Genome-wide association study identifies multiple susceptibility loci for multiple myeloma

Abstract

Multiple myeloma (MM) is a plasma cell malignancy with a significant heritable basis. Genome-wide association studies have transformed our understanding of MM predisposition, but individual studies have had limited power to discover risk loci. Here we perform a meta-analysis of these GWAS, add a new GWAS and perform replication analyses resulting in 9,866 cases and 239,188 controls. We confirm all nine known risk loci and discover eight new loci at 6p22.3 (rs34229995, P=1.31 × 10(-8)), 6q21 (rs9372120, P=9.09 × 10(-15)), 7q36.1 (rs7781265, P=9.71 × 10(-9)), 8q24.21 (rs1948915, P=4.20 × 10(-11)), 9p21.3 (rs2811710, P=1.72 × 10(-13)), 10p12.1 (rs2790457, P=1.77 × 10(-8)), 16q23.1 (rs7193541, P=5.00 × 10(-12)) and 20q13.13 (rs6066835, P=1.36 × 10(-13)), which localize in or near to JARID2, ATG5, SMARCD3, CCAT1, CDKN2A, WAC, RFWD3 and PREX1. These findings provide additional support for a polygenic model of MM and insight into the biological basis of tumour development.

Figure 1. Manhattan plot of association P-values.

Shown are the genome-wide P-values (two sided) of 12.4 million successfully imputed autosomal SNPs in 7,319 cases and 234,385 controls from the discovery phase. Labelled in blue are previously identified risk loci and labelled in red are newly identified risk loci. The red horizontal line represents the genome-wide significance threshold of P=5.0 × 10⁻⁸ and the blue horizontal line represents the threshold of P=1.0 × 10⁻⁶ used to define promising SNPs.

Figure 2. Regional plots of association results and recombination rates for the newly identified risk loci for multiple myeloma.

Results for 6p22.3 (rs34229995), 6q21 (rs9372120), 7q36.1 (rs7781265), 8q24.21 (rs1948915), 9p21.3 (rs2811710), 10p12.1 (rs2790457), 16q23.1 (rs7193541) and 20q13.13 (rs6066835). Plots (using visPig70) show association results of both genotyped (triangles) and imputed (circles) SNPs in the GWAS samples and recombination rates. −Log₁₀ P-values (y axes) of the SNPs are shown according to their chromosomal positions (x axes). The sentinel SNP in each combined analysis is shown as a large circle or triangle and is labelled by its rsID. The colour intensity of each symbol reflects the extent of LD with the top SNP, white (r²=0) through to dark red (r²=1.0). Genetic recombination rates, estimated using 1,000 Genomes Project samples, are shown with a light blue line. Physical positions are based on NCBI build 37 of the human genome. Also shown are the relative positions of genes and transcripts mapping to the region of association. Genes have been redrawn to show their relative positions; therefore, maps are not to physical scale. On the bottom is the chromatin-state segmentation track (ChromHMM) for lymphoblastoid cells using data from the HapMap ENCODE Project.