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

Tara C. Matise, Ravi Sachidanandam, Andrew G. Clark, Leonid Kruglyak, Ellen Wijsman, Jerzy Kakol, Steven Buyske, Buena Chui, Patrick Cohen, Claudia De Toma, Margaret Ehm, Stephen Glanowski, Chunsheng He, Jeremy Heil, Kyriacos Markianos, Ivy McMullen, Margaret A Pericak-Vance, Arkadiy Silbergleit, Lincoln Stein, Michael WagnerAlexander F. Wilson, Jeffrey D. Winick, Emily S. Winn-Deen, Carl T. Yamashiro, Howard M. Cann, Eric Lai, Arthur L. Holden

Research output: Contribution to journalArticle

99 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)271-284
Number of pages14
JournalAmerican Journal of Human Genetics
Volume73
Issue number2
DOIs
StatePublished - Aug 1 2003
Externally publishedYes

Fingerprint

Single Nucleotide Polymorphism
Asian Americans
Meiosis
Pedigree
Gene Frequency
African Americans
Microsatellite Repeats
Genetic Recombination
Chromosomes
Genome
Technology
Costs and Cost Analysis

ASJC Scopus subject areas

  • Genetics

Cite this

Matise, T. C., Sachidanandam, R., Clark, A. G., Kruglyak, L., Wijsman, E., Kakol, J., ... Holden, A. L. (2003). A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. American Journal of Human Genetics, 73(2), 271-284. https://doi.org/10.1086/377137

A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. / Matise, Tara C.; Sachidanandam, Ravi; Clark, Andrew G.; Kruglyak, Leonid; Wijsman, Ellen; Kakol, Jerzy; Buyske, Steven; Chui, Buena; Cohen, Patrick; De Toma, Claudia; Ehm, Margaret; Glanowski, Stephen; He, Chunsheng; Heil, Jeremy; Markianos, Kyriacos; McMullen, Ivy; Pericak-Vance, Margaret A; Silbergleit, Arkadiy; Stein, Lincoln; Wagner, Michael; Wilson, Alexander F.; Winick, Jeffrey D.; Winn-Deen, Emily S.; Yamashiro, Carl T.; Cann, Howard M.; Lai, Eric; Holden, Arthur L.

In: American Journal of Human Genetics, Vol. 73, No. 2, 01.08.2003, p. 271-284.

Research output: Contribution to journalArticle

Matise, TC, Sachidanandam, R, Clark, AG, Kruglyak, L, Wijsman, E, Kakol, J, Buyske, S, Chui, B, Cohen, P, De Toma, C, Ehm, M, Glanowski, S, He, C, Heil, J, Markianos, K, McMullen, I, Pericak-Vance, MA, Silbergleit, A, Stein, L, Wagner, M, Wilson, AF, Winick, JD, Winn-Deen, ES, Yamashiro, CT, Cann, HM, Lai, E & Holden, AL 2003, 'A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set', American Journal of Human Genetics, vol. 73, no. 2, pp. 271-284. https://doi.org/10.1086/377137
Matise TC, Sachidanandam R, Clark AG, Kruglyak L, Wijsman E, Kakol J et al. A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. American Journal of Human Genetics. 2003 Aug 1;73(2):271-284. https://doi.org/10.1086/377137
Matise, Tara C. ; Sachidanandam, Ravi ; Clark, Andrew G. ; Kruglyak, Leonid ; Wijsman, Ellen ; Kakol, Jerzy ; Buyske, Steven ; Chui, Buena ; Cohen, Patrick ; De Toma, Claudia ; Ehm, Margaret ; Glanowski, Stephen ; He, Chunsheng ; Heil, Jeremy ; Markianos, Kyriacos ; McMullen, Ivy ; Pericak-Vance, Margaret A ; Silbergleit, Arkadiy ; Stein, Lincoln ; Wagner, Michael ; Wilson, Alexander F. ; Winick, Jeffrey D. ; Winn-Deen, Emily S. ; Yamashiro, Carl T. ; Cann, Howard M. ; Lai, Eric ; Holden, Arthur L. / A 3.9-centimorgan-resolution human single-nucleotide polymorphism linkage map and screening set. In: American Journal of Human Genetics. 2003 ; Vol. 73, No. 2. pp. 271-284.
@article{045fee5596e94c95a6f006349d42bf8d,
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.",
author = "Matise, {Tara C.} and Ravi Sachidanandam and Clark, {Andrew G.} and Leonid Kruglyak and Ellen Wijsman and Jerzy Kakol and Steven Buyske and Buena Chui and Patrick Cohen and {De Toma}, Claudia and Margaret Ehm and Stephen Glanowski and Chunsheng He and Jeremy Heil and Kyriacos Markianos and Ivy McMullen and Pericak-Vance, {Margaret A} and Arkadiy Silbergleit and Lincoln Stein and Michael Wagner and Wilson, {Alexander F.} and Winick, {Jeffrey D.} and Winn-Deen, {Emily S.} and Yamashiro, {Carl T.} and Cann, {Howard M.} and Eric Lai and Holden, {Arthur L.}",
year = "2003",
month = "8",
day = "1",
doi = "10.1086/377137",
language = "English",
volume = "73",
pages = "271--284",
journal = "American Journal of Human Genetics",
issn = "0002-9297",
publisher = "Cell Press",
number = "2",

}

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.

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.

UR - http://www.scopus.com/inward/record.url?scp=0041488881&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0041488881&partnerID=8YFLogxK

U2 - 10.1086/377137

DO - 10.1086/377137

M3 - Article

C2 - 12844283

AN - SCOPUS:0041488881

VL - 73

SP - 271

EP - 284

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 2

ER -