Casey Dagnall

GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas

AbstractThe Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a prospective cohort study of nearly 155,000 U.S. volunteers aged 55–74 at enrollment in 1993–2001. We developed the PLCO Atlas Project, a large resource for multi-trait genome-wide association studies (GWAS), by genotyping participants with available DNA and genomic consent. Genotyping on high-density arrays and imputation was performed, and GWAS were conducted using a custom semi-automated pipeline. Association summary statistics were generated from a total of 110,562 participants of European, African and Asian ancestry. Application programming interfaces (APIs) and open-source software development kits (SKDs) enable exploring, visualizing and open data access through the PLCO Atlas GWAS Explorer website, promoting Findable, Accessible, Interoperable, and Re-usable (FAIR) principles. Currently the GWAS Explorer hosts association data for 90 traits and >78,000,000 genomic markers, focusing on cancer and cancer-related phenotypes. New traits will be posted as association data becomes available. The PLCO Atlas is a FAIR resource of high-quality genetic and phenotypic data with many potential reuse opportunities for cancer research and genetic epidemiology.

Validation of TypeSeq2, a Next-Generation–Based Sequencing Assay for the Detection of 46 Human Papillomavirus Genotypes, at the US National Cancer Institute and Costa Rica Laboratories

Abstract Background Cervical cancer is caused by persistent infection with carcinogenic human papillomavirus (HPV) genotypes. Prophylactic HPV vaccines are highly efficacious in preventing the acquisition of HPV infection. HPV vaccine trials and epidemiologic studies based on virologic endpoints rely on valid and reproducible measurements of HPV. We evaluated the second version of TypeSeq (TS2), a next-generation, sequencing-based assay that detects 46 HPV genotypes, in a historical phase 3 clinical trial. Methods We used 1214 stored cervical samples from women enrolled in the Costa Rica HPV Vaccine Trial with available HPV results from Short PCR Fragment 10- Line Probe Assay 25 (SPF10-LiPA25). TS2 was first validated at the National Cancer Institute (NCI) and transferred to the laboratory in Costa Rica, where we conducted a second validation study. We compared TS2 results generated at each laboratory to the SPF10-LiPA25 results. Results Overall, each laboratory demonstrated high positive agreement for most carcinogenic and noncarcinogenic genotypes between TS2 and SPF10-LiPA25. Intralaboratory comparisons revealed very high agreement in repeated testing. Interlaboratory comparisons showed high agreement for most carcinogenic and noncarcinogenic types. Overall, there were no statistically significant differences in vaccine efficacy in the according-to-protocol cohort using TS2 (either in NCI or Costa Rica) or SPF10-LiPA25 (McNemar P values >.05). Costa Rica produced similar vaccine efficacy estimates as NCI for HPV16/18, HPV31/33/45, and HPV35/39/51/52/56/58/59 as NCI (P values ≥.36). Conclusions Compared to SPF10-LiPA25, a well-established standard for HPV genotyping, TS2 demonstrated high accuracy. Inter- and intralaboratory comparisons demonstrated that TS2 is valid and reproducible. TS2 can accurately classify the presence of HPV, which is essential in HPV vaccine trials evaluating virological endpoints. Clinical Trials Registration NCT00128661.