TY - JOUR
T1 - Local Ancestry Inference in Large Pedigrees
AU - Wang, Heming
AU - Sofer, Tamar
AU - Zhang, Xiang
AU - Elston, Robert C.
AU - Redline, Susan
AU - Zhu, Xiaofeng
N1 - Funding Information:
The experiments reported here also feature in the doctoral thesis of H.W (https://etd.ohiolink.edu/ pg_10?0::NO:10:P10_ACCESSION_NUM:case1473439566976121). We thank Drs. Na than Morris and Xiaoyin Li for providing valuable comments and suggestions, and Dr. Matthew Goodman for editing the language. The work was supported by the NIH NHLBI grants R01HL113338 (to SR), R35HL135818 (to SR), the NHGRI grant R01HG003054 to (XZ), Sleep Research Society Foundation Career Development Award 018-JP-18 (to HW). The Cleveland Family Study was supported by NHLBI R01HL46380.
Publisher Copyright:
© 2020, The Author(s).
PY - 2020/12/1
Y1 - 2020/12/1
N2 - 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.
AB - 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.
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U2 - 10.1038/s41598-019-57039-w
DO - 10.1038/s41598-019-57039-w
M3 - Article
C2 - 31932708
AN - SCOPUS:85077785677
SN - 2045-2322
VL - 10
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 189
ER -