We conducted a genome-wide association study for testicular germ cell tumor (TGCT), genotyping 307,666 SNPs in 730 cases and 1,435 controls from the UK and replicating associations in a further 571 cases and 1,806 controls. We found strong evidence for susceptibility loci on chromosome 5 (per allele OR = 1.37 (95% CI = 1.19-1.58), P = 3 × 10 −13 ), chromosome 6 (OR = 1.50 (95% = CI = 1.28-1.75), P = 10 −13 ) and chromosome 12 (OR = 2.55 (95% CI = 2.05-3.19), P = 10 −31 ). KITLG, encoding the ligand for the receptor tyrosine kinase KIT, which has previously been implicated in the pathogenesis of TGCT and the biology of germ cells, may explain the association on chromosome 12.Testicular germ cell tumor (TGCT) is the most common malignancy in men aged 15-45 years. The worldwide incidence of the disease is 7.5 per 100,000, but the rates vary considerably between countries and ancestry groups1. Known risk factors include a family history of the disease, previous germ cell tumor, subfertility, undescended testis (UDT)2 and testicular microlithiasis3, the presence of small foci of intratesticular calcification. There are two main subclasses of TGCT: seminomas show histological features of primordial germ cells, whereas nonseminomas show varying degrees of differentiation toward embryonal and extraembryonal structures. Some tumors show features of both classes. TGCTs are believed to arise from progenitor germ cells through a preinvasive phase of intratubular germ cell neoplasia (ITGCN)4. The peak incidence of nonseminomas is between the ages of 20 and 30 Several studies have estimated the risk to brothers and fathers of individuals with TGCT to be eight-to tenfold and four-to sixfold, respectively7, much higher than the familial risks for most other cancer classes, which are generally approximately twofold8. However, most families with multiple cases of TGCT include only two affected individuals, usually sibpairs, and extended pedigrees with several cases are exceedingly rare9. A genome-wide genetic linkage study of 179 families by an international consortium did not provide strong evidence for the location of a gene predisposing to TGCT9. However, candidate association studies have indicated that deletions on the Y chromosome that are also associated with infertility are implicated in TGCT susceptibility10.We carried out a genome-wide association study for TGCT susceptibility alleles using subjects with TGCT from the UK and the Illumina 370K array. Table 2 online). SNPs on chromosomes 5, 6 and 12 showed convincing evidence of association after replication (Table 1).The strongest evidence was obtained for rs995030 and rs1508595, which are located within the same LD block on chromosome 12. SNPs located in adjacent LD blocks showed much weaker evidence of association, suggesting that the causative variant resides within this block. In a multiple regression analysis, there was evidence that both rs995030 and rs1508595 are independently associated with disease risk (P = 0.03 in stage 2, P = 0.0006 overall, compare...

We conducted a genome-wide association study for testicular germ cell tumor, genotyping 298,782 SNPs in 979 affected individuals and 4,947 controls from the UK and replicating associations in a further 664 cases and 3,456 controls. We identified three new susceptibility loci, two of which include genes that are involved in telomere regulation. We identified two independent signals within the TERT-CLPTM1L locus on chromosome 5, which has previously been associated with multiple other cancers (rs4635969, OR=1.54, P=1.14x10(-23); rs2736100, OR=1.33, P=7.55x10(-15)). We also identified a locus on chromosome 12 (rs2900333, OR=1.27, P=6.16x10(-10)) that contains ATF7IP, a regulator of TERT expression. Finally, we identified a locus on chromosome 9 (rs755383, OR=1.37, P=1.12x10(-23)), containing the sex determination gene DMRT1, which has been linked to teratoma susceptibility in mice.

Testicular germ cell tumor (TGCT) is the most common cancer in young men and is notable for its high familial risks1,2. To date, six loci associated with TGCT have been reported3-7. From GWAS analysis of 307,291 SNPs in 986 cases and 4,946 controls, we selected for follow-up 694 SNPs, which we genotyped in a further 1,064 TGCT cases and 10,082 controls from the UK. We identified SNPs at nine new loci showing association with TGCT (P<5×10−8), at 1q22, 1q24.1, 3p24.3, 4q24, 5q31.1, 8q13.3, 16q12.1, 17q22 and 21q22.3, which together account for an additional 4-6% of the familial risk of TGCT. The loci include genes plausibly related to TGCT development. PRDM14, at 8q13.3, is essential for early germ cell specification8 whilst DAZL, at 3p24.3, is required for regulation of germ cell development9. Furthermore, PITX1, at 5q31.1 regulates TERT expression, and is the third TGCT locus implicated in telomerase regulation10.

Immunotherapy prolongs survival in only a subset of melanoma patients, highlighting the need to better understand the driver tumor microenvironment. We conducted bioinformatic analyses of 703 transcriptomes to probe the immune landscape of primary cutaneous melanomas in a population-ascertained cohort. We identified and validated 6 immunologically distinct subgroups, with the largest having the lowest immune scores and the poorest survival. This poor-prognosis subgroup exhibited expression profiles consistent with β-catenin–mediated failure to recruit CD141+ DCs. A second subgroup displayed an equally bad prognosis when histopathological factors were adjusted for, while 4 others maintained comparable survival profiles. The 6 subgroups were replicated in The Cancer Genome Atlas (TCGA) melanomas, where β-catenin signaling was also associated with low immune scores predominantly related to hypomethylation. The survival benefit of high immune scores was strongest in patients with double-WT tumors for BRAF and NRAS, less strong in BRAF-V600 mutants, and absent in NRAS (codons 12, 13, 61) mutants. In summary, we report evidence for a β-catenin–mediated immune evasion in 42% of melanoma primaries overall and in 73% of those with the worst outcome. We further report evidence for an interaction between oncogenic mutations and host response to melanoma, suggesting that patient stratification will improve immunotherapeutic outcomes.

Genome-wide association studies (GWAS) have transformed our understanding of testicular germ cell tumour (TGCT) susceptibility but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totalling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, approximately 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 between all 44 TGCT risk SNPs and candidate causal genes. Our findings reveal widespread disruption of developmental transcriptional regulators as a basis of TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis1. Defective microtubule assembly and dysregulation of KIT-MAPK signalling also feature as recurrently disrupted pathways. Our findings support a polygenic model of risk and provide insight into the biological basis of TGCT.

Purpose Gene expression studies in melanoma have been few because tumors are small and cryopreservation is rarely possible. The purpose of this study was to evaluate the Illumina DASL Array Human Cancer Panel for gene expression studies in formalin-fixed melanoma primary tumors, and to identify prognostic biomarkers. Experimental Design Primary tumors from two studies were sampled using a tissue microarray needle. Study 1: 254 tumors from a melanoma cohort recruited 2000-2006. Study 2: 218 tumors from a case-control study of patients undergoing sentinel node biopsy. Results RNA was obtained from 76% of blocks. 1.4% of samples failed analysis (transcripts from less than 250 of the 502 genes on the DASL chip detected). Increasing age of the block and increased melanin in the tumor were associated with reduced number of genes detected. The gene whose expression was most differentially expressed in association with relapse free survival in study 1 was osteopontin (SPP1, p=2.11×10−6) and supportive evidence for this was obtained in study 2 used as a validation set (p=0.006) (unadjusted data). Osteopontin level in study 1 remained a significant predictor of relapse free survival when data were adjusted for age, sex, tumor site and histological predictors of relapse. Genes whose expression correlated most strongly with osteopontin were PBX1, BIRC5 (Survivin) and HLF. Conclusion Expression data were obtained from 74% of primary melanomas and provided confirmatory evidence that osteopontin expression is a prognostic biomarker. These results suggest that predictive biomarker studies may be possible using stored blocks from mature clinical trials.

This study investigated the extent of linkage disequilibrium (LD) in two genomic regions (on chromosomes 4 and 7) in five populations of domesticated pigs. LD was measured with DЈ and tested for significance with the Fisher exact test. Effects of genetic (linkage) distance, chromosome, population, and their interactions on DЈ were tested both through a linear model analysis of covariance and by a theoretical nonlinear model. The overall result was that (1) the distance explained most of the variability of DЈ, (2) the effect of chromosome was significant, and (3) the effect of population was significant. The significance of the chromosome effect may have resulted from selection and the significance of the population effect illustrates the effects of population structures and effective population sizes on LD. These results suggest that mapping methods based on LD may be valuable even with only moderately dense marker spacing in pigs.

1a,25-Dihydroxyvitamin D3 signals via the vitamin D receptor (VDR). Higher serum vitamin D is associated with thinner primary melanoma and better outcome, although a causal mechanism has not been established. As patients with melanoma commonly avoid sun exposure, and consequent vitamin D deficiency might worsen outcomes, we interrogated 703 primary melanoma transcriptomes to understand the role of vitamin D-VDR signaling and replicated the findings in The Cancer Genome Atlas metastases. VDR expression was independently protective for melanoma-related death in both primary and metastatic disease. High tumor VDR expression was associated with upregulation of pathways mediating antitumor immunity and corresponding with higher imputed immune cell scores and histologically detected tumor-infiltrating lymphocytes. High VDR-expressing tumors had downregulation of proliferative pathways, notably Wnt/b-catenin signaling. Deleterious low VDR levels resulted from promoter methylation and gene deletion in metastases. Vitamin D deficiency (<25 nmol/L $ 10 ng/mL) shortened survival in primary melanoma in a VDR-dependent manner. In vitro functional validation studies showed that elevated vitamin D-VDR signaling inhibited Wnt/b-catenin signaling genes. Murine melanoma cells overexpressing VDR produced fewer pulmonary metastases than controls in tail-vein metastasis assays. In summary, vitamin D-VDR signaling contributes to controlling pro-proliferative/immunosuppressive Wnt/ b-catenin signaling in melanoma and this is associated with less metastatic disease and stronger host immune responses. This is evidence of a causal relationship between vitamin D-VDR signaling and melanoma survival, which should be explored as a therapeutic target in primary resistance to checkpoint blockade.Significance: VDR expression could potentially be used as a biomarker to stratify patients with melanoma that may respond better to immunotherapy.