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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.