NDLI: Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Please wait, while we are loading the content...

Cell therapy using retinal progenitor cells shows therapeutic effect in a chemically-induced rotenone mouse model of Leber hereditary optic neuropathy

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Coffin–Siris Syndrome with obesity, macrocephaly, hepatomegaly and hyperinsulinism caused by a mutation in the ARID1B gene

Attenuated familial adenomatous polyposis manifests as autosomal dominant late-onset colorectal cancer

Biallelic MUTYH mutations can mimic Lynch syndrome

Clinical utility gene card for: Dent disease (Dent-1 and Dent-2)

Clinical utility gene card for: 15q13.3 microdeletion syndrome

Teeth anomalies and genetics, including genetic syndromes

Myhre and LAPS syndromes: clinical and molecular review of 32 patients

Year: 2014, Volume: 22, Issue: 10

Year: 2014, Volume: 22, Issue: 9

Year: 2014, Volume: 22, Issue: 8

Year: 2014, Volume: 22, Issue: 7

Year: 2014, Volume: 22, Issue: 6

Year: 2014, Volume: 22, Issue: 5

Year: 2014, Volume: 22, Issue: 4

Year: 2014, Volume: 22, Issue: 3

Year: 2014, Volume: 22, Issue: 2

Year: 2014, Volume: 22, Issue: 1

Year: 2013, Volume: 21

Year: 2012, Volume: 20

Year: 2011, Volume: 20

Year: 2011, Volume: 19

Year: 2010, Volume: 18

Year: 2009, Volume: 17

Year: 2008, Volume: 16

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Content Provider	PubMed Central
Author	Deelen, Patrick Menelaou, Androniki Leeuwen, Elisabeth M. Van Kanterakis, Alexandros Dijk, Freerk Van Carolina, Medina-gomez Francioli, Laurent C. Jan, Hottenga Jouke Karssen, Lennart C. Estrada, Karol Kreiner-møller, Eskil Rivadeneira, Fernando Setten, Jessica Van Javier, Gutierrez-achury Westra, Harm-jan Franke, Lude Van, Enckevort David Dijkstra, Martijn Byelas, Heorhiy Duijn, Cornelia M. Van Swertz, Morris A. Neerincx, Pieter B. T. Pulit, Sara L. Elbers, Clara C. Palamara, Pier Francesco Pe'er, Itsik Abdellaoui, Abdel Kloosterman, Wigard P. Oven, Mannis Van Vermaat, Martijn Li, Mingkun Laros, Jeroen F. J. Stoneking, Mark Knijff, Peter De Kayser, Manfred Veldink, Jan H. Berg, Leonard H. Van Den Den, Dunnen Johan T. Amin, Najaf Velde, K. Joeri Van Der Mathijs, Kattenberg Schaik, Barbera D. C. Van Bot, Jan Nijman, Isaäuc J. Mei, Hailiang Koval, Vyacheslav Ye, Kai Lameijer, Eric-wubbo Moed, Matthijs H. Hehir-kwa, Jayne Y. Handsaker, Robert E. Sunyaev, Shamil R. Sohail, Mashaal Hormozdiari, Fereydoun Marschall, Tobias Marschall, Schönhuth Guryev, Victor Slagboom, P. Eline Beekman, Marian B. Craen, Anton J. M. De Suchiman, H. Eka D. Hofman, Albert Duijn, Cornelia Van Willemsen, Gonneke Wolffenbuttel, Bruce H. Mathieu, Platteel Pitts, Steven J. Potluri, Shobha Cox, David R. Li, Qibin Li, Yingrui Du, Yuanping Chen, Ruoyan Cao, Hongzhi Li, Ning Cao, Sujie Wang, Jun Bovenberg, Jasper A. Wijmenga, Cisca Ommen, Gertjan B. Van De Bakker, Paul I. W. Boomsma, Dorret I. Committee, Steering
Copyright Year	2014
Abstract	Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with ‘true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05–0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r 2 , increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r 2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r 2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results.
Related Links	http://dx.doi.org/10.1038/ejhg.2014.19
Ending Page	1326
Page Count	6
Starting Page	1321
File Format	PDF
ISSN	10184813
e-ISSN	14765438
Journal	European Journal of Human Genetics
Issue Number	11
Volume Number	22
Language	English
Publisher	Nature Publishing Group
Publisher Date	2014-11-01
Access Restriction	Open
Rights Holder	Nature Publishing Group
Subject Keyword	Genetics(clinical) Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets

Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population

The effect of genome-wide association scan quality control on imputation outcome for common variants

NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Imputation of rare variants in next generation association studies

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Similar Documents

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Imputation of low-frequency variants using the HapMap3 benefits from large, diverse reference sets

Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population

The effect of genome-wide association scan quality control on imputation outcome for common variants

NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants

Imputation of rare variants in next generation association studies

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'