title: Joint analysis of sequence data and single-nucleotide polymorphism data using pedigree information for imputation and recombination inference.
abstract: We developed a general framework for family-based imputation using single-nucleotide polymorphism data and sequence data distributed by Genetic Analysis Workshop 18. By using PedIBD, we first inferred haplotypes and inheritance patterns of each family from SNP data. Then new variants in unsequenced family members can be obtained from sequenced relatives through their shared haplotypes. We then compared the results of our method against the imputation results provided by Genetic Analysis Workshop organizers. The results showed that our strategy uncovered more variants for more unsequenced relatives. We also showed that recombination breakpoints inferred by PedIBD have much higher resolution than those inferred from previous studies.
authors.affiliation: Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Sunah
authors.initials: S
authors.lastname: Song
authors.affiliation: Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Shields
authors.affiliation: Department of Pathology, Stanford University, Stanford, CA 94305, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Li