[Genetic-linkage] Linkage using 240S Illumina chips

Traynor, Bryan (NIH/NIMH) [E] via gen-link%40net.bio.net (by traynorb from mail.nih.gov)
Fri Aug 24 16:53:22 EST 2007

I was looking for help on how to use data from 240S Illumina chips for
linkage. I ran a family on these chips which genotype 240,000 SNPs
across the genome. Unfortunately none of the linkage programs that I
have looked at are able to handle this amount of data. Even SNPlink
which is designed to cut down the large numbers of SNPs does not work
with such a large dataset. One approach that I was thinking of following
is to match the SNPs on Illumina's linkage panel V to the SNPs that I
have generated using the 240S SNP chip. Problem is that not all of the
linkage panel V SNPs are on the 240S Illumina SNP chip, so I may have to
take nearby SNPs. My questions are as follows:

(1)    Has anyone any experience with using 240S or 550K Illumina SNP
chips for linkage studies?

(2)    Does anyone have a list of SNPs on the 240S SNP chip that they
know work for linkage?

Many thanks in advance,



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