TY - JOUR
T1 - A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set
AU - Matise, Tara C.
AU - Sachidanandam, Ravi
AU - Clark, Andrew G.
AU - Kruglyak, Leonid
AU - Wijsman, Ellen
AU - Kakol, Jerzy
AU - Buyske, Steven
AU - Chui, Buena
AU - Cohen, Patrick
AU - De Toma, Claudia
AU - Ehm, Margaret
AU - Glanowski, Stephen
AU - He, Chunsheng
AU - Heil, Jeremy
AU - Markianos, Kyriacos
AU - McMullen, Ivy
AU - Pericak-Vance, Margaret A.
AU - Silbergleit, Arkadiy
AU - Stein, Lincoln
AU - Wagner, Michael
AU - Wilson, Alexander F.
AU - Winick, Jeffrey D.
AU - Winn-Deen, Emily S.
AU - Yamashiro, Carl T.
AU - Cann, Howard M.
AU - Lai, Eric
AU - Holden, Arthur L.
N1 - Funding Information:
We thank the following individuals for valuable technical assistance: Victoria Appleton, Roxane Bonner, Amish Gandhi, Michael Gaskin, Penny Gwynne, Ken Harris, Miguel Hernandez, Xiangyang Kong, Annalee Ledesma, William Lee, Sandra Lew, Kerri McWeeny, Tom Perez, Gudmundur Thorisson, and Jeff Zdunek. We also thank Karl Broman, Linda Brzustowicz, Norman Doggett, Julie Douglas, Derek Gordon, Leigh Pascoe, Greg Schuler, Steve Sherry, Eric Sobel, and Daniel Weeks, as well as the anonymous reviewers, for helpful scientific input. The Laboratory for Computer Science Research of the Division of Computer and Information Sciences at Rutgers provided valuable time on their system. This project would not have been possible without the public resources provided by the American Diabetes Association (for the Japanese samples in the diversity panel), the Center for Medical Genetics at the Marshfield Clinic, NCBI, TSC, and deCode Genetics. This project was funded by TSC and Motorola Life Sciences.
PY - 2003/8/1
Y1 - 2003/8/1
N2 - 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.
AB - 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.
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U2 - 10.1086/377137
DO - 10.1086/377137
M3 - Article
C2 - 12844283
AN - SCOPUS:0041488881
SN - 0002-9297
VL - 73
SP - 271
EP - 284
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 2
ER -