A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set

Matise, T. C., Sachidanandam, R., Clark, A. G., Kruglyak, L., Wijsman, E., Kakol, J., Buyske, S., Chui, B., Cohen, P., de Toma, C., Ehm, M., Glanowski, S., He, C. S., Heil, J., Markianos, K., McMullen, I., Pericak-Vance, M. A., Silbergleit, A., Stein, L., Wagner, M., Wilson, A. F., Winick, J. D., Winn-Deen, E. S., Yamashiro, C. T., Cann, H. M., Lai, E., Holden, A. L. (August 2003) A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. American Journal of Human Genetics, 73 (2). pp. 271-284. ISSN 0002-9297

URL: http://www.ncbi.nlm.nih.gov/pubmed/12844283
DOI: 10.1086/377137

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 1770 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.

Item Type: Paper
Uncontrolled Keywords: HUMAN GENOME SEQUENCE VARIATION GENOTYPING ERRORS GENETIC MAPS MARKERS CONSTRUCTION PROGRAM IDENTIFICATION DISEQUILIBRIUM RECOMBINATION
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:
Communities: CSHL labs > Sachidanandam lab
CSHL labs > Stein lab
Depositing User: Matt Covey
Date: August 2003
Date Deposited: 11 Jun 2013 15:54
Last Modified: 11 Jun 2013 15:54
PMCID: PMC1180367
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27952

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving