MSI, Ploidy & Mutational Burden
Annotation of the cell models obtained through genomic analysis.
MSI estimation was performed using MSIsensor-pro. Samples with an MSI score >=7 were marked as MSI and remaining samples as MSS.
- MSI: Microsatellite Instable
- MSS: Microsatellite Stable
Multiple ploidy estimates are provided based on the underlying data source.
Determined using PureCN as a component of the Copy Number Dataset.
Determined using Purple as a component of the Copy Number Dataset.
Refers to the ploidy status of the cell model determined by using mean copy-number obtained from PICNIC using the Affymetrix SNP6 data.
Mutational burden describes the number of somatic mutations (SNV's/INDEL's) detected in a model relative to the total number of bases sequenced.
Total number of ‘PASS’ somatic variants * 10^6 / Genome Size
This is calculated using the models primary mutation data source, typically WES for cell lines and WGS for organoid models. Genome size is determined as:
- Whole Exome Sequencing: Fixed length 38Mb (Chalmers et al., 2017)
- Whole Genome Sequencing: Effective genome size for a the genome build and read length (Ref: Effective Genome Size).