Supplementary Figure 1. Subjects and single SNP exclusion schema for the GWAS Supplementary Figure 2. Principal component plot for the genotyped IFM cohort and 3 HapMap phase III reference populations. The first two components are plotted, each sample is represented by a colored circle. Magenta: IFM samples; Red : IFM outliers; Pink: Utah residents with Northern and Western European ancestry from the CEPH collection (CEU); Green: Han Chinese in Beijing, China (CHB); Blue: Yoruba in Ibadan, Nigeria (YRI). Supplementary Figure 3. OR for 6 SNPs associated with BiPN discovery study ; for each allele, OR and CI is drawn (left: 0 risk-allele, middle :1 risk-allele, right: 2 risk-allele). Supplementary Figure 4. Manhattan plots for association analyses. Genome-wide association test results are shown as -Log10 transformed P-values . Chromosomal location of SNPs is indicated on the x-axis. The five candidate gene SNPs are indicated.
ARTICLE ABSTRACTPurpose: Painful peripheral neuropathy is a frequent toxicity associated with bortezomib therapy. This study aimed to identify loci that affect susceptibility to this toxicity.Experimental Design: A genome-wide association study (GWAS) of 370,605 SNPs was performed to identify risk variants for developing severe bortezomib-induced peripheral neuropathy (BiPN) in 469 patients with multiple myeloma who received bortezomib–dexamethasone therapy prior to autologous stem cell in randomized clinical trials of the Intergroupe Francophone du Myelome (IFM) and findings were replicated in 114 patients with multiple myeloma of the HOVON-65/GMMG-HD4 clinical trial.Results: An SNP in the PKNOX1 gene was associated with BiPN in the exploratory cohort [rs2839629; OR, 1.89, 95% confidence interval (CI), 1.45–2.44; P = 7.6 × 10−6] and in the replication cohort (OR, 2.04; 95% CI, = 1.11–3.33; P = 8.3 × 10−3). In addition, rs2839629 is in strong linkage disequilibrium (r2 = 0.87) with rs915854, located in the intergenic region between PKNOX1 and cystathionine-ß-synthetase (CBS). Expression quantitative trait loci mapping showed that both rs2839629 and rs915854 genotypes have an impact on PKNOX1 expression in nerve tissue, whereas rs2839629 affects CBS expression in skin and blood.Conclusions: The use of GWAS in multiple myeloma pharmacogenomics has identified a novel candidate genetic locus mapping to PKNOX1 and in the immediate vicinity of CBS at 21q22.3 associated with the severe bortezomib-induced toxicity. The proximity of these two genes involved in neurologic pain whose tissue-specific expression is modified by the two variants provides new targets for neuroprotective strategies. Clin Cancer Res; 22(17); 4350–5. ©2016 AACR.