Mosaic structural variation sample

Mosaic Normal-Tumor genomes are generated from real normal-tumor pairs with validated somatic variants. In this case, validated variants from the GRIDSS2 paper. Mosaic genomes were generated using GenomeMosaicMaker, an open-source software tool designed and implemented for this specific purpose. The variants provided in the VCF truth file for each mosaic tumor/normal pair were annotated using funnSV for SVs and VEP for SNVs and indels. All CRAM files are aligned to GRCh37. Please see https://github.com/EUCANCan/oncoliner and https://github.com/Computational-Genomics-BSC/GenomeMosaicMaker for more information.

• Type: Whole Genome Sequencing
• Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 2 Publications 2 External Links

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000668	Simulated (based on real world data) tumor normal pair designed for benchmarking and optimisation of structural variation callers. The calls are derived from 12 patients in the hartwig database requested by the EUCANCan project. Paired-end sequencing data was imputed into the normal reference data to simulate real world variation like purity as well as technical impact of sequencing technologies. The dataset contains a tumor sequenced to ±90x depth and a normal control sequenced to ±30 x depth of these imputed events. The break junctions of all detected SVs in the original cases are imputed in this data from diagnostic WGS sequencing data.	Illumina NovaSeq 6000	1

Publications	Citations
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. Genome Biol 22: 2021 202	75
ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. Martín R, Gaitán N, Jarlier F, Feuerbach L, de Soyres H, Arbonés M, Gutman T, Puiggròs M, Ferriz A, Gonzalez A, Estelles L, Gut I, Capella-Gutierrez S, Stein LD, Brors B, Royo R, Hupé P, Torrents D. Cell Genom 4: 2024 100639	0

ONCOLINER ONCOLINER