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Rutgers Combined Linkage-Physical Map

We have constructed de novo a high-resolution genetic map that includes the largest set of polymorphic markers for which genotype data are publicly available: it combines genotype data from both the CEPH and deCODE pedigrees (for some markers), incorporates SNPs, also incorporates sequence-based positional information.

The position of most markers on our map is corroborated by both genomic sequence and recombination-based data. This specific combination of features maximizes marker inclusion, coverage, and resolution, making this map uniquely suited as a comprehensive resource for determining genetic map information (order and distances) for any large set of polymorphic markers.

Browse Rutgers Map | PubMed reference to Rutgers Combined Linkage-Physical Map.

Map Interpolator

Map Interpolator allows interpolation of map positions on the Rutgers second-generation combined linkage-physical map (Rutgers map v.2). This resource allows you to determine cM-scale linkage-based map positions for any marker, given only its physical position. For example, the marker rs884080 does not exist on our map. However, its position can be identified by interpolation using its physical position on chromosome 1 which is 2016609. The resulting interpolated sex-averaged linkage map position is: 4.1031 cM.

Interpolate Map positions


Our set of combined genotype data (exclusive of the deCODE data) and maps has been incorporated into the Map-O-Mat web-based linkage mapping server for analysis of human linkage maps. Map-O-Mat facilitates the verification of marker order and calculation of map distances for custom mapping sets by running the Cri-Map program for linkage analysis using the genotype data described in this manuscript.

This application is an automated marker-based linkage mapping server. The server uses publicly available genotype data for over 15,000 markers.

PubMed reference to Map-O-Mat.

Interpolated positions for the Affymetrix and Illumina GWA SNP panels

Use the following links to download files:

Build 37

Build 36

Interpolated positions of dbSNP Build 135 reference SNPs (39,521,116 rsID SNPs)

If you use these maps please be sure to cite one of our papers:

Rutgers Map v2 (second generation): Matise, TC et al. 2007. A second-generation combined linkage physical map of the human genome. Genome Res 17:1783-6.

Rutgers Map v3 (third generation): Nato, AQ, Buyske, S, and Matise, TC. 2011 (in prep). The Rutgers Map: A third-generation combined linkage-physical map of the human genome.

Use the following links to download files:

© 2012 Matise Laboratory of Computational Genetics.