Abstract 166P
Background
The aim of this study is to assess the performance of the accredited in-house NGS panel VHIO300 in the detection of gPV in tumor sequencing from patients with BC.
Methods
We selected 90 patients (pts) with BC with prior germline genetic diagnosis and available tumor tissue (primary tumor or metastatic samples); 45 had a gPV in a hereditary breast and ovarian cancer (HBOC) gene and 45 had no gPV detected. Blinded tumor sequencing was carried out using VHIO300 panel. Frequency of true positives (TP), true negatives (TN), false positives (FP) and false negatives (FN) of tumor sequencing was calculated, as well as sensitivity, specificity, positive and negative predictive value (PPV, NPV). A Cohen’s kappa coefficient of 0.80 was required.
Results
2 samples (1 from a pt with PALB2 gPV and 1 germline negative) did not fulfill technical requirements for tumor sequencing. So, 88 pts had germline and tumoral sequencing results. The VHIO300 identified the gPV in 40/44 (91%) tumor samples (TP). Four gPV were not identified in tumor sequencing (FN): 2 large rearrangements (LR) (100% of LR) and 2 intronic variants (29% of intronic variants). The 4 variants were identified after being revisited in a targeted manner (Table). Among the 44 pts with no gPV, the VHIO300 identified 3 HBOC-associated PV potentially of germline origin due to their variant allele frequency (1 BRCA1, 2 BRCA2). Ad hoc germline analysis of these 3 PV was negative, so they were considered as FP (7%) (Table). The sensitivity, specificity, PPV and NPV of the VHIO300 to detect gPV was 91%, 93%, 93%, and 91%, respectively. Cohen's kappa coefficient was 0.84 (95% CI 0.73 – 0.95). Table: 166P
| Gene | Variant | Type of variant | VAF | BC tumor | |
| gPV not detected by tumor sequencing (FN) | ATM | c.902-19_1065+869del1052 | LR | ---- | Lum B HER2 neg |
| gPV not detected by tumor sequencing (FN) | CHEK2 | Deletion of exons 3 and 4 | LR | ---- | Lum B HER2 neg |
| gPV not detected by tumor sequencing (FN) | CHEK2 | c.793-1G>A | Intronic variant | ---- | Lum A |
| gPV not detected by tumor sequencing (FN) | BRCA2 | c.8332-13T>G | Intronic variant | ---- | Lum B HER2 neg |
| PV in HBOC gene in tumoral sequencing not gPV (FP) | BRCA1 | c.5193+1G>T | Intronic variant | 45.32% | Triple neg |
| PV in HBOC gene in tumoral sequencing not gPV (FP) | BRCA2 | c.8695C>T | Point mt nonsense | 57.66% | Lum B HER2 neg |
| PV in HBOC gene in tumoral sequencing not gPV (FP) | BRCA2 | c.8023A>G | Point mt missense | 35.19% | Lum A |
Conclusions
The VHIO300 panel demonstrated acceptable sensitivity and specificity in this BC population, validating its clinical use as a surrogate initial method to identify patients with HBOC gPV. However, if there is a high clinical suspicion of HBOC, germline testing should be performed if no putative gPV is identified in tissue.
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
M. Cruellas Lapena: Financial Interests, Personal, Invited Speaker: Roche; Other, Personal, Other, Travel grant: Lilly. C. Saura Manich: Financial Interests, Personal, Advisory Board: AstraZeneca, Daiichi Sankyo, Eisai, Exact Sciences, Exeter Pharma, F. Hoffmann - La Roche Ltd., Gilead, Lilly, Merck Sharp & Dohme, Novartis, Pfizer, Philips, Pierre Fabre, PintPharma, Puma, Roche Farma, Sanofi Avenits, Seagen, Zymeworks, Pharmalex Spain SLU; Financial Interests, Personal, Expert Testimony: Boehringer Ingelheim, Bristol Meyers Squibb, Genentech, Innoup, Millenium; Financial Interests, Personal, Other, SC: Byondis B.V., GSK, Macrogenics, Menarini, Merus, Synthon Biopharpaceuticals; Financial Interests, Institutional, Research Grant: AstraZeneca, Bayer Pharma, Boehringer Ingelheim, Bristol Myers Squibb (BMS), Cytomx Therapeutics, Daiichi Sankyo, Eli Lilly and Company, F. Hoffmann-La Roche Ltd., Genentech, GSK, Immunomedics, Innoup Farma, Macrogenics, Menarini Ricerche, Merus, Novartis, Pfizer, Puma, Roche, Sanofi-Aventis, Seattle Genetics; Financial Interests, Institutional, Invited Speaker: Byondis B.V.; Non-Financial Interests, Member: Spanish Society of Medical Oncology (SEOM), American Society for Clinical Oncology (ASCO), Geicam (Spanish Breast Cancer Research Group), European Society for Medical Oncology (ESMO), Sinology Society of the Official College of Physicians of Barcelona (COMB); Non-Financial Interests, Member, Junta Directiva y Comité Científico: SOLTI group (Academic research group in breast cancer). A. Vivancos: Financial Interests, Personal, Advisory Board: Roche, Bristol Myers Squibb, Guardant Health, Bayer, INCYTE; Financial Interests, Personal, Stocks/Shares: Reveal Genomics; Financial Interests, Institutional, Research Grant, Preclinical Research Grant: Bristol Myers Squibb, Roche, INCYTE. M. Oliveira: Financial Interests, Personal, Advisory Board: AstraZeneca, Daiichi Sankyo / AstraZeneca, Gilead, Lilly, MSD, Relay Therapeutics, Roche, Seagen, Cureo Science, iOne, Pfizer; Financial Interests, Personal, Invited Speaker: Eisai, Gilead, Pfizer, Roche, Seagen, AstraZeneca, Lilly, Medscape, AstraZeneca, AstraZeneca; Financial Interests, Personal, Other, Educational activity: Libbs; Financial Interests, Institutional, Invited Speaker: AstraZeneca, Boehringer-Ingelheim, GSK, Roche, Seattle Genetics, Zenith Epigenetics, Gilead, Ayala Pharmaceuticals, Pfizer; Financial Interests, Invited Speaker: Roche; Non-Financial Interests, Member of Board of Directors, Head: SOLTI Breast Cancer Research; Other, Travel Grant: Pierre Fabre, Eisai, Gilead, AstraZeneca. J. Balmaña: Financial Interests, Personal, Invited Speaker: AstraZeneca; Financial Interests, Institutional, Other, Educational programs: AstraZeneca-MSD; Financial Interests, Institutional, Invited Speaker: AstraZeneca, MedSir. All other authors have declared no conflicts of interest.