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,...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0068604&type=printable |
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| 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 |
| 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 |
| collection | DOAJ |
| 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%. |
| format | Article |
| id | doaj-art-907409466cd94df49150bc46dd9dcc97 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-907409466cd94df49150bc46dd9dcc972025-08-20T03:09:45ZengPublic 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%.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0068604&type=printable |
| 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 |
| title | 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_short | 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 |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0068604&type=printable |
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