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https://doi.org/10.1038/s41598-017-06905-6
DC Field | Value | |
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dc.title | Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy | |
dc.contributor.author | Ahmad, M | |
dc.contributor.author | Sinha, A | |
dc.contributor.author | Ghosh, S | |
dc.contributor.author | Kumar, V | |
dc.contributor.author | Davila, S | |
dc.contributor.author | Yajnik, C.S | |
dc.contributor.author | Chandak, G.R | |
dc.date.accessioned | 2020-10-20T09:09:36Z | |
dc.date.available | 2020-10-20T09:09:36Z | |
dc.date.issued | 2017 | |
dc.identifier.citation | Ahmad, M, Sinha, A, Ghosh, S, Kumar, V, Davila, S, Yajnik, C.S, Chandak, G.R (2017). Inclusion of Population-specific Reference Panel from India to the 1000 Genomes Phase 3 Panel Improves Imputation Accuracy. Scientific Reports 7 (1) : 6733. ScholarBank@NUS Repository. https://doi.org/10.1038/s41598-017-06905-6 | |
dc.identifier.issn | 20452322 | |
dc.identifier.uri | https://scholarbank.nus.edu.sg/handle/10635/178310 | |
dc.description.abstract | Imputation is a computational method based on the principle of haplotype sharing allowing enrichment of genome-wide association study datasets. It depends on the haplotype structure of the population and density of the genotype data. The 1000 Genomes Project led to the generation of imputation reference panels which have been used globally. However, recent studies have shown that population-specific panels provide better enrichment of genome-wide variants. We compared the imputation accuracy using 1000 Genomes phase 3 reference panel and a panel generated from genome-wide data on 407 individuals from Western India (WIP). The concordance of imputed variants was cross-checked with next-generation re-sequencing data on a subset of genomic regions. Further, using the genome-wide data from 1880 individuals, we demonstrate that WIP works better than the 1000 Genomes phase 3 panel and when merged with it, significantly improves the imputation accuracy throughout the minor allele frequency range. We also show that imputation using only South Asian component of the 1000 Genomes phase 3 panel works as good as the merged panel, making it computationally less intensive job. Thus, our study stresses that imputation accuracy using 1000 Genomes phase 3 panel can be further improved by including population-specific reference panels from South Asia. © 2017 The Author(s). | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.source | Unpaywall 20201031 | |
dc.subject | controlled clinical trial | |
dc.subject | controlled study | |
dc.subject | female | |
dc.subject | gene frequency | |
dc.subject | genome | |
dc.subject | human | |
dc.subject | India | |
dc.subject | major clinical study | |
dc.subject | male | |
dc.subject | phase 3 clinical trial | |
dc.subject | stress | |
dc.subject | allele | |
dc.subject | Asia | |
dc.subject | Asian continental ancestry group | |
dc.subject | biology | |
dc.subject | Caucasian | |
dc.subject | genetic variation | |
dc.subject | genome-wide association study | |
dc.subject | haplotype | |
dc.subject | high throughput sequencing | |
dc.subject | human genome | |
dc.subject | human genome project | |
dc.subject | population genetics | |
dc.subject | reference value | |
dc.subject | statistics and numerical data | |
dc.subject | Alleles | |
dc.subject | Asia | |
dc.subject | Asian Continental Ancestry Group | |
dc.subject | Computational Biology | |
dc.subject | European Continental Ancestry Group | |
dc.subject | Gene Frequency | |
dc.subject | Genetic Variation | |
dc.subject | Genetics, Population | |
dc.subject | Genome, Human | |
dc.subject | Genome-Wide Association Study | |
dc.subject | Haplotypes | |
dc.subject | High-Throughput Nucleotide Sequencing | |
dc.subject | Human Genome Project | |
dc.subject | Humans | |
dc.subject | Reference Values | |
dc.type | Article | |
dc.contributor.department | DUKE-NUS MEDICAL SCHOOL | |
dc.description.doi | 10.1038/s41598-017-06905-6 | |
dc.description.sourcetitle | Scientific Reports | |
dc.description.volume | 7 | |
dc.description.issue | 1 | |
dc.description.page | 6733 | |
Appears in Collections: | Elements Staff Publications |
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