Journal: medRxiv

Article Title: Combination of BRCA deep targeted sequencing and shallow whole genome sequencing to detect homologous recombination deficiency in ovarian cancer

doi: 10.1101/2024.09.10.24313378

Figure Lengend Snippet: Sensitivity of the HRD INSIGHT assay to detect (A) germline and somatic SNV and small Indel mutations, (B) germline large genomic rearrangements (LGRs) of BRCA1/2 genes in reference standards. (C) Concordance of the HRD INSIGHT assay to determine the genomic instability score and status of the reference standards. (D) Positive-, negative- and overall-percent agreement (NPA, PPA, Overall) of the HRD INSIGHT assay with the HRD Focus Panel (AmoyDx), TruSight Oncology TSO 500 HRD (Illumina) and SOPHiA DDM HRD Solutions (Sophia Genetics) to determine HRD status of clinical FFPE ovarian samples. For 4 conflicting samples, the results of individual assays were shown.

Article Snippet: While the PPA and NPA among all assays were mostly above 90%, the HRD INSI assay shared the lowest PPA with the AmoyDx kit (94.7%) and the lowest NPA with the Illumina TSO kit (81.3%).

Techniques:

Journal: medRxiv

Article Title: Combination of BRCA deep targeted sequencing and shallow whole genome sequencing to detect homologous recombination deficiency in ovarian cancer

doi: 10.1101/2024.09.10.24313378

Figure Lengend Snippet: (A) The successful rate of each assay to determine HRD status of clinical samples. (B) Distribution of noise index and DNA integrity number among samples that failed AmoyDx test. (C) Noise reduction algorithm improved the correlation of wGI score with TSO genomic instability (GIS) score. (D) Tumor fraction (TF) was determined in-silico and compared with AmoyDx and TSO kits. (E) In-silico simulation of TF serial dilution at different levels showed stable wGI scores at a minimum TF of 30%. (F) wGI score measurement was robust and reproducible among different runs across different sequencing platforms.

Article Snippet: While the PPA and NPA among all assays were mostly above 90%, the HRD INSI assay shared the lowest PPA with the AmoyDx kit (94.7%) and the lowest NPA with the Illumina TSO kit (81.3%).

Techniques: In Silico, Serial Dilution, Sequencing