Validation and functional characterization of GWAS-identified variants for chronic lymphocytic leukemia: a CRuCIAL study.

Abstract

During the past years, considerable efforts have been made to uncover the genetic component of chronic lymphocytic leukemia (CLL) susceptibility. To date, several genome-wide association studies (GWAS) and their meta- analysis have identified not only single-nucleotide polymorphisms (SNPs) associated with CLL risk [1] but also patient survival [2]. However, despite these noticeable results, it becomes evident that both validation and functional characterization of the genetic variations identified are still required before they can be used in a clinical setting. Hence, we decided to validate the association of 41 GWAS-identified hits for CLL in 1158 CLL cases and 1947 controls ascertained through the Consortium for Research in Chronic lymphocytIc Leukemia (CRuCIAL) and to investigate their impact on modulating host immune responses and their utility to predict disease onset. Study participants were of European ancestry and gave their written informed consent to participate in the study, which was approved by the ethical review committee of participant institutions. CLL patients had often Binet stage A and Rai stage I (67.00% and 79.83%) and, compared to controls, had a higher mean age (66.19 ± 12.66 vs. 55.60 ± 11.50) and an increased male/female ratio (1.54 vs. 0.91). SNPs selection was based on published GWAS, functionality according to HaploReg data, and linkage disequilibrium between the SNPs. Genotyping of genetic variants was performed using KASPTM and Taqman® assays. Hardy–Weinberg equilibrium was assessed in the controls (P > 0.001) and the association between CLL and SNPs was tested using a multivariate unconditional logistic regression analysis adjusted for age, sex, and country of origin. A meta-analysis of the CRuCIAL results with those from previous GWAS was conducted to validate genetic associations and the I [2] statistic was used to assess statistical heterogeneity between the studies (PHet > 0.01).