دورية أكاديمية
A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples
| العنوان: | A combined reference panel from the 1000 Genomes and UK10K projects improved rare variant imputation in European and Chinese samples |
|---|---|
| المؤلفون: | Chou, Wen-Chi, Zheng, Hou-Feng, Cheng, Chia-Ho, Yan, Han, Wang, Li, Han, Fang, Richards, J. Brent, Karasik, David, Kiel, Douglas P., Hsu, Yi-Hsiang |
| المساهمون: | Hsu, YH (reprint author), Beth Israel Deaconess Med Ctr, Dept Med, Hebrew SeniorLife, Inst Aging Res, Boston, MA 02215 USA., Hsu, YH (reprint author), Harvard Med Sch, Boston, MA 02115 USA., Hsu, YH (reprint author), Broad Inst MIT & Harvard, Cambridge, MA 02142 USA., Hsu, YH (reprint author), Harvard Sch Publ Hlth, Mol & Integrat Physiol Sci, Boston, MA 02115 USA., Beth Israel Deaconess Med Ctr, Dept Med, Hebrew SeniorLife, Inst Aging Res, Boston, MA 02215 USA., Harvard Med Sch, Boston, MA 02115 USA., Broad Inst MIT & Harvard, Cambridge, MA 02142 USA., Hangzhou Normal Univ, Sch Med, Inst Aging Res, Hangzhou, Zhejiang, Peoples R China., Hangzhou Normal Univ, Affiliated Hosp, Hangzhou, Zhejiang, Peoples R China., Peking Univ, Peoples Hosp, Dept Pulm Crit Care Med, Beijing, Peoples R China., McGill Univ, Jewish Gen Hosp, Lady Davis Inst Med Res, Dept Med Human Genet Epidemiol & Biostat, Montreal, PQ, Canada., Kings Coll London, Twin Res & Genet Epidemiol, London, England., Harvard Sch Publ Hlth, Mol & Integrat Physiol Sci, Boston, MA 02115 USA. |
| المصدر: | SCI |
| بيانات النشر: | SCIENTIFIC REPORTS |
| سنة النشر: | 2016 |
| المجموعة: | Peking University Institutional Repository (PKU IR) / 北京大学机构知识库 |
| مصطلحات موضوعية: | WIDE ASSOCIATION, GENOTYPE-IMPUTATION, LOW-FREQUENCY, POWER |
| الوصف: | Imputation using the 1000 Genomes haplotype reference panel has been widely adapted to estimate genotypes in genome wide association studies. To evaluate imputation quality with a relatively larger reference panel and a reference panel composed of different ethnic populations, we conducted imputations in the Framingham Heart Study and the North Chinese Study using a combined reference panel from the 1000 Genomes (N = 1,092) and UK10K (N = 3,781) projects. For rare variants with 0.01% < MAF = 0.5%, imputation in the Framingham Heart Study with the combined reference panel increased well-imputed genotypes (with imputation quality score >= 0.4) from 62.9% to 76.1% when compared to imputation with the 1000 Genomes. For the North Chinese samples, imputation of rare variants with 0.01% < MAF <= 0.5% with the combined reference panel increased well-imputed genotypes by from 49.8% to 61.8%. The predominant European ancestry of the UK10K and the combined reference panels may explain why there was less of an increase in imputation success in the North Chinese samples. Our results underscore the importance and potential of larger reference panels to impute rare variants, while recognizing that increasing ethnic specific variants in reference panels may result in better imputation for genotypes in some ethnic groups. ; NHLBI; Boston University (BU) [N01-HC-25195]; Affymetrix, Inc. [N02-HL-6-4278]; NIAMS [R01 AR/AG 41398, R01 AR 061162, R01 AR 061445] ; SCI(E) ; ARTICLE ; YiHsiangHsu@hsl.harvard.edu ; 6 |
| نوع الوثيقة: | journal/newspaper |
| اللغة: | English |
| تدمد: | 2045-2322 |
| العلاقة: | SCIENTIFIC REPORTS.2016,6.; 1515909; http://hdl.handle.net/20.500.11897/457995Test; WOS:000390306100001 |
| DOI: | 10.1038/srep39313 |
| الإتاحة: | https://doi.org/20.500.11897/457995Test https://doi.org/10.1038/srep39313Test https://hdl.handle.net/20.500.11897/457995Test |
| رقم الانضمام: | edsbas.173F836B |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 20452322 |
|---|---|
| DOI: | 10.1038/srep39313 |