Computational protocol: Common variants at 2q37.3, 8q24.21, 15q21.3, and 16q24.1 influence chronic lymphocytic leukemia risk

Similar protocols

Protocol publication

[…] We used Haploview software (v3.2) to infer the LD structure of the genome in the regions containing loci associated with disease risk. We applied two in silico algorithms, PolyPhen and SIFT, to predict the impact of non-synonymous SNPs on protein function. [...] To examine for a relationship between SNP genotype and expression levels of MYC, FARP2, NEDD4, MBD1, and CPEB1 in lymphocytes we made use of publicly available expression data generated from analysis of 90 Caucasian derived Epstein-Barr virus–transformed lymphoblastoid cell lines using Sentrix Human-6 Expression BeadChips (Illumina, San Diego, USA),. Online recovery of data was performed using WGAViewer Version 1.25 Software. Differences in the distribution of levels of mRNA expression between SNP genotypes were compared using a Wilcoxon-type test for trend. […]

Pipeline specifications

Software tools Haploview, PolyPhen, SIFT, WGAViewer
Application GWAS
Diseases Leukemia, Lymphocytic, Chronic, B-Cell, Hematologic Neoplasms