DNA was analyzed using the recently described next-generation sequencing-based assay to generate genome-wide SNP profiles from which the three components of the HRD score are calculated (20 (link)). A custom enrichment panel was developed, which targets 54,091 single-nucleotide polymorphisms (SNP) distributed across the complete human genome. The panel also includes an additional 685 probes targeting the complete coding region of BRCA1 and BRCA2. A detailed description of the panel design and development and the assay process is provided in Timms and colleagues (20 (link)).
MIP SNP arrays have been previously described in detail (27 (link)). For PrECOG 0105, MIP SNP array data had previously been generated on 55 samples from this study. In 31 samples with HRD scores from both arrays and sequencing, the Pearson correlation was 0.94. The sequencing-based HRD assay was used for molecular data for 60 of the 70 samples in the analysis set and a whole genome MIP array was used to generate data for the remaining 10 where sequencing data were not available (3 with insufficient tissue and 7 where sequencing failed). The sequencing-based HRD assay was used for all of the cisplatin trial cohort samples.
To determine BRCA1/2 mutation status, variant and large rearrangement detection was performed on sequence from BRCA1 and BRCA2. Complete descriptions of the sequence alignment and mutation detection methods are provided in Timms and colleagues (20 (link)). Mutations identified were only included in the analysis if classified as deleterious or suspected deleterious based on previously described criteria (28 (link)).
To calculate the HRD score for samples analyzed by custom hybridization sequencing assay, reads covering SNP positions were used to generate allelic imbalance profiles as described by Timms and colleagues (20 (link)). HRD score was defined as the unweighted sum of LOH, TAI, and LST scores: HRD = LOH + TAI + LST. Details of the individual LOH, TAI, and LST scores, as well as the combined HRD score, are described in theSupplementary Material .
HR deficiency status was determined on the basis of the combination of the dichotomized HRD score using the predefined HRD threshold and tumor BRCA1/2 status (scored as mutated if deleterious or suspected deleterious mutations in BRCA1/2 were present; nonmutated if otherwise, including variants of uncertain significance). HR deficiency was defined as high HRD score (above the HRD threshold, > 42) and/or mutated tumor BRCA1/2. HR nondeficiency was defined as low HRD score (below the HRD threshold, < 42) and nonmutated orfailed tumor BRCA1/2 mutation analysis. HR status could not be determined if HRD score analysis failed and tumor BRCA1/2 analysis was negative or failed.
MIP SNP arrays have been previously described in detail (27 (link)). For PrECOG 0105, MIP SNP array data had previously been generated on 55 samples from this study. In 31 samples with HRD scores from both arrays and sequencing, the Pearson correlation was 0.94. The sequencing-based HRD assay was used for molecular data for 60 of the 70 samples in the analysis set and a whole genome MIP array was used to generate data for the remaining 10 where sequencing data were not available (3 with insufficient tissue and 7 where sequencing failed). The sequencing-based HRD assay was used for all of the cisplatin trial cohort samples.
To determine BRCA1/2 mutation status, variant and large rearrangement detection was performed on sequence from BRCA1 and BRCA2. Complete descriptions of the sequence alignment and mutation detection methods are provided in Timms and colleagues (20 (link)). Mutations identified were only included in the analysis if classified as deleterious or suspected deleterious based on previously described criteria (28 (link)).
To calculate the HRD score for samples analyzed by custom hybridization sequencing assay, reads covering SNP positions were used to generate allelic imbalance profiles as described by Timms and colleagues (20 (link)). HRD score was defined as the unweighted sum of LOH, TAI, and LST scores: HRD = LOH + TAI + LST. Details of the individual LOH, TAI, and LST scores, as well as the combined HRD score, are described in the
HR deficiency status was determined on the basis of the combination of the dichotomized HRD score using the predefined HRD threshold and tumor BRCA1/2 status (scored as mutated if deleterious or suspected deleterious mutations in BRCA1/2 were present; nonmutated if otherwise, including variants of uncertain significance). HR deficiency was defined as high HRD score (above the HRD threshold, > 42) and/or mutated tumor BRCA1/2. HR nondeficiency was defined as low HRD score (below the HRD threshold, < 42) and nonmutated orfailed tumor BRCA1/2 mutation analysis. HR status could not be determined if HRD score analysis failed and tumor BRCA1/2 analysis was negative or failed.
