Showing posts with label biomarker. Show all posts
Showing posts with label biomarker. Show all posts

Thursday, June 05, 2014

check points when reviewing a genetic screening report


  1. title and footnote, ensuring it describes the analysis population, the outcome variable and the class of genetic markers; 
  2. eyeball examples:
    • 1 example of x chr snp
    • 1 example of autosomal snp with only 2 genotypes
    • 1 example of top association 
    • 1 example of a random association
  3. use the excel output to check the value ranges for each column, pay attention to
    • extreme values
    • empty cells
    • characters indicating missing: -,NA, 0
  4. Cosmetic issues
    • decimal places
    • check line ends for character cut off

Saturday, May 18, 2013

Prioritizing GWAS Results

This review paper mentioned 3 analytic methods to prioritizing GWAS results (for follow-up studies):
  • Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable.

  • Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact.

  • Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases.