A cancer genomics resource built on GA4GH standards

Rahel Paloots, Michael Baudis

CGC St Louis 2022

Progenetix is a cancer genomics resource that includes genomic profiling data as well as biomedical annotations and provenance data for cancer studies. The main goal of the Progenetix database is to provide easy, open access for research studies and clinical diagnostics. To facilitate sharing of genomic data, Progenetix complies with and contributes to GA4GH and Beacon data standards. Beacon, developed with the support from ELXIR (the European bioinformatics infrastructure organization), started out as protocol to share genomic variants over federated queries.

Candidate targets of copy number deletion events across 17 cancer types

Huang Q and Baudis M

Progenetix, BeaconPlus & GA4GH

A cancer genomics reference resource powered by GA4GH standards

Michael Baudis

Roche Data Science Seminar

The presentation reports about the Progenetix cancer genomics resource and its role in the GA4GH ecosystem & the Beacon genomics API development process.

The GA4GH Phenopacket schema defines a computable representation of clinical data

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Axton M, Babb L, Boerkoel CF, Chaudhari BP, Chin H-L, Dumontier M, Gazzaz N, Hansen DP, Hochheiser H, Kinsler VA, Lochmüller H, Mankovich AR, Saunders GI, Sergouniotis PI, Thompson R, Zankl A, Haendel MA, Robinson PN, The GAGHPMC.

Cancer cell line variant knowledge resource for facilitated cell line identification

Rahel Paloots, Michael Baudis

ESHG Vienna 2022

One of the known features of cancer is the instability of its genome. Vast changes in the genome lead to duplications and deletions in the chromosome, that can be detected in most types of cancer. These chromosomal aberrations are also called copy number variants. Cancer cell lines are necessary tools for understanding the disease mechanisms as well as the development of new cancer treatments. However, they may not always be the best representation of their neoplasm of origin, due to cell line contamination and misidentification, as well as higher numbers of accumulated mutations in the cancer cell line genome.