MONSTAR-1 data overview - Githubissues

icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing

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MONSTAR-1 data overview #442

Closed lindaxiang closed 2 months ago

lindaxiang commented 5 months ago

MONSTAR-1 Data Overview and Ingestion

2224 patients with advanced solid tumours for metastatic recurrent cancer
755 have both liquid and tissue sequencing data

Molecular data

Targeted Sequencing.
Tissue targeted panel (FoundationOne CDx)
ctDNA targeted panel (FoundationOne Liquid CDx)
Panel size: 324 genes
No FASTQ but BAM (convertible) file available from FMI. Monstar can only provide variant files in XML format.
Genome build: GRCh19

Clinical data

Use the date of enrollment as the date of diagnosis.
Exceptions are needed for 43/70 core fields
Major concern: miss cancer staging information
Gather some level of treatment information
Gather relatively detail information for biomarker, exposure and comorbidity