Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor

Abstract

Genome-wide association studies (GWAS) have transformed understanding of susceptibility to testicular germ cell tumors (TGCTs), but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totaling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, roughly doubling the number of known TGCT risk loci to 44. By performing in situ Hi-C in TGCT cells, we provide evidence for a network of physical interactions among all 44 TGCT risk SNPs and candidate causal genes. Our findings implicate widespread disruption of developmental transcriptional regulators as a basis of TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis. Defective microtubule assembly and dysregulation of KIT-MAPK signaling also feature as recurrently disrupted pathways. Our findings support a polygenic model of risk and provide insight into the biological basis of TGCT.

Figure 1

Study design.

Figure 2

Circos plot of integrated functional analysis for all 44 TGCT risk loci. Inner-most ring represents the presence of a Hi-C contact in the NTERA2 cell line, the next four rings (H3k9me3, H3k9ac, H3k4me1, H3k4me3) are narrow-peak histone ChIP-seq tracks for NTERA2, the sixth ring represents -log P values of TGCT risk association from the Oncoarray GWAS data with green line denoting genome-wide significance and the seventh ring (outer-most) is the functional classification of candidate causal genes (green= transctiptional regulation, blue= microtubule/chromosomal assembly, purple= KIT-MAPK), the size of bar represents the strength of functional data. Candidate causal genes are also annotated around the outside of the plot.

Figure 3

A-C – Regional plots of three new TGCT loci at A) 8p23.1, B) 15q25.2 and C) 15q22.31. Shown by triangles are the −log10 association P values of genotyped SNPs, based on Oncoarray data. Shown by circles are imputed SNPs at each locus. The intensity of red shading indicates the strength of LD with the sentinel SNP (labelled). Also shown are the SNP build 37 coordinates in mega-bases (Mb), recombination rates in centi-morgans (cM) per mega-base (Mb) (in light blue) and the genes in the region (in dark blue). Below the gene transcripts are Hi-C next generation sequencing read pair counts (intervals are determined by HindIII cut points, with average 3Kb resolution), where gaps represent bait locations, which are plotted along with significant Hi-C interactions, where colour and depth of ribbons represent the score. Below the axis is a zoomed-in section displaying the surrounding genes for each SNP, with the sentinel SNP marked with a red triangle and any significant regulatory markers denoted with a blue circle. Finally the predicted chromHMM states are shown (coloured as per the legend) along with a zoomed-in arc depiction of the same Hi-C contact(s).

Figure 3

A-C – Regional plots of three new TGCT loci at A) 8p23.1, B) 15q25.2 and C) 15q22.31. Shown by triangles are the −log10 association P values of genotyped SNPs, based on Oncoarray data. Shown by circles are imputed SNPs at each locus. The intensity of red shading indicates the strength of LD with the sentinel SNP (labelled). Also shown are the SNP build 37 coordinates in mega-bases (Mb), recombination rates in centi-morgans (cM) per mega-base (Mb) (in light blue) and the genes in the region (in dark blue). Below the gene transcripts are Hi-C next generation sequencing read pair counts (intervals are determined by HindIII cut points, with average 3Kb resolution), where gaps represent bait locations, which are plotted along with significant Hi-C interactions, where colour and depth of ribbons represent the score. Below the axis is a zoomed-in section displaying the surrounding genes for each SNP, with the sentinel SNP marked with a red triangle and any significant regulatory markers denoted with a blue circle. Finally the predicted chromHMM states are shown (coloured as per the legend) along with a zoomed-in arc depiction of the same Hi-C contact(s).

Figure 3

A-C – Regional plots of three new TGCT loci at A) 8p23.1, B) 15q25.2 and C) 15q22.31. Shown by triangles are the −log10 association P values of genotyped SNPs, based on Oncoarray data. Shown by circles are imputed SNPs at each locus. The intensity of red shading indicates the strength of LD with the sentinel SNP (labelled). Also shown are the SNP build 37 coordinates in mega-bases (Mb), recombination rates in centi-morgans (cM) per mega-base (Mb) (in light blue) and the genes in the region (in dark blue). Below the gene transcripts are Hi-C next generation sequencing read pair counts (intervals are determined by HindIII cut points, with average 3Kb resolution), where gaps represent bait locations, which are plotted along with significant Hi-C interactions, where colour and depth of ribbons represent the score. Below the axis is a zoomed-in section displaying the surrounding genes for each SNP, with the sentinel SNP marked with a red triangle and any significant regulatory markers denoted with a blue circle. Finally the predicted chromHMM states are shown (coloured as per the legend) along with a zoomed-in arc depiction of the same Hi-C contact(s).