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Journal of Biomolecular Screening
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Genome-wide Linkage Analysis with Clustered SNP Markers

Kaja K. Selmer

Institute of Medical Genetics, University of Oslo, Oslo, Norway, Department of Medical Genetics, UllevÅl University Hospital, Oslo, Norway, k.k.selmer{at}medisin.uio.no

Kristin Brandal

Institute of Medical Genetics, University of Oslo, Oslo, Norway

Ole K. Olstad

Department of Clinical Chemistry, UllevÅl University Hospital, Oslo, Norway

Bård Birkenes

Institute of Medical Genetics, University of Oslo, Oslo, Norway

Dag E. Undlien

Institute of Medical Genetics, University of Oslo, Oslo, Norway, Department of Medical Genetics, UllevÅl University Hospital, Oslo, Norway

Thore Egeland

Department of Medical Genetics, UllevÅl University Hospital, Oslo, Norway, Oslo University College, Oslo, Norway

Single nucleotide polymorphisms (SNPs) have recently replaced microsatellites as the genetic markers of choice in linkage analysis, primarily because they are more abundant and the genotypes more amenable for automatic calling. One of the most recently launched linkage mapping sets (LMS) is the Applied Biosystems Human LMS 4K, which is a genome-wide linkage set based on the SNPlexTM technology and the use of clustered SNPs. In this article the authors report on their experience with this set and the associated genotyping software GeneMapper® version 4.0, which they have used for linkage analyses in 17 moderate to large families with assumed monogenic disease. For comparison of methods, they also performed a genome-wide linkage analysis in 1 of the 17 families using the Affymetrix GeneChip® Human Mapping 10K 2.0 array. The conclusion is that both methods performed technically well, with high call rates and comparable and low rates of Mendelian inconsistencies. However, genotyping is less automated in GeneMapper® version 4.0 than in the Affymetrix software and thus more time consuming. (Journal of Biomolecular Screening 2009:92-96)

Key Words: genome wide • linkage analysis • single nucleotide polymorphisms • large pedigrees • software

Journal of Biomolecular Screening, Vol. 14, No. 1, 92-96 (2009)
DOI: 10.1177/1087057108327327
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O. Skare, N. Sheehan, and T. Egeland
Identification of distant family relationships
Bioinformatics, September 15, 2009; 25(18): 2376 - 2382.
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