Skip to main content

Table 1 Genomic scars of homologous recombination deficiency and relationships to drug response

From: Genomic scars as biomarkers of homologous recombination deficiency and drug response in breast and ovarian cancers

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) [33, 45]
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) [29, 44, 45]
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) [35, 45]
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) [1, 47]
Larger breast cancer data set (879)
  1. AOCS, Australian Ovarian Cancer Study; BLBC, basal-like breast cancer; HGSC, high-grade serous ovarian cancer; HR, homologous recombination; LOH, loss of heterozygosity; MDACC, MD Anderson Cancer Center; Nmut, number of coding mutation; SNP, single-nucleotide polymorphism; TCGA, The Cancer Genome Atlas; TNBC, triple-negative breast cancer; UPMC, University of Pittsburgh Medical Center.