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Prieto-Potin I, Idrovo F, Suárez-Gauthier A, Díaz-Blázquez M, Astilleros-Blanco de Córdova L, Chamizo C, Zazo S, Carvajal N, López-Sánchez A, Pérez-Buira S, Aúz-Alexandre CL, Manso R, Plaza-Sánchez J, de Lucas-López V, Pérez-González N, Martín-Valle S, Cristóbal I, Casado V, García-Foncillas J, Rojo F. Comprehensive Approach to Genomic and Immune Profiling: Insights of a Real-World Experience in Gynecological Tumors. Diagnostics (Basel) 2022; 12:diagnostics12081903. [PMID: 36010253 PMCID: PMC9406465 DOI: 10.3390/diagnostics12081903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
Gynecological cancer accounts for an elevated incidence worldwide requiring responsiveness regarding its care. The comprehensive genomic approach agrees with the classification of certain tumor types. We evaluated 49 patients with gynecological tumors undergoing high-throughput sequencing to explore whether identifying alterations in cancer-associated genes could characterize concrete histological subtypes. We performed immune examination and analyzed subsequent clinical impact. We found 220 genomic aberrations mostly distributed as single nucleotide variants (SNV, 77%). Only 3% were classified as variants of strong clinical significance in BRCA1 and BRCA2 of ovarian high-grade serous (HGSC) and uterine endometrioid carcinoma. TP53 and BRCA1 occurred in 72% and 28% of HGSC. Cervical squamous cell carcinoma was entirely HPV-associated and mutations occurred in PIK3CA (60%), as well as in uterine serous carcinoma (80%). Alterations were seen in PTEN (71%) and PIK3CA (60%) of uterine endometrioid carcinoma. Elevated programmed death-ligand 1 (PD-L1) was associated with high TILs. Either PD-L1 augmented in deficient mis-matched repair (MMR) proteins or POLE mutated cases when compared to a proficient MMR state. An 18% received genotype-guided therapy and a 4% immunotherapy. The description of tumor subtypes is plausible through high-throughput sequencing by recognizing clinically relevant alterations. Additional concomitant assessment of immune biomarkers identifies candidates for immunotherapy.
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Affiliation(s)
- Iván Prieto-Potin
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Franklin Idrovo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Ana Suárez-Gauthier
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - María Díaz-Blázquez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | | | - Cristina Chamizo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Sandra Zazo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Nerea Carvajal
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Almudena López-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Sandra Pérez-Buira
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Carmen Laura Aúz-Alexandre
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Rebeca Manso
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Jenifer Plaza-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Virginia de Lucas-López
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Nuria Pérez-González
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Sara Martín-Valle
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Ion Cristóbal
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
- Translational Oncology Division, Oncohealth Institute, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Victoria Casado
- Translational Oncology Division, Oncohealth Institute, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Jesús García-Foncillas
- Cancer Unit for Research on Novel Therapeutic Targets, Oncohealth Institute, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
- Translational Oncology Division, Oncohealth Institute, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
| | - Federico Rojo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, 28040 Madrid, Spain
- Correspondence:
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Prieto-Potin I, Carvajal N, Plaza-Sánchez J, Manso R, Aúz-Alexandre CL, Chamizo C, Zazo S, López-Sánchez A, Rodríguez-Pinilla SM, Camacho L, Longarón R, Bellosillo B, Somoza R, Hernández-Losa J, Fernández-Soria VM, Ramos-Ruiz R, Cristóbal I, García-Foncillas J, Rojo F. Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ 2020; 8:e10069. [PMID: 33083132 PMCID: PMC7546223 DOI: 10.7717/peerj.10069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/09/2020] [Indexed: 01/29/2023] Open
Abstract
Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
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Affiliation(s)
- Iván Prieto-Potin
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Nerea Carvajal
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jenifer Plaza-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Rebeca Manso
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Carmen Laura Aúz-Alexandre
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Cristina Chamizo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Sandra Zazo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Almudena López-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | | | - Laura Camacho
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Raquel Longarón
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Rosa Somoza
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | | | - Ion Cristóbal
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jesús García-Foncillas
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Federico Rojo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
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