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Papadopoulou K, Koliou GA, Tsimiliotis D, Kotoula V, Foukas P, Goussia A, Tsiatas M, Visvikis A, Chatzopoulos K, Nifora M, Charchanti A, Koumarianou A, Christodoulou C, Pectasides D, Psyrri A, Fostira F, Fountzilas G, Samantas E. Investigation of prognostic biomarkers in patients with urothelial carcinoma treated with platinum-based regimens. Urol Oncol 2022; 40:538.e15-538.e24. [PMID: 36041976 DOI: 10.1016/j.urolonc.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Bladder cancer (BC) is a heterogeneous malignancy with dismal outcome. PATIENTS AND METHODS Mutations in genes, altered or linked to platinum sensitivity in BC, were examined in 66 patients' tumors along with tumor infiltrating lymphocytes (TILs) density and MMR, PD-L1 and CD8 protein expression, as well as basal and luminal subtypes, defined by protein expression of markers, including CK5/6 and GATA3 or CK20, respectively. RESULTS 41 tumors harbored mutations, mainly in TP53 (38%), ARID1A (17%) and the DNA damage response and repair (DDR) genes ERCC2 (17%) and BRCA2 (15%). Mutations in other DDR relevant genes were also present. Age showed unfavorable prognosis for overall survival (HR=1.07, P = 0.026); no benefit was seen for patients with TP53, ARID1A, ERCC2 or BRCA2 mutations or mutations in 1 or more DDR genes. PD-L1 status positively correlated with stromal (rho=0.46, P < 0.001) and intratumoral (rho=0.53, P < 0.001) CD8 expression or TILs (rho=0.29, P = 0.018); none associated with overall survival (OS). A statistically significant difference was observed between PD-L1 status and immunohistochemistry (IHC)‑based subtypes, with tumors classified as luminal (GATA3+ and/or CK20+ and CK5/6-) showing lower PD-L1 expression relative to basal (CK5/6+ and GATA3- and/or CK20-) (median value 0 vs. 2.5, P = 0.029). Concerning OS, no statistically significant difference was seen among patients with basal or luminal tumors. CONCLUSION No association was seen herein between DDR mutations, TILs, PD-L1, CD8 expression or IHC-based subtypes and patient survival; these observations warrant validation within a larger cohort.
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Affiliation(s)
- Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | | | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Periklis Foukas
- Second Department of Pathology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Haidari, Greece
| | - Anna Goussia
- Department of Pathology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Marinos Tsiatas
- Department of Oncology, Athens Medical Center, Marousi, Greece
| | - Anastasios Visvikis
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Kyriakos Chatzopoulos
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Martha Nifora
- Second Department of Pathology, National and Kapodistrian University of Athens, School of Medicine, Attikon University Hospital, Haidari, Greece
| | - Antonia Charchanti
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Anna Koumarianou
- Hematology Oncology Unit, Fourth Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Section of Medical Oncology, Athens, Greece
| | - Amanda Psyrri
- Attikon University Hospital, Faculty of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece; Aristotle University of Thessaloniki, Thessaloniki, Greece; Department of Medical Oncology, German Oncology Center, Limassol, Cyprus
| | - Epaminontas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
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Kotoula V, Papadopoulou K, Tikas I, Fostira F, Vrettou E, Chrisafi S, Fountzilas E, Koliou GA, Apostolou P, Papazisis K, Zaramboukas T, Asimaki-Vlachopoulou A, Miliaras S, Ananiadis A, Poulios C, Natsiopoulos I, Tsiftsoglou A, Demiri E, Fountzilas G. Follow-up of tissue genomics in BRCA1/2 carriers who underwent prophylactic surgeries. Breast Cancer 2021; 28:1367-1382. [PMID: 34304347 DOI: 10.1007/s12282-021-01276-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE The genomic status of non-malignant tissues from carriers of pathogenic germline BRCA1/2 (gBRCA1/2) variants may reveal information towards individualized prophylaxis. We performed spatiotemporal tissue genotype comparisons in a real-life cohort of gBRCA1/2 carriers of Greek origin, who underwent multiple risk-reducing/prophylactic surgeries at various time points. METHODS Fifty-three women (median age 36 years) within cancer families were observed for up to 37.5 years; 43 were cancer carriers and 10 were healthy carriers. Histology review and genotyping were performed for 187 paraffin tissues (average: 3.5 per carrier) including 46 carcinomas (40 breast) and 141 non-malignant breast and gynecological samples. RESULTS High allelic imbalance (AI) and somatic pathogenic TP53 variants were present in cancer carriers only (p values < 0.0001). High AI was associated with gBRCA1/2 indels (p < 0.0001) and gBRCA2 alterations (p = 0.0109). Somatic (pathogenic) variants were infrequently shared between non-malignant tissues and matched carcinomas. Aberrations of gBRCA1 variant heterozygosity were noticed in tissues from cancer carriers only (13/43, 30.2%). These pertained to classic LOH (neoplastic lesions in 9/43 carriers, 20.9%) and under-representation of the germline variants (5 samples, 4 non-malignant, all in the breast). Both aberrations coexisted in matched samples in one case. Over time, germline variant heterozygosity prevailed in non-malignant tissues; intra-carrier genomic alterations were aggravated (21.1%), ameliorated (26.3%) or remained stable. CONCLUSION This real-life case study supports the need to address tissue genotypes from prophylactic surgeries in combination with polygenic scores towards personalized prophylaxis. To this end, knowing the traditionally classified pathogenic potential of a gBRCA1/2 variant may not be enough.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece. .,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Ioannis Tikas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Eleni Vrettou
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic of Thessaloniki, Thessaloníki, Greece.,European University of Cyprus, Nicosia, Cyprus
| | | | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research NCSR Demokritos, Athens, Greece
| | - Konstantinos Papazisis
- Department of Medical Oncology, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Thomas Zaramboukas
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | | | - Spyros Miliaras
- First Department of Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | | | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, University Campus, bld. 17b, 54124, Thessaloníki, Greece
| | - Ioannis Natsiopoulos
- Department of Breast Surgery, Interbalkan European Medical Center, Thessaloníki, Greece
| | - Aris Tsiftsoglou
- Department of Surgery, St. Luke's Hospital, Thessaloníki, Greece
| | - Efterpi Demiri
- Department of Plastic Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloníki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloníki, Greece.,Aristotle University of Thessaloniki, Thessaloníki, Greece.,German Oncology Center, Limassol, Cyprus
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3
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Fountzilas E, Kotoula V, Koliou GA, Liontos M, Papadopoulou K, Giannoulatou E, Papanikolaou A, Tikas I, Chrisafi S, Mauri D, Chatzopoulos K, Fostira F, Pectasides D, Oikonomopoulos G, Aivazi D, Andrikopoulou A, Visvikis A, Aravantinos G, Zagouri F, Fountzilas G. Tumor Genotyping and Homologous Recombination Repair Gene Variants in Patients With Epithelial Ovarian Cancer: Is Pathogenic Enough? Front Oncol 2021; 11:683057. [PMID: 34141624 PMCID: PMC8204021 DOI: 10.3389/fonc.2021.683057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Our hypothesis was that the predictive accuracy of pathogenic variants in genes participating in the homologous recombination repair (HRR) system in patients with epithelial ovarian cancer (EOC) could be improved by considering additional next-generation sequencing (NGS) metrics. NGS genotyping was performed in tumor tissue, retrospectively and prospectively collected from patients with EOC, diagnosed from 8/1998 to 10/2016. Variants were considered clonal when variant allele frequencies corresponded to >25%. The primary endpoint was overall survival (OS). This study included 501 patients with EOC, predominantly with high-grade serous (75.2%) and advanced stage tumors (81.7%); median age was 58 years (22-84). Pathogenic and clonal pathogenic variants in HRR and/or TP53 genes were identified in 72.8% and 66.5% tumors, respectively. With a median follow-up of 123.9 months, the presence of either pathogenic or clonal pathogenic HRR-only variants was associated with longer OS compared to HRR/TP53 co-mutation (HR=0.54; 95% CI, 0.34-0.87, Wald's p=0.012 and HR=0.45; 95% CI, 0.27-0.78, Wald's p=0.004, respectively). However, only the presence of clonal HRR-only variants was independently associated with improved OS (HR=0.55; 95% CI, 0.32-0.94, p=0.030). Variant clonality and co-occuring TP53 variants affect the predictive value of HRR pathogenic variants for platinum agents in patients with EOC. Clinical Trial Registration [ClinicalTrials.gov], identifier [NCT04716374].
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Affiliation(s)
- Elena Fountzilas
- Second Department of Medical Oncology, Euromedica General Clinic of Thessaloniki, Thessaloniki, Greece
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Michalis Liontos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Alexios Papanikolaou
- First Department of Obstetrics and Gynecology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Davide Mauri
- Department of Medical Oncology, Medical School, University of Ioannina, Ioannina, Greece.,Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, InRASTES, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | | | - Dimitra Aivazi
- First Department of Obstetrics and Gynecology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Angeliki Andrikopoulou
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Anastasios Visvikis
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Medical Oncology, German Oncology Center, Limassol, Cyprus
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4
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Lakis S, Kotoula V, Koliou GA, Efstratiou I, Chrisafi S, Papanikolaou A, Zebekakis P, Fountzilas G. Multisite Tumor Sampling Reveals Extensive Heterogeneity of Tumor and Host Immune Response in Ovarian Cancer. Cancer Genomics Proteomics 2021; 17:529-541. [PMID: 32859631 DOI: 10.21873/cgp.20209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND/AIM Ovarian cancer (OVCA) is characterized by genomic/molecular intra-patient heterogeneity (IPH). Tissue histology and morphological features are surrogates of the underlying genomic/molecular contexture. We assessed the morphological IPH of OVCA tumor compartments and of lymphocytic infiltrates in multiple matched samples per patient. MATERIALS AND METHODS We examined 294 hematoxylin & eosin (H&E) OVCA tumor whole sections from 70 treatment-naïve patients who had undergone cytoreductive surgery. We assessed morphological subtypes as immunoreactive (IR), solid - proliferative (SD), papilloglandular (PG), and mesenchymal transition (MT); subtype load per patient; stromal tumor-infiltrating lymphocyte (sTIL) density as average per sample; and, as maximal sTIL values (max-TILs) among all samples per patient, ovaries and implants. RESULTS Among all 294 tumor sections, the most frequent primary morphological subtype was PG (n=150, 51.0%), followed by MT (71, 24.1%), SD (48, 16.3%) and IR (15, 5.1%). Subtype combinations were observed in 67/294 sections (22.8%) and IPH in 48/70 patients (68.6%). PG prevailed in ovaries (p<0.001), SD and MT in implants (p=0.023 and p<0.001, respectively). sTILs were higher in SD compared to non-SD (p=0.019) and lower in PG, respectively (p<0.001). sTIL density was higher in implants than in ovaries (p<0.001). Higher max-TILs were associated with stage IV disease (p=0.043), upper abdominal dissemination (p=0.024), endometrioid histology (p=0.013), and grade 3 tumors (p=0.021). Favorable prognosticators were higher max-TILs per patient (PFS, OS) and higher SD-load (PFS). CONCLUSION Clinically relevant morphological and host immune-response IPH appear to be the norm in OVCA. This may complicate efforts to decipher sensitivity of the tumor to certain treatment modalities from a single pre-operative biopsy.
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Affiliation(s)
- Sotirios Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexios Papanikolaou
- First Department of Obstetrics and Gynecology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Pantelis Zebekakis
- First Department of Internal Medicine, AHEPA Hospital, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece.,German Oncology Center, Limassol, Cyprus
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Genotyping data of routinely processed matched primary/metastatic tumor samples. Data Brief 2020; 34:106646. [PMID: 33365374 PMCID: PMC7749371 DOI: 10.1016/j.dib.2020.106646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/05/2023] Open
Abstract
Genotypic and phenotypic comparisons of tumors in multiple tissue samples from the same patient are important for understanding disease evolution and treatment possibilities. Panel NGS genotyping is currently widely used in this context, whereby NGS variant filtering and final evaluation constitute the basis for meaningful comparisons. Here, we present the genotype data used for genotype / phenotype comparisons between matched primary / metastatic colorectal tumors in the work by Chatzopoulos et al (doi: 10.1016/j.humpath.2020.10.009), as well as the process followed for obtaining these data. We describe key issues while processing routinely formalin-fixed paraffin-embedded (FFPE) tumors for genotyping, NGS application (Ion Torrent), a stringent variant filtering algorithm for genotype analyses in FFPE tissues and particularly in matched tumor samples, and provide the respective datasets. Apart from research, tumor NGS genotyping is currently applied for clinical diagnostic purposes in Oncology. The datasets and method description provided herein (a) are important for comprehending the peculiarities of FFPE tumor genotyping, which is still mostly based on principles of germline DNA genotyping; (b) can be used in pooled analyses, e.g., of primary / metastatic tumors for the investigation of tumor evolution.
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6
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Fountzilas E, Kotoula V, Koliou GA, Giannoulatou E, Gogas H, Papadimitriou C, Tikas I, Zhang J, Papadopoulou K, Zagouri F, Christodoulou C, Koutras A, Makatsoris T, Chrisafi S, Linardou H, Varthalitis I, Papatsibas G, Razis E, Papakostas P, Samantas E, Aravantinos G, Bafaloukos D, Kosmidis P, Koumarianou A, Psyrri A, Pentheroudakis G, Pectasides D, Futreal A, Fountzilas G, Tsimberidou AM. Pathogenic mutations and overall survival in 3,084 patients with cancer: the Hellenic Cooperative Oncology Group Precision Medicine Initiative. Oncotarget 2020; 11:1-14. [PMID: 32002119 PMCID: PMC6967777 DOI: 10.18632/oncotarget.27338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/19/2019] [Indexed: 12/22/2022] Open
Abstract
Background: We evaluated the association between pathogenic mutations and overall survival (OS) in patients with cancer referred to Hellenic Cooperative Oncology Group–affiliated Departments.
Patients and methods: Patients referred from 12/1980 to 1/2017 had molecular testing (for research) of archival tumor tissue collected at the time of first diagnosis (non-metastatic, 81%; metastatic, 19%). Tumor-specific gene panels (16-101 genes) were used to identify pathogenic mutations in clinically relevant genes. NGS genotyping was performed at the Laboratory of Molecular Oncology, Aristotle University of Thessaloniki. Annotation of mutations was performed at MD Anderson Cancer Center.
Results: We analyzed 3,084 patients (median age, 57 years; men, 22%) with sequencing data. Overall, 1,775 (58% of 3,084) patients had pathogenic mutations. The median follow-up was 7.52 years (95% CI, 7.39-7.61). In patients with non-metastatic tumors, after stratification by tumor type, increasing age, higher grade, and histology other than adenocarcinoma were associated with shorter OS. OS was also shorter in patients with pathogenic TP53 (HR=1.36; p<0.001), MLL3 (HR=1.64; p=0.005), and BRCA1 (HR=1.46; p=0.047) mutations compared to wild-type genes. In multivariate analyses, independent prognostic factors predicting shorter OS were pathogenic mutations in TP53 (HR=1.37, p=0.002) and MLL3 (HR=1.50, p=0.027); increasing age (HR=1.02, p<0.001); and increasing grade (HR=1.46, p<0.001). In patients with metastatic cancer, older age and higher grade were associated with shorter OS and maintained their independent prognostic significance (increasing age, HR=1.03, p<0.001 and higher grade, HR=1.73, p<0.001).
Conclusions: Analysis of molecular data reveals prognostic biomarkers, regardless of tissue or organ of origin to improve patient management.
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Affiliation(s)
- Elena Fountzilas
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics, Houston, TX, USA.,Current address: Hellenic Cooperative Oncology Group, Athens, Greece
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Christos Papadimitriou
- Oncology Unit, Aretaieion Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Thomas Makatsoris
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - George Papatsibas
- Oncology Department, University General Hospital of Larissa, Larissa, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | - Epaminontas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Anna Koumarianou
- Fourth Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Amanda Psyrri
- Section of Medical Oncology, Department of Internal Medicine, Attikon University Hospital, Faculty of Medicine, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Georgios Pentheroudakis
- Department of Medical Oncology, Medical School, University of Ioannina, Ioannina, Greece.,Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Department of Genomic Medicine, Houston, TX, USA
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Apostolia M Tsimberidou
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics, Houston, TX, USA
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7
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Wang Q, Kotoula V, Hsu PC, Papadopoulou K, Ho JWK, Fountzilas G, Giannoulatou E. Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data. BMC Med Genomics 2019; 12:181. [PMID: 31874647 PMCID: PMC6929331 DOI: 10.1186/s12920-019-0636-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Background The application of next-generation sequencing in cancer has revealed the genomic landscape of many tumour types and is nowadays routinely used in research and clinical settings. Multiple algorithms have been developed to detect somatic variation from sequencing data using either paired tumour-blood or tumour-only samples. Most of these methods have been developed and evaluated for the identification of somatic variation using Illumina sequencing datasets of moderate coverage. However, a comprehensive evaluation of somatic variant detection algorithms on Ion Torrent targeted deep sequencing data has not been performed. Methods We have applied three somatic detection algorithms, Torrent Variant Caller, MuTect2 and VarScan2, on a large cohort of ovarian cancer patients comprising of 208 paired tumour-blood samples and 253 tumour-only samples sequenced deeply on Ion Torrent Proton platform across 330 amplicons. Subsequently, the concordance and performance of the three somatic variant callers were assessed. Results We have observed low concordance across the algorithms with only 0.5% of SNV and 0.02% of INDEL calls in common across all three methods. The intersection of all methods showed better performance when assessed using correlation with known mutational signatures, overlap with COSMIC variation and by examining the variant characteristics. The Torrent Variant Caller also performed well with the advantage of not eliminating a high number of variants that could lead to high type II error. Conclusions Our results suggest that caution should be taken when applying state-of-the-art somatic variant algorithms to Ion Torrent targeted deep sequencing data. Better quality control procedures and strategies that combine results from multiple methods should ensure that higher accuracy is achieved. This is essential to ensure that results from bioinformatics pipelines using Ion Torrent deep sequencing can be robustly applied in cancer research and in the clinic.
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Affiliation(s)
- Qing Wang
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Pei-Chen Hsu
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,School of Computer Science and Engineering, UNSW, Sydney, Australia
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, China.,St Vincent's Clinical School, UNSW, Sydney, Australia
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia. .,St Vincent's Clinical School, UNSW, Sydney, Australia.
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