[rat-forum] genome-wide genotyping in rats

Moreno-Quinn, Carol quinn at mcw.edu
Tue Feb 7 10:43:31 CST 2012

It depends on how dense you want to genotype and how much you want to
spend. The rat SNP chip is available through Affymetrix, it is very
dense (probably more than you need for a backcross), but expensive.
Also, if your strains are very closely related phylogenetically, it may
be hard to find polymorphic SSLP markers. You can find polymorphic
information between strains for both SSLPs and SNPs in RGD (rgd.mcw.edu)


Carol Moreno Quinn MD PhD

Associate Professor

Physiology. Human and Molecular Genetics Center

Medical College of Wisconsin




From: rat-forum-bounces at mcw.edu [mailto:rat-forum-bounces at mcw.edu] On
Behalf Of Remmers, Elaine (NIH/NHGRI) [E]
Sent: Tuesday, February 07, 2012 10:26 AM
To: 'rat-forum at mcw.edu'
Subject: [rat-forum] genome-wide genotyping in rats


What is the current best way to do genome-wide genotyping in rats?  Is
there a SNP chip that can be used for mapping in a backcross collection?




Elaine F. Remmers, Ph.D.

Staff Scientist

Inflammatory Disease Section, NHGRI, NIH, DHHS

Building 10 CRC East/Room B2-5235A

10 Center Drive - MSC 1849

Bethesda, MD 20892-1849


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