Linkage using 240S Illumina chips

[Traynor, Bryan (NIH/NIMH) [E]]

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,

Best,

Bryan