Input | Name | Demonstrated objective(s) | Output | Data sets used (sample size) | References |
---|---|---|---|---|---|
Segmented allele-specific copy number from SNP microarray data | Telomeric allelic imbalance score (NtAi) | 1. Indicate sensitivity to platinum drugs | Integer between 0 and 46 per sample | Breast cancer cell lines (10 + 24) | |
2. Indicate BRCA1/2 dysfunction | Cisplatin-1 TNBC trial (27) | ||||
Cisplatin-2 TNBC trial (37) | |||||
TCGA HGSCs (218) | |||||
Homologous recombination defect (HRD) score | 1. Indicate HR dysfunction | Integer from 0 upper sample | MDACC ovarian cancers (152) | ||
2. Indicate sensitivity to platinum drugs | UPMC ovarian cancers (152) | ||||
TCGA ovarian cancers (435) | |||||
Cancer cell lines (57) | |||||
Cisplatin-1 TNBC trial (27) | |||||
Cisplatin-2 TNBC trial (37) | |||||
PreECOG TNBC/BRCA1/2 trial (80) | |||||
Large-scale transition (LST) score | 1. Indicate HR dysfunction | Integer from 0 upper sample | BLBC discovery set (65) | ||
2. Indicate sensitivity to platinum drugs | BLBC validation set (55) | ||||
BLBC cell lines (17) | |||||
Cisplatin-1 TNBC trial (27) | |||||
Cisplatin-2 TNBC trial (37) | |||||
LOH clustering | 1. Indicate sensitivity to platinum drugs | Three clusters of tumors: HiA, | Boston HGSCs (47) | [34] | |
2. Indicate BRCA1/2 dysfunction | HiB, and Lo | Boston TNBCs (50) | |||
3. Provide prognostic information | AOCS HGSCs (85) | ||||
TCGA HGSCs (116) | |||||
Single-nucleotide variant calls from exome sequencing data | Total number of somatic, synonymous, and non-synonymous coding mutations (Nmut) | 1. Indicate sensitivity to platinum drugs | Integer from 0 upper sample | TCGA HGSCs (316) | [46] |
2. Indicate BRCA1/2 dysfunction | |||||
3. Provide prognostic information | |||||
Mutational catalogue from whole-genome sequencing data | Mutational signature 3/Mutational signature D | Indicate BRCA1/2 dysfunction | Proportion of mutational spectrum contributed by mutational signature 3 per sample | Initial breast cancer data set (21) | |
Larger breast cancer data set (879) |