Laurie J. Ozelius &

    • Inga Peter


  7. Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA


    • Kinnari Upadhyay,

    • Dan Ben-Avraham,

    • Nir Barzilai,

    • Harry Ostrer &

    • Gil Atzmon


  8. Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA


    • Dan Ben-Avraham,

    • Nir Barzilai &

    • Gil Atzmon


  9. Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA


    • Tinu Thomas,

    • Joseph Vijai &

    • Kenneth Offit


  10. Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA


    • Tinu Thomas,

    • Joseph Vijai &

    • Kenneth Offit


  11. VIB Department of Molecular Genetics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium


    • Marc Cruts &

    • Christine Van Broeckhoven


  12. VIB Center for the Biology of Disease, KU Leuven, Herestraat 49, bus 602, 3000 Leuven, Belgium


    • Guy Froyen


  13. VIB Vesalius Research Center, KU Leuven, Herestraat 49, bus 912, 3000 Leuven, Belgium


    • Diether Lambrechts &

    • Philip Van Damme


  14. VIB BioInformatics Training and Services facility, Rijvisschestraat 120, 9052 Gent, Belgium


    • Stéphane Plaisance &

    • Herwig Van Marck


  15. Neurology Department, University Hospital Leuven, 3000 Leuven, Belgium


    • Philip Van Damme


  16. Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel


    • Ariel Darvasi


  17. Department of Neurology, Beth Israel Medical Center, New York, New York 10003, USA


    • Susan Bressman


  18. Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA


    • Harry Ostrer


  19. 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


    • Lorraine N. Clark


  20. Departments of Psychiatry and Molecular Medicine, Hofstra University School of Medicine, Hempstead, New York 11550, USA


    • Todd Lencz


  21. Center for Computational Biology and Bioinformatics, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA


    • Itsik Pe’er


Contributions

S.C. was the primary analysis and manuscript-writing person. K.Y.H., E.K., X.L., J.X., F.G., S.G., K.U., D.B.-A., S.M., B.M.B., T.T. and J.V. conducted analysis and provided input for the manuscript. M.C., G.F., D.L., S.P., C.V.B, P.V.D., and H.V.M. contributed the Flemish genomes. N.B. contributed Ashkenazi DNA samples. A.D., K.O., S.B., I.Peter, J.H.C., H.O., L.J.O., G.A., L.N.C., T.L., and I.Pe’er initiated and funded the study. I.Peter, J.H.C., H.O., G.A., L.N.C., and T.L. supervised analysis and provided comments on the manuscript. G.A. and L.N.C. conducted lab work. T.L. led the funding of the study. I.Pe’er led the analysis and the writing of the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:



Tags: israel, khazaria, khazars
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