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

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...

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Main Authors:	Carmi, Shai, Hui, Ken Y., Kochav, Ethan, Liu, Xinmin, Xue, James, Grady, Fillan, Guha, Saurav, Upadhyay, Kinnari, Ben-Avraham, Dan, Mukherjee, Semanti, Bowen, B. Monica, Thomas, Tinu, Vijai, Joseph, Cruts, Marc, Froyen, Guy, Lambrechts, Diether, Plaisance, Stéphane, Van Broeckhoven, Christine, Van Damme, Philip, Van Marck, Herwig, Barzilai, Nir, Darvasi, Ariel, Offit, Kenneth, Bressman, Susan, Ozelius, Laurie J., Peter, Inga, Cho, Judy H., Ostrer, Harry, Atzmon, Gil, Clark, Lorraine N., Lencz, Todd, Pe’er, Itsik
Format:	Online
Language:	English
Published:	Nature Pub. Group 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164776/

id	pubmed-4164776
recordtype	oai_dc
spelling	pubmed-41647762014-09-22 Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins Carmi, Shai Hui, Ken Y. Kochav, Ethan Liu, Xinmin Xue, James Grady, Fillan Guha, Saurav Upadhyay, Kinnari Ben-Avraham, Dan Mukherjee, Semanti Bowen, B. Monica Thomas, Tinu Vijai, Joseph Cruts, Marc Froyen, Guy Lambrechts, Diether Plaisance, Stéphane Van Broeckhoven, Christine Van Damme, Philip Van Marck, Herwig Barzilai, Nir Darvasi, Ariel Offit, Kenneth Bressman, Susan Ozelius, Laurie J. Peter, Inga Cho, Judy H. Ostrer, Harry Atzmon, Gil Clark, Lorraine N. Lencz, Todd Pe’er, Itsik Article 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. Nature Pub. Group 2014-09-09 /pmc/articles/PMC4164776/ /pubmed/25203624 http://dx.doi.org/10.1038/ncomms5835 Text en Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by-nc-sa/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Carmi, Shai Hui, Ken Y. Kochav, Ethan Liu, Xinmin Xue, James Grady, Fillan Guha, Saurav Upadhyay, Kinnari Ben-Avraham, Dan Mukherjee, Semanti Bowen, B. Monica Thomas, Tinu Vijai, Joseph Cruts, Marc Froyen, Guy Lambrechts, Diether Plaisance, Stéphane Van Broeckhoven, Christine Van Damme, Philip Van Marck, Herwig Barzilai, Nir Darvasi, Ariel Offit, Kenneth Bressman, Susan Ozelius, Laurie J. Peter, Inga Cho, Judy H. Ostrer, Harry Atzmon, Gil Clark, Lorraine N. Lencz, Todd Pe’er, Itsik
spellingShingle	Carmi, Shai Hui, Ken Y. Kochav, Ethan Liu, Xinmin Xue, James Grady, Fillan Guha, Saurav Upadhyay, Kinnari Ben-Avraham, Dan Mukherjee, Semanti Bowen, B. Monica Thomas, Tinu Vijai, Joseph Cruts, Marc Froyen, Guy Lambrechts, Diether Plaisance, Stéphane Van Broeckhoven, Christine Van Damme, Philip Van Marck, Herwig Barzilai, Nir Darvasi, Ariel Offit, Kenneth Bressman, Susan Ozelius, Laurie J. Peter, Inga Cho, Judy H. Ostrer, Harry Atzmon, Gil Clark, Lorraine N. Lencz, Todd Pe’er, Itsik Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
author_facet	Carmi, Shai Hui, Ken Y. Kochav, Ethan Liu, Xinmin Xue, James Grady, Fillan Guha, Saurav Upadhyay, Kinnari Ben-Avraham, Dan Mukherjee, Semanti Bowen, B. Monica Thomas, Tinu Vijai, Joseph Cruts, Marc Froyen, Guy Lambrechts, Diether Plaisance, Stéphane Van Broeckhoven, Christine Van Damme, Philip Van Marck, Herwig Barzilai, Nir Darvasi, Ariel Offit, Kenneth Bressman, Susan Ozelius, Laurie J. Peter, Inga Cho, Judy H. Ostrer, Harry Atzmon, Gil Clark, Lorraine N. Lencz, Todd Pe’er, Itsik
author_sort	Carmi, Shai
title	Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
title_short	Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
title_full	Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
title_fullStr	Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
title_full_unstemmed	Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins
title_sort	sequencing an ashkenazi reference panel supports population-targeted personal genomics and illuminates jewish and european origins
description	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.
publisher	Nature Pub. Group
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4164776/
_version_	1613134097431920640

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

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