Project description:High-quality evidence shows that MRI in biopsy-naive men can reduce the number of men who need prostate biopsy and can reduce the number of diagnoses of clinically insignificant cancers that are unlikely to cause harm. In men with prior negative biopsy results who remain under persistent suspicion, MRI improves the detection and localization of life-threatening prostate cancer with greater clinical utility than the current standard of care, systematic transrectal US-guided biopsy. Systematic analyses show that MRI-directed biopsy increases the effectiveness of the prostate cancer diagnosis pathway. The incorporation of MRI-directed pathways into clinical care guidelines in prostate cancer detection has begun. The widespread adoption of the Prostate Imaging Reporting and Data System (PI-RADS) for multiparametric MRI data acquisition, interpretation, and reporting has promoted these changes in practice. The PI-RADS MRI-directed biopsy pathway enables the delivery of key diagnostic benefits to men suspected of having cancer based on clinical suspicion. Herein, the PI-RADS Steering Committee discusses how the MRI pathway should be incorporated into routine clinical practice and the challenges in delivering the positive health impacts needed by men suspected of having clinically significant prostate cancer.

| S-EPMC6677282 | biostudies-literature

A Haplotype GWAS in Syndromic Familial Colorectal Cancer.

Project description:A previous genome-wide association study (GWAS) in colorectal cancer (CRC) patients with gastric and/or prostate cancer in their families suggested genetic loci with a shared risk for these three cancers. A second haplotype GWAS was undertaken in the same colorectal cancer patients and different controls with the aim of confirming the result and finding novel loci. The haplotype GWAS analysis involved 685 patients with colorectal cancer cases and 1642 healthy controls from Sweden. A logistic regression model was used with a sliding window haplotype approach. Whole-genome and exome sequencing datawere used to find candidate SNPs to be tested in a nested case-control study. In the analysis of 685 colorectal cancer cases and 1642 controls, all ten candidate loci from the previous study were confirmed. Fifty candidate loci were suggested with a p-value < 5 × 10-6 and odds ratios between 1.35-6.52. Two of the 50 loci, on 13q33.3 and 16q23.3, were the same as in the previous study. Whole-genome or exome data from 122 colorectal cancer patients was used to search for candidate variants in these 50 loci. A nested case-control study was performed to test genetic variants at 11 loci in a cohort of 827 familial colorectal cancer and a sub-cohort of 293 familial CRC cases with colorectal, gastric, and/or prostate cancer within their families and 1530 healthy controls. One SNP, rs115943733 on 10q11.21, reached statistical significance (OR = 3.26, p = 0.009). Seven SNPs in 4 loci had a higher OR in the smaller cohort compared to the larger study CRC cases. The results in this GWAS gave support for suggested loci with an increased shared risk of CRC, gastric, and/or prostate cancer. Further studies are needed to confirm the shared risk to be able to use this information in cancer prevention.

| S-EPMC11765965 | biostudies-literature

Japan PBC-GWAS Haplotype Study

Project description:Primary biliary cholangitis (PBC) susceptibility loci have largely been discovered through single SNP association testing. In this study, we report genic haplotype patterns associated with PBC risk genome-wide in two Japanese cohorts. Among the 74 genic PBC risk haplotype candidates we detected with a novel methodological approach in a discovery cohort of 1,937 Japanese, nearly two-thirds were replicated (49 haplotypes, Bonferroni-corrected P<6.8x10-4) in an independent Japanese cohort (N=949). Along with corroborating known PBC-associated loci (TNFSF15, HLA-DRA), risk haplotypes may potentially model cis-interactions that regulate gene expression. For example, one replicated haplotype association (9q32-9q33.1, OR=1.7, P=3.0x10-21) consists of intergenic SNPs outside of the human leukocyte antigen (HLA) region that overlap regulatory histone mark peaks in liver and blood cells, and are significantly associated with TNFSF8 expression in whole blood. We also replicated a novel haplotype association involving non-HLA SNPs mapped to UMAD1 (7p21.3; OR=15.2, P=3.9x10-9) that overlap enhancer peaks in liver and memory Th cells. Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.

| EGAS00001002915 | EGA

St. Jude Children’s Research Hospital – Washington University Pediatric Cancer Genome Project Steering Committee

Project description:Data Access Committee EGAC00001000044

| EGAC00001000044 | EGA