GWAS Tutorial Insights
Discover key insights from the GWAS tutorial presented by Shubhabrata Joey Mukherjee, PhD, Laura E. Gibbons, PhD, and Elizabeth Sanders. Gain knowledge about genotyped data, SNP selection, and phenotypes such as ADNI-Mem, ADNI-Exec, and WMH. Explore beyond the tutorial for additional resources on Box and collaborative folders.
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Presentation Transcript
Disclaimers for all talks Friday Harbor 2017
Disclaimer This conference is supported by a grant from the National Institute on Aging (NIA) of the National Institutes of Health (NIH) Any views expressed are the personal views of the speaker and do not imply endorsement by the NIA, the NIH, or the United States Department of Health and Human Services
GWAS Tutorial Shubhabrata Joey Mukherjee, PhD Laura E. Gibbons, PhD Elizabeth Sanders (Paul K. Crane, MD MPH)
Stuff Joey said to tell you about the GWAS Software: R and PLINK installer/binary files are provided for people who have not installed them SNP data: what we have are genotyped (not imputed) data from people with appropriate consent and European ethnicity from ADNI1 (not ADNIGO, ADNI2, or ADNI3). Conscious choices to avoid crashing your computer (about 550,000 SNPs) Many thanks to Kwangsik Nho for his assistance The plan will be to perform QC and perform a GWAS with a phenotype / covariate file
Phenotypes in the GWAS What is in there: ADNI-Mem, ADNI-Exec, WMH Note that WMH is non-normally distributed, which may be an issue
Stuff Joey said to tell you beyond the GWAS On Box there is a file with ADNI data. I received an email called Dan Mungas has added you to a collaborated folder on Box
Notes It should be straightforward to create a new phenotype file to go along with the genetic data that are in the tutorial Elizabeth, Laura, and Joey spoil me tremendously (and you too!) Note that imaging data may be profoundly not normally distributed and you may want to consider that in genetic analyses Have fun!!!
