title: High-accuracy haplotype imputation using unphased genotype data as the references.
abstract: Enormously growing genomic datasets present a new challenge on missing data imputation, a notoriously resource-demanding task. Haplotype imputation requires ethnicity-matched references. However, to date, haplotype references are not available for the majority of populations in the world. We explored to use existing unphased genotype datasets as references; if it succeeds, it will cover almost all of the populations in the world. The results showed that our HiFi software successfully yields 99.43% accuracy with unphased genotype references. Our method provides a cost-effective solution to breakthrough the bottleneck of limited reference availability for haplotype imputation in the big data era.
authors.affiliation: Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China; Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA.
authors.forename: Wenzhi
authors.initials: W
authors.lastname: Li
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.affiliation: 4DGenome Inc, Atlanta, GA, USA.
authors.forename: Guoxing
authors.initials: G
authors.lastname: Fu
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA; 4DGenome Inc, Atlanta, GA, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Ma
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA.
authors.forename: Jendai
authors.initials: J
authors.lastname: Richards
authors.affiliation: 4DGenome Inc, Atlanta, GA, USA.
authors.forename: Weinian
authors.initials: W
authors.lastname: Rao
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA.
authors.forename: Tameka
authors.initials: T
authors.lastname: Bythwood
authors.affiliation: Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China. Electronic address: gsw1962@126.com.
authors.forename: Shiwen
authors.initials: S
authors.lastname: Guo
authors.affiliation: Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, USA; 4DGenome Inc, Atlanta, GA, USA; First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, China. Electronic address: qsong@msm.edu.
authors.forename: Qing
authors.initials: Q
authors.lastname: Song
mesh_terms: D005828:Genetics, Population / Q000592:standards*; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000191:economics / Q000592:standards*; D012984:Software
keywords: Big data; Imputation; References