A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set.
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.
Matise
Tara C
TC
Department of Genetics, Rutgers University, Piscataway, NJ, 08840, USA. matise@biology.rutgers.edu
Sachidanandam
Ravi
R
Clark
Andrew G
AG
Kruglyak
Leonid
L
Wijsman
Ellen
E
Kakol
Jerzy
J
Buyske
Steven
S
Chui
Buena
B
Cohen
Patrick
P
de Toma
Claudia
C
Ehm
Margaret
M
Glanowski
Stephen
S
He
Chunsheng
C
Heil
Jeremy
J
Markianos
Kyriacos
K
McMullen
Ivy
I
Pericak-Vance
Margaret A
MA
Silbergleit
Arkadiy
A
Stein
Lincoln
L
Wagner
Michael
M
Wilson
Alexander F
AF
Winick
Jeffrey D
JD
Winn-Deen
Emily S
ES
Yamashiro
Carl T
CT
Cann
Howard M
HM
Lai
Eric
E
Holden
Arthur L
AL
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
D004247:DNA