Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.
The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation,...
| Main Authors: | , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3712964?pdf=render |
| id |
doaj-907409466cd94df49150bc46dd9dcc97 |
|---|---|
| record_format |
Article |
| spelling |
doaj-907409466cd94df49150bc46dd9dcc972020-11-25T00:08:40ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0187e6860410.1371/journal.pone.0068604Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies.Peter K JoshiJames PrendergastRoss M FraserJennifer E HuffmanVeronique VitartCaroline HaywardRuth McQuillanDominik GlodzikOzren PolašekNicholas D HastieIgor RudanHarry CampbellAlan F WrightChris S HaleyJames F WilsonPau NavarroThe analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10%) in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.http://europepmc.org/articles/PMC3712964?pdf=render |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Peter K Joshi James Prendergast Ross M Fraser Jennifer E Huffman Veronique Vitart Caroline Hayward Ruth McQuillan Dominik Glodzik Ozren Polašek Nicholas D Hastie Igor Rudan Harry Campbell Alan F Wright Chris S Haley James F Wilson Pau Navarro |
| spellingShingle |
Peter K Joshi James Prendergast Ross M Fraser Jennifer E Huffman Veronique Vitart Caroline Hayward Ruth McQuillan Dominik Glodzik Ozren Polašek Nicholas D Hastie Igor Rudan Harry Campbell Alan F Wright Chris S Haley James F Wilson Pau Navarro Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. PLoS ONE |
| author_facet |
Peter K Joshi James Prendergast Ross M Fraser Jennifer E Huffman Veronique Vitart Caroline Hayward Ruth McQuillan Dominik Glodzik Ozren Polašek Nicholas D Hastie Igor Rudan Harry Campbell Alan F Wright Chris S Haley James F Wilson Pau Navarro |
| author_sort |
Peter K Joshi |
| title |
Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| title_short |
Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| title_full |
Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| title_fullStr |
Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| title_full_unstemmed |
Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| title_sort |
local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. |
| publisher |
Public Library of Science (PLoS) |
| series |
PLoS ONE |
| issn |
1932-6203 |
| publishDate |
2013-01-01 |
| description |
The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10%) in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%. |
| url |
http://europepmc.org/articles/PMC3712964?pdf=render |
| work_keys_str_mv |
AT peterkjoshi localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT jamesprendergast localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT rossmfraser localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT jenniferehuffman localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT veroniquevitart localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT carolinehayward localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT ruthmcquillan localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT dominikglodzik localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT ozrenpolasek localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT nicholasdhastie localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT igorrudan localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT harrycampbell localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT alanfwright localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT chrisshaley localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT jamesfwilson localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies AT paunavarro localexomesequencesfacilitateimputationoflesscommonvariantsandincreasepowerofgenomewideassociationstudies |
| _version_ |
1725414988417335296 |