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Samsom KG, Bosch LJW, Schipper LJ, Schout D, Roepman P, Boelens MC, Lalezari F, Klompenhouwer EG, de Langen AJ, Buffart TE, van Linder BMH, van Deventer K, van den Burg K, Unmehopa U, Rosenberg EH, Koster R, Hogervorst FBL, van den Berg JG, Riethorst I, Schoenmaker L, van Beek D, de Bruijn E, van der Hoeven JJM, van Snellenberg H, van der Kolk LE, Cuppen E, Voest EE, Meijer GA, Monkhorst K. Optimized whole-genome sequencing workflow for tumor diagnostics in routine pathology practice. Nat Protoc 2024; 19:700-726. [PMID: 38092944 DOI: 10.1038/s41596-023-00933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/19/2023] [Indexed: 03/10/2024]
Abstract
Two decades after the genomics revolution, oncology is rapidly transforming into a genome-driven discipline, yet routine cancer diagnostics is still mainly microscopy based, except for tumor type-specific predictive molecular tests. Pathology laboratories struggle to quickly validate and adopt biomarkers identified by genomics studies of new targeted therapies. Consequently, clinical implementation of newly approved biomarkers suffers substantial delays, leading to unequal patient access to these therapies. Whole-genome sequencing (WGS) can successfully address these challenges by providing a stable molecular diagnostic platform that allows detection of a multitude of genomic alterations in a single cost-efficient assay and facilitating rapid implementation, as well as by the development of new genomic biomarkers. Recently, the Whole-genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE) study demonstrated that WGS is a feasible and clinically valid technique in routine clinical practice with a turnaround time of 11 workdays. As a result, WGS was successfully implemented at the Netherlands Cancer Institute as part of routine diagnostics in January 2021. The success of implementing WGS has relied on adhering to a comprehensive protocol including recording patient information, sample collection, shipment and storage logistics, sequencing data interpretation and reporting, integration into clinical decision-making and data usage. This protocol describes the use of fresh-frozen samples that are necessary for WGS but can be challenging to implement in pathology laboratories accustomed to using formalin-fixed paraffin-embedded samples. In addition, the protocol outlines key considerations to guide uptake of WGS in routine clinical care in hospitals worldwide.
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Affiliation(s)
- Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Linda J W Bosch
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Luuk J Schipper
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
| | - Daoin Schout
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ferry Lalezari
- Department of Radiology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Adrianus J de Langen
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tineke E Buffart
- Department of Medical Oncology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Berit M H van Linder
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kelly van Deventer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Kay van den Burg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Unga Unmehopa
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Efraim H Rosenberg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roelof Koster
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Frans B L Hogervorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Immy Riethorst
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Lieke Schoenmaker
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Daphne van Beek
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | - Ewart de Bruijn
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
| | | | | | | | - Edwin Cuppen
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
- Hartwig Medical Foundation, Science Park, Amsterdam, the Netherlands
- Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Emile E Voest
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM), Utrecht, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
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Koster R, Schipper LJ, Giesbertz NAA, van Beek D, Mendeville M, Samsom KG, Rosenberg EH, Hogervorst FBL, Roepman P, Boelens MC, Bosch LJW, van den Berg JG, Meijer GA, Voest EE, Cuppen E, Ruijs MWG, van Wezel T, van der Kolk L, Monkhorst K. Impact of genetic counseling strategy on diagnostic yield and workload for genome-sequencing-based tumor diagnostics. Genet Med 2024; 26:101032. [PMID: 38006283 DOI: 10.1016/j.gim.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023] Open
Abstract
PURPOSE Genome sequencing (GS) enables comprehensive molecular analysis of tumors and identification of hereditary cancer predisposition. According to guidelines, directly determining pathogenic germline variants (PGVs) requires pretest genetic counseling, which is cost-ineffective. Referral for genetic counseling based on tumor variants alone could miss relevant PGVs and/or result in unnecessary referrals. METHODS We validated GS for detection of germline variants and simulated 3 strategies using paired tumor-normal GS data of 937 metastatic patients. In strategy-1, genetic counseling before tumor testing allowed direct PGV analysis. In strategy-2 and -3, germline testing and referral for post-test genetic counseling is based on tumor variants using Dutch (strategy-2) or Europen Society for Medical Oncology (ESMO) Precision Medicine Working Group (strategy-3) guidelines. RESULTS In strategy-1, PGVs would be detected in 50 patients (number-needed-to counsel; NTC = 18.7). In strategy-2, 86 patients would have been referred for genetic counseling and 43 would have PGVs (NTC = 2). In strategy-3, 94 patients would have been referred for genetic counseling and 32 would have PGVs (NTC = 2.9). Hence, 43 and 62 patients, respectively, were unnecessarily referred based on a somatic variant. CONCLUSION Both post-tumor test counseling strategies (2 and 3) had significantly lower NTC, and strategy-2 had the highest PGV yield. Combining pre-tumor test mainstreaming and post-tumor test counseling may maximize the clinically relevant PGV yield and minimize unnecessary referrals.
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Affiliation(s)
- Roelof Koster
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Luuk J Schipper
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Kris G Samsom
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Linda J W Bosch
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Gerrit A Meijer
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emile E Voest
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Tom van Wezel
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Kim Monkhorst
- The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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3
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Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, Fiandalo M, Foti M, Khotskaya Y, Lee J, Peters N, Sweeney S, Abraham J, Brenton JD, Caldas C, Doherty G, Nimmervoll B, Pinilla K, Martin JE, Rueda OM, Sammut SJ, Silva D, Cao K, Heath AP, Li M, Lilly J, MacFarland S, Maris JM, Mason JL, Morgan AM, Resnick A, Welsh M, Zhu Y, Johnson B, Li Y, Sholl L, Beaudoin R, Biswas R, Cerami E, Cushing O, Dand D, Ducar M, Gusev A, Hahn WC, Haigis K, Hassett M, Janeway KA, Jänne P, Jawale A, Johnson J, Kehl KL, Kumari P, Laucks V, Lepisto E, Lindeman N, Lindsay J, Lueders A, Macconaill L, Manam M, Mazor T, Miller D, Newcomb A, Orechia J, Ovalle A, Postle A, Quinn D, Reardon B, Rollins B, Shivdasani P, Tramontano A, Van Allen E, Van Nostrand SC, Bell J, Datto MB, Green M, Hubbard C, McCall SJ, Mettu NB, Strickler JH, Andre F, Besse B, Deloger M, Dogan S, Italiano A, Loriot Y, Ludovic L, Michels S, Scoazec J, Tran-Dien A, Vassal G, Freeman CE, Hsiao SJ, Ingham M, Pang J, Rabadan R, Roman LC, Carvajal R, DuBois R, Arcila ME, Benayed R, Berger MF, Bhuiya M, Brannon AR, Brown S, Chakravarty D, Chu C, de Bruijn I, Galle J, Gao J, Gardos S, Gross B, Kundra R, Kung AL, Ladanyi M, Lavery JA, Li X, Lisman A, Mastrogiacomo B, McCarthy C, Nichols C, Ochoa A, Panageas KS, Philip J, Pillai S, Riely GJ, Rizvi H, Rudolph J, Sawyers CL, Schrag D, Schultz N, Schwartz J, Sheridan R, Solit D, Wang A, Wilson M, Zehir A, Zhang H, Zhao G, Ahmed L, Bedard PL, Bruce JP, Chow H, Cooke S, Del Rossi S, Felicen S, Hakgor S, Jagannathan P, Kamel-Reid S, Krishna G, Leighl N, Lu Z, Nguyen A, Oldfield L, Plagianakos D, Pugh TJ, Rizvi A, Sabatini P, Shah E, Singaravelan N, Siu L, Srivastava G, Stickle N, Stockley T, Tang M, Virtaenen C, Watt S, Yu C, Bernard B, Bifulco C, Cramer JL, Lee S, Piening B, Reynolds S, Slagel J, Tittel P, Urba W, VanCampen J, Weerasinghe R, Acebedo A, Guinney J, Guo X, Hunter-Zinck H, Yu T, Dang K, Anagnostou V, Baras A, Brahmer J, Gocke C, Scharpf RB, Tao J, Velculescu VE, Alexander S, Bailey N, Gold P, Bierkens M, de Graaf J, Hudeček J, Meijer GA, Monkhorst K, Samsom KG, Sanders J, Sonke G, ten Hoeve J, van de Velde T, van den Berg J, Voest E, Steinhardt G, Kadri S, Pankhuri W, Wang P, Segal J, Moung C, Espinosa-Mendez C, Martell HJ, Onodera C, Quintanar Alfaro A, Sweet-Cordero EA, Talevich E, Turski M, Van’t Veer L, Wren A, Aguilar S, Dienstmann R, Mancuso F, Nuciforo P, Tabernero J, Viaplana C, Vivancos A, Anderson I, Chaugai S, Coco J, Fabbri D, Johnson D, Jones L, Li X, Lovly C, Mishra S, Mittendorf K, Wen L, Yang YJ, Ye C, Holt M, LeNoue-Newton ML, Micheel CM, Park BH, Rubinstein SM, Stricker T, Wang L, Warner J, Guan M, Jin G, Liu L, Topaloglu U, Urtis C, Zhang W, D’Eletto M, Hutchison S, Longtine J, Walther Z. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Sci Rep 2022; 12:19055. [PMID: 36351964 PMCID: PMC9646734 DOI: 10.1038/s41598-022-21448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
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Affiliation(s)
- Debra Van Egeren
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Systems Biology, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Stem Cell Program, Boston Children’s Hospital, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Khushi Kohli
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Jeremy L. Warner
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
| | - Philippe L. Bedard
- grid.17063.330000 0001 2157 2938Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Gregory Riely
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eva Lepisto
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.429426.f0000 0000 9350 5788Present Address: Multiple Myeloma Research Foundation, Norwalk, CT USA
| | - Deborah Schrag
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michele LeNoue-Newton
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paul Catalano
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Kenneth L. Kehl
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Franziska Michor
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.65499.370000 0001 2106 9910The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XThe Ludwig Center at Harvard, Boston, MA USA
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Samsom KG, Schipper LJ, Roepman P, Bosch LJ, Lalezari F, Klompenhouwer EG, de Langen AJ, Buffart TE, Riethorst I, Schoenmaker L, Schout D, van der Noort V, van den Berg JG, de Bruijn E, van der Hoeven JJ, van Snellenberg H, van der Kolk LE, Cuppen E, Voest EE, Meijer GA, Monkhorst K. Feasibility of whole genome sequencing based tumor diagnostics in routine pathology practice. J Pathol 2022; 258:179-188. [PMID: 35792649 PMCID: PMC9546477 DOI: 10.1002/path.5988] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 02/21/2022] [Revised: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/09/2022]
Abstract
The current increase in number and diversity of targeted anticancer agents poses challenges to the logistics and timeliness of molecular diagnostics (MolDx), resulting in underdiagnosis and treatment. Whole‐genome sequencing (WGS) may provide a sustainable solution for addressing current as well as future diagnostic challenges. The present study therefore aimed to prospectively assess feasibility, validity, and value of WGS in routine clinical practice. WGS was conducted independently of, and in parallel with, standard of care (SOC) diagnostics on routinely obtained tumor samples from 1,200 consecutive patients with metastatic cancer. Results from both tests were compared and discussed in a dedicated tumor board. From 1,200 patients, 1,302 samples were obtained, of which 1,216 contained tumor cells. WGS was successful in 70% (854/1,216) of samples with a median turnaround time of 11 days. Low tumor purity (<20%) was the main reason for not completing WGS. WGS identified 99.2% and SOC MolDx 99.7% of the total of 896 biomarkers found in genomic regions covered by both tests. Actionable biomarkers were found in 603/848 patients (71%). Of the 936 associated therapy options identified by WGS, 343 were identified with SOC MolDx (36.6%). Biomarker‐based therapy was started in 147 patients. WGS revealed 49 not previously identified pathogenic germline variants. Fresh‐frozen, instead of formalin‐fixed and paraffin‐embedded, sample logistics were easily adopted as experienced by the professionals involved. WGS for patients with metastatic cancer is well feasible in routine clinical practice, successfully yielding comprehensive genomic profiling for the vast majority of patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Kris G. Samsom
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Luuk J. Schipper
- Department of Molecular Oncology Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM) Jaarbeursplein 6 3521 AL Utrecht The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Science Park, 1098 XH Amsterdam The Netherlands
| | - Linda J.W. Bosch
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Ferry Lalezari
- Department of Radiology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | | | - Adrianus J. de Langen
- Department of Thoracic Oncology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Tineke E. Buffart
- Department of Gastrointestinal Oncology Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
| | - Immy Riethorst
- Hartwig Medical Foundation, Science Park, 1098 XH Amsterdam The Netherlands
| | - Lieke Schoenmaker
- Hartwig Medical Foundation, Science Park, 1098 XH Amsterdam The Netherlands
| | - Daoin Schout
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Vincent van der Noort
- Department of Biometrics Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
| | - Jose G. van den Berg
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Ewart de Bruijn
- Hartwig Medical Foundation, Science Park, 1098 XH Amsterdam The Netherlands
| | | | | | - Lizet E. van der Kolk
- Family Cancer Clinic Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Science Park, 1098 XH Amsterdam The Netherlands
- Center for Molecular Medicine University Medical Centre Utrecht 3584 CX Heidelberglaan 100 Utrecht The Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM) Jaarbeursplein 6 3521 AL Utrecht The Netherlands
| | - Emile E. Voest
- Department of Molecular Oncology Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
- Department of Medical Oncology Netherlands Cancer Institute 1066 CX Plesmanlaan 121 Amsterdam The Netherlands
- Oncode Institute, Office Jaarbeurs Innovation Mile (JIM) Jaarbeursplein 6 3521 AL Utrecht The Netherlands
| | - Gerrit A. Meijer
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
| | - Kim Monkhorst
- Department of Pathology Netherlands Cancer Institute Plesmanlaan 121 1066 CX Amsterdam The Netherlands
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5
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Schipper LJ, Monkhorst K, Samsom KG, Bosch LJ, Snaebjornsson P, van Boven H, Roepman P, van der Kolk LE, van Houdt WJ, van der Graaf WT, Meijer GA, Voest EE. Clinical Impact of Prospective Whole Genome Sequencing in Sarcoma Patients. Cancers (Basel) 2022; 14:436. [PMID: 35053600 PMCID: PMC8773512 DOI: 10.3390/cancers14020436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 12/21/2022] Open
Abstract
With more than 70 different histological sarcoma subtypes, accurate classification can be challenging. Although characteristic genetic events can largely facilitate pathological assessment, large-scale molecular profiling generally is not part of regular diagnostic workflows for sarcoma patients. We hypothesized that whole genome sequencing (WGS) optimizes clinical care of sarcoma patients by detection of diagnostic and actionable genomic characteristics, and of underlying hereditary conditions. WGS of tumor and germline DNA was incorporated in the diagnostic work-up of 83 patients with a (presumed) sarcomas in a tertiary referral center. Clinical follow-up data were collected prospectively to assess impact of WGS on clinical decision making. In 12/83 patients (14%), the genomic profile led to revision of cancer diagnosis, with change of treatment plan in eight. All twelve patients had undergone multiple tissue retrieval procedures and immunohistopathological assessments by regional and expert pathologists prior to WGS analysis. Actionable biomarkers with therapeutic potential were identified for 30/83 patients. Pathogenic germline variants were present in seven patients. In conclusion, unbiased genomic characterization with WGS identifies genomic biomarkers with direct clinical implications for sarcoma patients. Given the diagnostic complexity and high unmet need for new treatment opportunities in sarcoma patients, WGS can be an important extension of the diagnostic arsenal of pathologists.
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Affiliation(s)
- Luuk J. Schipper
- Department of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Kris G. Samsom
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Linda J.W. Bosch
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Petur Snaebjornsson
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Hester van Boven
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Paul Roepman
- Hartwig Medical Foundation, 1098 XH Amsterdam, The Netherlands;
| | - Lizet E. van der Kolk
- Family Cancer Clinic, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | - Winan J. van Houdt
- Department of Surgical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
| | | | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; (K.M.); (K.G.S.); (L.J.W.B.); (P.S.); (H.v.B.); (G.A.M.)
| | - Emile E. Voest
- Department of Molecular Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
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6
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Roepman P, de Bruijn E, van Lieshout S, Schoenmaker L, Boelens MC, Dubbink HJ, Geurts-Giele WRR, Groenendijk FH, Huibers MMH, Kranendonk MEG, Roemer MGM, Samsom KG, Steehouwer M, de Leng WWJ, Hoischen A, Ylstra B, Monkhorst K, van der Hoeven JJM, Cuppen E. Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics. J Mol Diagn 2021; 23:816-833. [PMID: 33964451 DOI: 10.1016/j.jmoldx.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/17/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing (WGS) using fresh-frozen tissue and matched blood samples from cancer patients may become the most complete genetic tumor test. With the increasing availability of small biopsies and the need to screen more number of biomarkers, the use of a single all-inclusive test is preferable over multiple consecutive assays. To meet high-quality diagnostics standards, we optimized and clinically validated WGS sample and data processing procedures, resulting in a technical success rate of 95.6% for fresh-frozen samples with sufficient (≥20%) tumor content. Independent validation of identified biomarkers against commonly used diagnostic assays showed a high sensitivity (recall; 98.5%) and precision (positive predictive value; 97.8%) for detection of somatic single-nucleotide variants and insertions and deletions (across 22 genes), and high concordance for detection of gene amplification (97.0%; EGFR and MET) as well as somatic complete loss (100%; CDKN2A/p16). Gene fusion analysis showed a concordance of 91.3% between DNA-based WGS and an orthogonal RNA-based gene fusion assay. Microsatellite (in)stability assessment showed a sensitivity of 100% with a precision of 94%, and virus detection (human papillomavirus), an accuracy of 100% compared with standard testing. In conclusion, whole genome sequencing has a >95% sensitivity and precision compared with routinely used DNA techniques in diagnostics, and all relevant mutation types can be detected reliably in a single assay.
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Affiliation(s)
- Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands.
| | | | | | | | - Mirjam C Boelens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Margaretha G M Roemer
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
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7
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Radonic T, Geurts-Giele WRR, Samsom KG, Roemen GMJM, von der Thüsen JH, Thunnissen E, Meijssen IC, Sleddens HFBM, Dinjens WNM, Boelens MC, Weijers K, Speel EJM, Finn SP, O'Brien C, van Wezel T, Cohen D, Monkhorst K, Roepman P, Dubbink HJ. RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer. J Thorac Oncol 2021; 16:798-806. [PMID: 33588111 DOI: 10.1016/j.jtho.2021.01.1619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
INTRODUCTION RET gene fusions are established oncogenic drivers in 1% of NSCLC. Accurate detection of advanced patients with RET fusions is essential to ensure optimal therapy choice. We investigated the performance of fluorescence in situ hybridization (FISH) as a diagnostic test for detecting functional RET fusions. METHODS Between January 2016 and November 2019, a total of 4873 patients with NSCLC were routinely screened for RET fusions using either FISH (n = 2858) or targeted RNA next-generation sequencing (NGS) (n = 2015). If sufficient material was available, positive cases were analyzed by both methods (n = 39) and multiple FISH assays (n = 17). In an independent cohort of 520 patients with NSCLC, whole-genome sequencing data were investigated for disruptive structural variations and functional fusions in the RET and compared with ALK and ROS1 loci. RESULTS FISH analysis revealed RET rearrangement in 48 of 2858 cases; of 30 rearranged cases double tested with NGS, only nine had a functional RET fusion. RNA NGS yielded RET fusions in 14 of 2015 cases; all nine cases double tested by FISH had RET locus rearrangement. Of these 18 verified RET fusion cases, 16 had a split signal and two a complex rearrangement by FISH. By whole-genome sequencing, the prevalence of functional fusions compared with all disruptive events was lower in the RET (4 of 9, 44%) than the ALK (27 of 34, 79%) and ROS1 (9 of 12, 75%) loci. CONCLUSIONS FISH is a sensitive but unspecific technique for RET screening, always requiring a confirmation using an orthogonal technique, owing to frequently occurring RET rearrangements not resulting in functional fusions in NSCLC.
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Affiliation(s)
- Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kris G Samsom
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido M J M Roemen
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin Weijers
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands; School for Oncology and Developmental Biology (GROW), Maastricht, The Netherlands
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Cathal O'Brien
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Tom van Wezel
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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8
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Samsom KG, Bosch LJW, Schipper LJ, Roepman P, de Bruijn E, Hoes LR, Riethorst I, Schoenmaker L, van der Kolk LE, Retèl VP, Frederix GWJ, Buffart TE, van der Hoeven JJM, Voest EE, Cuppen E, Monkhorst K, Meijer GA. Study protocol: Whole genome sequencing Implementation in standard Diagnostics for Every cancer patient (WIDE). BMC Med Genomics 2020; 13:169. [PMID: 33167975 PMCID: PMC7654005 DOI: 10.1186/s12920-020-00814-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND 'Precision oncology' can ensure the best suitable treatment at the right time by tailoring treatment towards individual patient and comprehensive tumour characteristics. In current molecular pathology, diagnostic tests which are part of the standard of care (SOC) only cover a limited part of the spectrum of genomic changes, and often are performed in an iterative way. This occurs at the expense of valuable patient time, available tissue sample, and interferes with 'first time right' treatment decisions. Whole Genome Sequencing (WGS) captures a near complete view of genomic characteristics of a tumour in a single test. Moreover, WGS facilitates faster implementation of new treatment relevant biomarkers. At present, WGS mainly has been applied in study settings, but its performance in a routine diagnostic setting remains to be evaluated. The WIDE study aims to investigate the feasibility and validity of WGS-based diagnostics in clinical practice. METHODS 1200 consecutive patients in a single comprehensive cancer centre with (suspicion of) a metastasized solid tumour will be enrolled with the intention to analyse tumour tissue with WGS, in parallel to SOC diagnostics. Primary endpoints are (1) feasibility of implementation of WGS-based diagnostics into routine clinical care and (2) clinical validation of WGS by comparing identification of treatment-relevant variants between WGS and SOC molecular diagnostics. Secondary endpoints entail (1) added clinical value in terms of additional treatment options and (2) cost-effectiveness of WGS compared to SOC diagnostics through a Health Technology Assessment (HTA) analysis. Furthermore, the (3) perceived impact of WGS-based diagnostics on clinical decision making will be evaluated through questionnaires. The number of patients included in (experimental) therapies initiated based on SOC or WGS diagnostics will be reported with at least 3 months follow-up. The clinical efficacy is beyond the scope of WIDE. Key performance indicators will be evaluated after every 200 patients enrolled, and procedures optimized accordingly, to continuously improve the diagnostic performance of WGS in a routine clinical setting. DISCUSSION WIDE will yield the optimal conditions under which WGS can be implemented in a routine molecular diagnostics setting and establish the position of WGS compared to SOC diagnostics in routine clinical care.
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Affiliation(s)
- Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Linda J W Bosch
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Luuk J Schipper
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Louisa R Hoes
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Tineke E Buffart
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Emile E Voest
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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9
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Samsom KG, Levy S, van Veenendaal LM, Roepman P, Kodach LL, Steeghs N, Valk GD, Wouter Dercksen M, Kuhlmann KFD, Verbeek WHM, Meijer GA, Tesselaar MET, van den Berg JG. Driver mutations occur frequently in metastases of well-differentiated small intestine neuroendocrine tumours. Histopathology 2020; 78:556-566. [PMID: 32931025 DOI: 10.1111/his.14252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/09/2020] [Indexed: 12/13/2022]
Abstract
AIMS To investigate the clinicopathological significance of driver mutations in metastatic well-differentiated small intestine neuroendocrine tumours (SI-NETs). METHODS AND RESULTS Whole genome sequencing (WGS) of 35 metastatic SI-NETs and next-generation sequencing (NGS) of eight metastatic SI-NETs were performed. Biopsies were obtained between 2015 and 2019. Tumours were classified according to the 2019 World Health Organization classification. WGS included assessment of somatic mutations in all cancer-related driver genes, the tumour mutational burden (TMB), and microsatellite status. NGS entailed a cancer hotspot panel of 58 genes. Our cohort consisted of 21% grade 1, 60% grade 2 and 19% grade 3 SI-NETs. Driver mutations were identified in ~50% of SI-NETs. In total, 27 driver mutations were identified, of which 74% were in tumour suppressor genes (e.g. TP53, RB1, and CDKN1B) and 22% were in proto-oncogenes (e.g. KRAS, NRAS, and MET). Allelic loss of chromosome 18 (63%), complete loss of CDKN2A and CDKN1B (both 6%) and CDKN1B mutations (9%) were most common. Potential targetable genetic alterations were detected in 21% of metastasised SI-NETs. All tumours were microsatellite-stable and showed low TMBs (median 1.10; interquartile range 0.87-1.35). The Ki67 proliferation index was significantly associated with the presence of driver mutations (P = 0.015). CONCLUSION Driver mutations occur in 50% of metastasised SI-NETs, and their presence is associated with a high Ki67 proliferation index. The identification of targetable mutations make these patients potentially eligible for targeted therapy.
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Affiliation(s)
- Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sonja Levy
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Linde M van Veenendaal
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Neeltje Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Centre for Personalised Cancer Treatment, University Medical Centre, Utrecht, The Netherlands
| | - Gerlof D Valk
- Department of Endocrine Oncology, University Medical Centre, Utrecht, The Netherlands
| | - M Wouter Dercksen
- Department of Medical Oncology, Maxima Medical Centre, Eindhoven, The Netherlands
| | - Koert F D Kuhlmann
- Department of Surgery, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wieke H M Verbeek
- Department of Gastroenterology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Margot E T Tesselaar
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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10
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Samsom KG, van Veenendaal LM, Valk GD, Vriens MR, Tesselaar MET, van den Berg JG. Molecular prognostic factors in small-intestinal neuroendocrine tumours. Endocr Connect 2019; 8:906-922. [PMID: 31189127 PMCID: PMC6599083 DOI: 10.1530/ec-19-0206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Small-intestinal neuroendocrine tumours (SI-NETs) represent a heterogeneous group of rare tumours. In recent years, basic research in SI-NETs has attempted to unravel the molecular events underlying SI-NET tumorigenesis. AIM We aim to provide an overview of the current literature regarding prognostic and predictive molecular factors in patients with SI-NETs. METHOD A PubMed search was conducted on (epi)genetic prognostic factors in SI-NETs from 2000 until 2019. RESULTS The search yielded 1522 articles of which 20 reviews and 35 original studies were selected for further evaluation. SI-NETs are mutationally quiet tumours with a different genetic make-up compared to pancreatic NETs. Loss of heterozygosity at chromosome 18 is the most frequent genomic aberration (44-100%) followed by mutations of CDKN1B in 8%. Prognostic analyses were performed in 16 studies, of which 8 found a significant (epi)genetic association for survival or progression. Loss of heterozygosity at chromosome 18, gains of chromosome 4, 5, 7, 14 and 20p, copy gain of the SRC gene and low expression of RASSF1A and P16 were associated with poorer survival. In comparison with genetic mutations, epigenetic alterations are significantly more common in SI-NETs and may represent more promising targets in the treatment of SI-NETs. CONCLUSION SI-NETs are mutationally silent tumours. No biomarkers have been identified yet that can easily be adopted into current clinical decision making. SI-NETs may represent a heterogeneous disease and larger international studies are warranted to translate molecular findings into precision oncology.
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Affiliation(s)
- K G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L M van Veenendaal
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - G D Valk
- Department of Endocrine Oncology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Correspondence should be addressed to G D Valk:
| | - M R Vriens
- Department of Surgical Oncology and Endocrine Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - M E T Tesselaar
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J G van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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