title: A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set.
abstract: Recent advances in technologies for high-throughout single-nucleotide polymorphism (SNP)-based genotyping have improved efficiency and cost so that it is now becoming reasonable to consider the use of SNPs for genomewide linkage analysis. However, a suitable screening set of SNPs and a corresponding linkage map have yet to be described. The SNP maps described here fill this void and provide a resource for fast genome scanning for disease genes. We have evaluated 6,297 SNPs in a diversity panel composed of European Americans, African Americans, and Asians. The markers were assessed for assay robustness, suitable allele frequencies, and informativeness of multi-SNP clusters. Individuals from 56 Centre d'Etude du Polymorphisme Humain pedigrees, with >770 potentially informative meioses altogether, were genotyped with a subset of 2,988 SNPs, for map construction. Extensive genotyping-error analysis was performed, and the resulting SNP linkage map has an average map resolution of 3.9 cM, with map positions containing either a single SNP or several tightly linked SNPs. The order of markers on this map compares favorably with several other linkage and physical maps. We compared map distances between the SNP linkage map and the interpolated SNP linkage map constructed by the deCode Genetics group. We also evaluated cM/Mb distance ratios in females and males, along each chromosome, showing broadly defined regions of increased and decreased rates of recombination. Evaluations indicate that this SNP screening set is more informative than the Marshfield Clinic's commonly used microsatellite-based screening set.
authors.affiliation: Department of Genetics, Rutgers University, Piscataway, NJ, 08840, USA. matise@biology.rutgers.edu
authors.forename: Tara C
authors.initials: TC
authors.lastname: Matise
authors.forename: Ravi
authors.initials: R
authors.lastname: Sachidanandam
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Clark
authors.forename: Leonid
authors.initials: L
authors.lastname: Kruglyak
authors.forename: Ellen
authors.initials: E
authors.lastname: Wijsman
authors.forename: Jerzy
authors.initials: J
authors.lastname: Kakol
authors.forename: Steven
authors.initials: S
authors.lastname: Buyske
authors.forename: Buena
authors.initials: B
authors.lastname: Chui
authors.forename: Patrick
authors.initials: P
authors.lastname: Cohen
authors.forename: Claudia
authors.initials: C
authors.lastname: de Toma
authors.forename: Margaret
authors.initials: M
authors.lastname: Ehm
authors.forename: Stephen
authors.initials: S
authors.lastname: Glanowski
authors.forename: Chunsheng
authors.initials: C
authors.lastname: He
authors.forename: Jeremy
authors.initials: J
authors.lastname: Heil
authors.forename: Kyriacos
authors.initials: K
authors.lastname: Markianos
authors.forename: Ivy
authors.initials: I
authors.lastname: McMullen
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Pericak-Vance
authors.forename: Arkadiy
authors.initials: A
authors.lastname: Silbergleit
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Wilson
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Winick
authors.forename: Emily S
authors.initials: ES
authors.lastname: Winn-Deen
authors.forename: Carl T
authors.initials: CT
authors.lastname: Yamashiro
authors.forename: Howard M
authors.initials: HM
authors.lastname: Cann
authors.forename: Eric
authors.initials: E
authors.lastname: Lai
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Holden
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D005820:Genetic Testing; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide
chemical_list: D004247:DNA