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

   

Authors:	Carmi, S.; Hui, K. Y.; Kochav, E.; Liu, X. M.; Xue, J.; Grady, F.; Guha, S.; Upadhyay, K.; Ben-Avraham, D.; Mukherjee, S.; Bowen, B. M.; Thomas, T.; Vijai, J.; Cruts, M.; Froyen, G.; Lambrechts, D.; Plaisance, S.; Van Broeckhoven, C.; Van Damme, P.; Van Marck, H.; Barzilai, N.; Darvasi, A.; Offit, K.; Bressman, S.; Ozelius, L. J.; Peter, I.; Cho, J. H.; Ostrer, H.; Atzmon, G.; Clark, L. N.; Lencz, T.; Pe'Er, I.
Article Title:	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 approximate to 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 approximate to 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 approximate to 12-25 Kyr, suggesting a predominantly Near Eastern source for the repopulation of Europe after the Last Glacial Maximum.
Keywords:	jews; mutations; association; wide; parkinsons-disease; frequency; genetic-variation; identity-by-descent; genotype-imputation; demographic history; ancestry
Journal Title:	Nature Communications
Volume:	5
ISSN:	2041-1723
Publisher:	Nature Publishing Group
Date Published:	2014-09-09
Start Page:	4835
Language:	English
ACCESSION:	WOS:000342929300006
DOI:	10.1038/ncomms5835
PROVIDER:	wos
PMCID:	PMC4164776
PUBMED:	25203624
Notes:	Article -- 4835 -- Source: Wos

https://synapse.mskcc.org/synapse/works/has_related_data_chk/66019