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a tough GWAS study design ? which software to use?

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#1 weihua



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Posted 29 October 2012 - 03:13 AM

I have a genotyping data from Affy SNP6.0 which includes 30 pairs of afftected siblings, 20 sporadic affetced cases from some population and 30 afftced sibpairs from other populations (do not know exactly). for controls I have 200 controls from the same population using the same chip and 1000 population controls using illumina 610 chip. The disease prevalence is around 0.001 in EU.

I was wondering how to analyse this data? I have several concerns:
1. the sample size is too small. I remove the cases from other populations and only include 30 sibpairs and 20 sporadic cases. I devide them into 2 case groups which contains 40 cases each and compare with controls. But the plot does not show a peak only sporadic ones.

2. does any body know any software which can consider related samples? a lot of them only can concern one affected and one unaffetd sibs but in my case all the cases are affted?
ROADtrips seem to have a different input format other than plink? does anyone know how to transfer?
ANYBODY has any suggestions about the study design? Thank you.

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