Identifying germline pathogenic variants in breast cancer using tumor sequencing
Related Experiment Video
Updated: Aug 11, 2026
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
Mara Cruellas1, Andri Papakonstantinou2, Adrià López-Fernández1
1Medical Oncology Service, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Institute of Oncology (VHIO), Spain; Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Spain.
Purpose:
To investigate the performance of an in-house tumor sequencing panel to identify patients with breast cancer and a germline pathogenic variant (gPV).
Patients And Methods:
Retrospective and blinded tumor sequencing analysis in 90 patients with breast cancer and prior germline genetic testing (45 non-carriers and 45 carriers of a gPV) using an in-house panel (VHIO-300). Sensitivity (S), specificity (Sp), positive predictive value (PPV), and negative predictive value (NPV) of tumor sequencing were calculated. A Cohen's kappa coefficient ≥0.80 was predefined as minimum to be reliably acceptable for clinical implementation.
Results:
The cohort included 84 women and 6 men with a median age of 48 years (29-84). Tumors of germline carriers were mainly stage II (47 % vs 31 %, P = 0.047), luminal B-like (56 % vs 31 %, p = 0.037) or triple negative (22 % vs 16 %, = 0.037). The in-house tumor panel identified 91 % (40/44) of the gPV. The analysis did not detect any of the 2 patients with germline large rearrangement alterations nor 2 of the 7 patients with intronic variants included. The tumor sequencing panel yielded 7 % of false positive results (ie, genetic alterations suggestive of germline origin). Hence, S was 91 %, Sp 93 % and Cohen's kappa coefficient between tumor and germline testing was 0.84 (95 % CI 0.73-0.95).
Conclusion:
Tumor tissue sequencing with our in-house panel demonstrated an acceptable performance to identify patients with breast cancer carriers of a gPV.
