Local Ancestry Inference in Large Pedigrees

Heming Wang, Tamar Sofer, Xiang Zhang, Robert C. Elston, Susan Redline, Xiaofeng Zhu

Research output: Contribution to journalArticle

Abstract

Local ancestry, defined as the genetic ancestry at a genomic location of an admixed individual, is widely used as a genetic marker in genetic association and evolutionary genetics studies. Many methods have been developed to infer the local ancestries in a set of unrelated individuals, a few of them have been extended to small nuclear families, but none can be applied to large (e.g. three-generation) pedigrees. In this study, we developed a method, FamANC, that can improve the accuracy of local ancestry inference in large pedigrees by: (1) using an existing algorithm to infer local ancestries for all individuals in a family, assuming (contrary to fact) they are unrelated, and (2) improving its accuracy by correcting inference errors using pedigree structure. Applied on African-American pedigrees from the Cleveland Family Study, FamANC was able to correct all identified Mendelian errors and most of double crossovers.

Original languageEnglish (US)
Article number189
JournalScientific reports
Volume10
Issue number1
DOIs
StatePublished - Dec 1 2020

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Wang, H., Sofer, T., Zhang, X., Elston, R. C., Redline, S., & Zhu, X. (2020). Local Ancestry Inference in Large Pedigrees. Scientific reports, 10(1), [189]. https://doi.org/10.1038/s41598-019-57039-w