Common genetic variation contributes significantly to the risk of developing chronic lymphocytic leukemia.

Recent genome-wide association studies (GWAS) have identified common genetic risk variants for chronic lymphocytic leukemia (CLL). Testing SNPs individually for an association in GWAS necessitates the imposition of a very stringent P value to address multiple testing. While this reduces false positives, it may result in true associations being missed. Thus, any overall estimate of the total heritability, that is, the proportion of the CLL risk ascribable to genetic variation, will be negatively biased. An alternative approach is to fit all the SNPs simultaneously providing an unbiased estimate of the heritability explained by all SNPs. We have applied this methodology to a GWAS of CLL. Briefly, 517 CLL cases were genotyped using HumanCNV370-Duo BeadChips (Illumina). For controls, we made use of Hap1.2M-Duo Custom array data generated on 2,930 individuals from Wellcome Trust CaseControl Consortium 2 (WTCCC2). We excluded samples with call rates below 90%, non-European background and cryptic relatedness assessed by estimation of identity by descent, along with SNPs having call rate below 95%, minor allele frequency (MAF) less than 1% in cases and controls, and evidence of departure from Hardy-Weinberg equilibrium (P<10 cases; P<0.05 controls). Performing a differential missingness test between cases and controls we excluded those SNPs with P<0.05. In addition, using PLINK we excluded individuals having a relatedness score over 0.05. This filtering resulted in 238,870 SNPs used for the analysis. A total of 63 samples were removed during quality control. We estimated heritability using the methodology of Yang et al. and Lee et al. Briefly, the method fits a linear mixed model of the form: y=m+g+e where y is the vector of disease status, m is the mean vector, g is a vector of random additive genetic effects obtained from SNP data, and e is a vector of residual effects. The covariance structure fitted in the data is the individual relationship estimated from the SNPs, defined by: