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However, the results are often suboptimal in populations underrepresented in existing reference panels and array designs, since the selected single nucleotide polymorphisms (SNPs) may fail to capture population-specific haplotype structures, hence the full extent of common genetic variation. Here, we propose to sequence the full genomes of a small subset of an underrepresented study cohort to inform the selection of population-specific add-on tag SNPs and to generate an internal population-specific imputation reference panel, such that the remaining array-genotyped cohort could be more accurately imputed. Using a Tanzania-based cohort as a proof-of-concept, we demonstrate the validity of our approach by showing improvements in imputation accuracy after the addition of our designed add-on tags to the base H3Africa array.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1009628","type":"journal-article","created":{"date-parts":[[2022,1,13]],"date-time":"2022-01-13T14:32:08Z","timestamp":1642084328000},"page":"e1009628","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":12,"title":["Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5021-8823","authenticated-orcid":true,"given":"Zhi 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