Cancer Cell Line Genomics

The cancercelllines.org genomic information resource contains genome profiling data, somatic mutation information and associated metadata for thousands of human cancer cell lines. It has its origins in genomic copy number variation (CNV) profiling data of cell lines originally collected as part of the more than 100’000 individual datasets in the Progenetix oncogenomic resource. However, by providing genome mapped, annotated data for many types of genomic mutations, together with CNV profiles for a subset of the overall more than 16‘000 cell lines, cancercelllines.org provides a unique entry point for the comparative analysis of genomic variants in cell lines as well as for the exploration of related publications.

Cell Line Data CNV Frequency Plot The CNV histogram above represents CNV data from a randomly selected set of samples - either instances of a common cell line or with a shared diagnosis. In this example the frequencies of regional gains and losses in 18 samples from pgx:icdom-959 (Malignant lymphomas, NOS or diffuse) are on display.

In cancercelllines.org genomic variation data collected from a variaty of external resources and from original data (re-) analyses has been mapped to GRCh38 genome coordinates and is queryable using the Beacon v2 API . The resource contains data of 16340 individual cancer cell lines from 382 different cancer types (NCIt neoplasm classification).

A large amount of the cancer cell line data has been collected based on annotations and pointers from Cellosaurus , a reference knowledge resource on cell lines.

Citation
  • cancercelllines.org: Cancer cell line oncogenomic online resource (2023)
  • Paloots R and Baudis M. (2023): cancercelllines.org - a Novel Resource for Genomic Variants in Cancer Cell Lines bioRxiv DOI 10.1101/2023.12.12.571281 2023 Dec 13
  • Huang Q, Carrio-Cordo P, Gao B, Paloots R, Baudis M. (2021): The Progenetix oncogenomic resource in 2021. Database (Oxford). 2021 Jul 17