title: Chromosomal haplotypes by genetic phasing of human families.
abstract: Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Jared C
authors.initials: JC
authors.lastname: Roach
authors.forename: Gustavo
authors.initials: G
authors.lastname: Glusman
authors.forename: Robert
authors.initials: R
authors.lastname: Hubley
authors.forename: Stephen Z
authors.initials: SZ
authors.lastname: Montsaroff
authors.forename: Alisha K
authors.initials: AK
authors.lastname: Holloway
authors.forename: Denise E
authors.initials: DE
authors.lastname: Mauldin
authors.forename: Deepak
authors.initials: D
authors.lastname: Srivastava
authors.forename: Vidu
authors.initials: V
authors.lastname: Garg
authors.forename: Katherine S
authors.initials: KS
authors.lastname: Pollard
authors.forename: David J
authors.initials: DJ
authors.lastname: Galas
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
authors.forename: Arian F A
authors.initials: AF
authors.lastname: Smit
mesh_terms: D000465:Algorithms; D002877:Chromosomes, Human / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D040582:Inheritance Patterns / Q000235:genetics*; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D010375:Pedigree; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software