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Juan Ramon A, Parmar C, Carrasco-Zevallos OM, Csiszer C, Yip SSF, Raciti P, Stone NL, Triantos S, Quiroz MM, Crowley P, Batavia AS, Greshock J, Mansi T, Standish KA. Development and deployment of a histopathology-based deep learning algorithm for patient prescreening in a clinical trial. Nat Commun 2024; 15:4690. [PMID: 38824132 PMCID: PMC11144215 DOI: 10.1038/s41467-024-49153-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/24/2024] [Indexed: 06/03/2024] Open
Abstract
Accurate identification of genetic alterations in tumors, such as Fibroblast Growth Factor Receptor, is crucial for treating with targeted therapies; however, molecular testing can delay patient care due to the time and tissue required. Successful development, validation, and deployment of an AI-based, biomarker-detection algorithm could reduce screening cost and accelerate patient recruitment. Here, we develop a deep-learning algorithm using >3000 H&E-stained whole slide images from patients with advanced urothelial cancers, optimized for high sensitivity to avoid ruling out trial-eligible patients. The algorithm is validated on a dataset of 350 patients, achieving an area under the curve of 0.75, specificity of 31.8% at 88.7% sensitivity, and projected 28.7% reduction in molecular testing. We successfully deploy the system in a non-interventional study comprising 89 global study clinical sites and demonstrate its potential to prioritize/deprioritize molecular testing resources and provide substantial cost savings in the drug development and clinical settings.
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Affiliation(s)
- Albert Juan Ramon
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, San Diego, CA, USA.
| | - Chaitanya Parmar
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, San Diego, CA, USA
| | | | - Carlos Csiszer
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, Titusville, NJ, USA
| | - Stephen S F Yip
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, Cambridge, MA, USA
| | - Patricia Raciti
- Janssen R&D, LLC, a Johnson & Johnson Company. Oncology, Spring House, PA, USA
| | - Nicole L Stone
- Janssen R&D, LLC, a Johnson & Johnson Company. Oncology, Spring House, PA, USA
| | - Spyros Triantos
- Janssen R&D, LLC, a Johnson & Johnson Company. Oncology, Spring House, PA, USA
| | - Michelle M Quiroz
- Janssen R&D, LLC, a Johnson & Johnson Company. Oncology, Spring House, PA, USA
| | - Patrick Crowley
- Janssen R&D, LLC, a Johnson & Johnson Company. Global Development, High Wycombe, UK
| | - Ashita S Batavia
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, Titusville, NJ, USA
| | - Joel Greshock
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, Spring House, PA, USA
| | - Tommaso Mansi
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, Titusville, NJ, USA
| | - Kristopher A Standish
- Janssen R&D, LLC, a Johnson & Johnson Company. Data Science and Digital Health, San Diego, CA, USA
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Sticht F, Malfertheiner MV, Wiest C, Schulz C, Fisser C, Mamilos A. Comparison of transbronchial biopsy techniques using needle and forceps biopsies in lung cancer for molecular diagnostics: a prospective, randomized crossover trial. Transl Cancer Res 2024; 13:2464-2474. [PMID: 38881945 PMCID: PMC11170508 DOI: 10.21037/tcr-23-2320] [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: 12/18/2023] [Accepted: 03/14/2024] [Indexed: 06/18/2024]
Abstract
Background In lung cancer, molecular testing and next-generation sequencing (NGS) are needed to identify therapeutic targets and are increasingly being used in earlier stages of the disease. Despite its longstanding use, it remains unclear whether transbronchial needle aspiration (TBNA) of peripheral lung lesions provides as adequate material for genetic testing as transbronchial forceps biopsies (TBFBs). In this study, we aim to analyze the use of TBNA using median viable cell area (MVCA) as a surrogate parameter to analyze sample quality. Methods This prospective single-center study analyzed biopsy specimens or aspirates of patients who underwent bronchoscopy with transbronchial biopsy. Patients underwent bronchoscopy with TBFB and TBNA for suspected lung cancer in peripheral lung lesions. Patients were randomized 1:1 to receive either TBFB or TBNA as the first biopsy technique and then switched to the other. After routine workup, sample slides were digitally scanned, and MVCA was calculated by a pathologist blinded to the biopsy technique used. The primary endpoint was MVCA of TBNA versus TBFB. Secondary endpoints were complications categorized as bleeding, pneumothorax, and other. Results Between August 2021 and April 2022, 15 patients were included in the per-protocol analysis. Six patients were included in cohort 1 and nine patients in cohort 2. A malignant diagnosis was confirmed in 11/15 (73.3%) cases, of which nine were primary lung malignancies. Overall, MVCA in samples obtained by TBFB was significantly larger than TBNA samples {TBFB-MVCA 9.80 mm2 [interquartile range (IQR), 2.70-10.39 mm2] vs. TBNA-MVCA 2.70 mm2 (IQR, 0.14-8.21 mm2), P=0.008}. Despite this difference, molecular testing was feasible in both TBNA and TBFB samples. No major complications were observed. Conclusions Despite a significantly smaller MVCA provided by TBNA, samples were still considered feasible for NGS, indicating that TBNA represents an alternative method to obtain sufficient tumor tissue in peripheral nodules as part of the diagnosis of suspected lung cancer.
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Affiliation(s)
- Florian Sticht
- Clinic and Polyclinic of Internal Medicine, Department of Pneumology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
- Department of Internal Medicine II, Pneumology, Bad Reichenhall District Hospital, Bad Reichenhall, Germany
| | | | - Clemens Wiest
- Clinic and Polyclinic of Internal Medicine, Department of Pneumology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Christian Schulz
- Clinic and Polyclinic of Internal Medicine, Department of Pneumology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Christoph Fisser
- Clinic and Polyclinic of Internal Medicine, Department of Pneumology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Andreas Mamilos
- Department of Pathology, University Regensburg, Regensburg, Germany
- Department of Pathology, German Oncology Center, Limassol, Cyprus
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Okojie J, O’Neal N, Burr M, Worley P, Packer I, Anderson D, Davis J, Kearns B, Fatema K, Dixon K, Barrott JJ. DNA Quantity and Quality Comparisons between Cryopreserved and FFPE Tumors from Matched Pan-Cancer Samples. Curr Oncol 2024; 31:2441-2452. [PMID: 38785464 PMCID: PMC11119490 DOI: 10.3390/curroncol31050183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024] Open
Abstract
Personalized cancer care requires molecular characterization of neoplasms. While the research community accepts frozen tissues as the gold standard analyte for molecular assays, the source of tissue for testing in clinical cancer care comes almost universally from formalin-fixed, paraffin-embedded tissue (FFPE). As newer technologies emerge for DNA characterization that requires higher molecular weight DNA, it was necessary to compare the quality of DNA in terms of DNA length between FFPE and cryopreserved samples. We hypothesized that cryopreserved samples would yield higher quantity and superior quality DNA compared to FFPE samples. We analyzed DNA metrics by performing a head-to-head comparison between FFPE and cryopreserved samples from 38 human tumors representing various cancer types. DNA quantity and purity were measured by UV spectrophotometry, and DNA from cryopreserved tissue demonstrated a 4.2-fold increase in DNA yield per mg of tissue (p-value < 0.001). DNA quality was measured on a fragment microelectrophoresis analyzer, and again, DNA from cryopreserved tissue demonstrated a 223% increase in the DNA quality number and a 9-fold increase in DNA fragments > 40,000 bp (p-value < 0.0001). DNA from the cryopreserved tissues was superior to the DNA from FFPE samples in terms of DNA yield and quality.
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Affiliation(s)
- Jeffrey Okojie
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Nikole O’Neal
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Mackenzie Burr
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Peyton Worley
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Isaac Packer
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - DeLaney Anderson
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Jack Davis
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Bridger Kearns
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
| | - Kaniz Fatema
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
| | - Ken Dixon
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
| | - Jared J. Barrott
- Department of Cell Biology & Physiology, Brigham Young University, Provo, UT 84602, USA; (J.O.); (M.B.); (P.W.); (I.P.); (D.A.); (J.D.); (B.K.)
- Department of Biomedical and Pharmaceutical Sciences, Idaho State University, Pocatello, ID 83209, USA; (N.O.); (K.F.)
- Specicare, 690 Medical Park Ln, Gainesville, GA 30501, USA
- Simmons Center for Cancer Research, Brigham Young University, Provo, UT 84602, USA
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da Silveira Corrêa B, De-Paris F, Viola GD, Andreis TF, Rosset C, Vianna FSL, da Rosa Rivero LF, de Oliveira FH, Ashton-Prolla P, de Souza Macedo G. Challenges to the effectiveness of next-generation sequencing in formalin-fixed paraffin-embedded tumor samples for non-small cell lung cancer. Ann Diagn Pathol 2024; 69:152249. [PMID: 38150865 DOI: 10.1016/j.anndiagpath.2023.152249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 12/29/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) of Formalin-Fixed and Paraffin-Embedded (FFPE) specimens is routine in precision oncology practice. However, results are not always conclusive, and it is important to identify which factors may influence FFPE tumor sequencing success. MATERIALS AND METHODS Here, we evaluated the influence of pre-analytical factors on 705 samples of non-small cell lung cancer specimens that underwent NGS testing. Factors such as tumor site, tumor cell percentage, fragment size, primary tumor or metastasis, presence of necrosis, DNA purity, DNA concentration, sample origin and year of testing. RESULTS The overall NGS success rate was 84.9 % (n = 599). Bone site specimens had a very low success rate (42.1 %), differing from lung samples (79.8 %) (P < 0.05). Samples with tumor percentages <5 % (success rate of 44.4 %) represented 14.1 % of failed sequencings. Moreover, samples with tumor percentages >10 %-20 % (82 %) did not differ from those with >30 % (88.9 %) on sequencing outcomes (P = 0.086). Specimens that provided DNA concentrations >2.0 ng/uL, 1.0-2.0 ng/uL, 0.5-1.0 ng/uL and <0.5 ng/uL had success rates of 92 %, 77.1 %, 61.3 % and 20.4 %, respectively. Small fragments (≤0.2 cm2) had a success rate of 74.7 % and were more prevalent in the unsuccessful group (P < 0.05). CONCLUSIONS Our results suggest that tumor percentage, fragment size, decalcified bone specimens, and DNA concentration are potential modifiers of NGS success rates. Interestingly, specimens with tumor percentages between 10 % and 20 % have the same sequencing outcome than specimens with >30 %. These results can strengthen the understanding of factors that lead to NGS success variability.
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Affiliation(s)
- Bruno da Silveira Corrêa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil.
| | - Fernanda De-Paris
- Serviço de Diagnóstico Laboratorial, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Guilherme Danielski Viola
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Unidade de Pesquisa Laboratorial, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernanda Sales Luiz Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Luis Fernando da Rosa Rivero
- Serviço de Patologia Cirúrgica - Hospital de Clínicas de Porto Alegre - Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Francine Hehn de Oliveira
- Serviço de Patologia Cirúrgica - Hospital de Clínicas de Porto Alegre - Universidade Federal do Rio Grande do Sul, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Agronomia, Porto Alegre 91501-970, Rio Grande do Sul, Brazil; Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriel de Souza Macedo
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Serviço de Diagnóstico Laboratorial, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil; Programa de Medicina Personalizada, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Santa Cecília, Porto Alegre 90035-903, Rio Grande do Sul, Brazil
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Kim MH, Kim SH, Lee G, Mok J, Lee MK, Song JS, Eom JS. Next-generation sequencing using tissue specimen collected with a 1.1 mm-diameter cryoprobe in patients with lung cancer. Respirology 2024; 29:333-339. [PMID: 38379178 DOI: 10.1111/resp.14680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND AND OBJECTIVE Next-generation sequencing (NGS) analysis is considered standard for lung cancer diagnosis in clinical practice. Little is known about the feasibility of NGS using tumour tissue sampled with a 1.1 mm-diameter cryoprobe. We aimed to investigate the suitability of specimens obtained by transbronchial cryobiopsy (TBC) using a 1.1 mm-diameter cryoprobe for NGS analysis. METHODS Patients with lung cancer who underwent TBC using a 1.1 mm-diameter cryoprobe for NGS testing between October 2020 and April 2023 were enrolled. A 4.0- or 3.0 mm-diameter bronchoscope with radial probe endobronchial ultrasound and virtual bronchoscopic navigation was used to detect peripheral lung lesions. All procedures were performed under fluoroscopic guidance. Data were analysed retrospectively. RESULTS A total of 56 patients underwent TBC using a 1.1 mm cryoprobe for NGS testing, during the study period. Most patients (98%) were in the advanced stage of lung cancer (recurrent or inoperable disease of stages III or IV). The diagnostic yield of NGS for DNA and RNA sequencing was 95% each (53 of 56). Moderate bleeding was noted in three patients (5%) and none of the study patients developed life-threatening complications, such as pneumothorax or lung infection. CONCLUSION TBC using a 1.1 mm-diameter cryoprobe is a useful and safe tool for NGS analysis, for both DNA and RNA sequencing.
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Affiliation(s)
- Mi-Hyun Kim
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Soo Han Kim
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Geewon Lee
- Department of Radiology, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Radiology, Pusan National University Hospital, Busan, Republic of Korea
| | - Jeongha Mok
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Min Ki Lee
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Ju Sun Song
- GC Genome Corporation, Yongin, Republic of Korea
| | - Jung Seop Eom
- Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
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Stenzinger A, Vogel A, Lehmann U, Lamarca A, Hofman P, Terracciano L, Normanno N. Molecular profiling in cholangiocarcinoma: A practical guide to next-generation sequencing. Cancer Treat Rev 2024; 122:102649. [PMID: 37984132 DOI: 10.1016/j.ctrv.2023.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cholangiocarcinomas (CCA) are a heterogeneous group of tumors that are classified as intrahepatic, perihilar, or distal according to the anatomic location within the biliary tract. Each CCA subtype is associated with distinct genomic alterations, including single nucleotide variants, copy number variants, and chromosomal rearrangements or gene fusions, each of which can influence disease prognosis and/or treatment outcomes. Molecular profiling using next-generation sequencing (NGS) is a powerful technique for identifying unique gene variants carried by an individual tumor, which can facilitate their accurate diagnosis as well as promote the optimal selection of gene variant-matched targeted treatments. NGS is particularly useful in patients with CCA because between one-third and one-half of these patients have genomic alterations that can be targeted by drugs that are either approved or in clinical development. NGS can also provide information about disease evolution and secondary resistance alterations that can develop during targeted therapy, and thus facilitate assessment of prognosis and choice of alternative targeted treatments. Pathologists play a critical role in assessing the viability of biopsy samples for NGS, and advising treating clinicians whether NGS can be performed and which of the available platforms should be used to optimize testing outcomes. This review aims to provide clinical pathologists and other healthcare professionals with practical step-by-step guidance on the use of NGS for molecular profiling of patients with CCA, with respect to tumor biopsy techniques, pre-analytic sample preparation, selecting the appropriate NGS panel, and understanding and interpreting results of the NGS test.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology Heidelberg (IPH), Center for Molecular Pathology, University Hospital Heidelberg, In Neuenheimer Feld 224, 69120 Heidelberg, Building 6224, Germany.
| | - Arndt Vogel
- Division of Gastroenterology and Hepatology, Toronto General Hospital Medical Oncology, Princess Margaret Cancer Centre, Schwartz Reisman Liver Research Centre, 200 Elizabeth Street, Office: 9 EB 236 Toronto, ON, M5G 2C4, Canada.
| | - Ulrich Lehmann
- Institute for Pathology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Angela Lamarca
- Department of Medical Oncology, Oncohealth Institute, Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital, Av. de los Reyes Católicos, 2, 28040 Madrid, Spain; Department of Medical Oncology, The Christie NHS Foundation Trust, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, IHU RespirERA, Siège de l'Université: Grand Château, 28 Avenue de Valrose, 06103 Nice CEDEX 2, France.
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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Steiert TA, Parra G, Gut M, Arnold N, Trotta JR, Tonda R, Moussy A, Gerber Z, Abuja P, Zatloukal K, Röcken C, Folseraas T, Grimsrud M, Vogel A, Goeppert B, Roessler S, Hinz S, Schafmayer C, Rosenstiel P, Deleuze JF, Gut I, Franke A, Forster M. A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 2023; 51:7143-7162. [PMID: 37351572 PMCID: PMC10415133 DOI: 10.1093/nar/gkad519] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/24/2023] Open
Abstract
In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.
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Affiliation(s)
- Tim A Steiert
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Genís Parra
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Marta Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Jean-Rémi Trotta
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Raúl Tonda
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Alice Moussy
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
| | - Zuzana Gerber
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Peter M Abuja
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Center for Molecular Biomedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz 8010, Austria
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel 24105, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
| | - Marit M Grimsrud
- Norwegian PSC Research Center Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo 0372, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo 0372, Norway
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hanover 30625, Germany
| | - Benjamin Goeppert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, Ludwigsburg 71640, Germany
| | - Stephanie Roessler
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Sebastian Hinz
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Clemens Schafmayer
- Department of General Surgery, University Medicine Rostock, Rostock 18057, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Jean-François Deleuze
- Le Centre de référence, d’innovation, d’expertise et de transfert (CRefIX), PFMG 2025, Évry 91057, France
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Évry 91057, France
| | - Ivo G Gut
- Center for Genomic Regulation, Centro Nacional de Análisis Genómico, Barcelona 08028, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Kiel 24105, Germany
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8
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Grypari IM, Tzelepi V, Gyftopoulos K. DNA Damage Repair Pathways in Prostate Cancer: A Narrative Review of Molecular Mechanisms, Emerging Biomarkers and Therapeutic Targets in Precision Oncology. Int J Mol Sci 2023; 24:11418. [PMID: 37511177 PMCID: PMC10380086 DOI: 10.3390/ijms241411418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer (PCa) has a distinct molecular signature, including characteristic chromosomal translocations, gene deletions and defective DNA damage repair mechanisms. One crucial pathway involved is homologous recombination deficiency (HRD) and it is found in almost 20% of metastatic castrate-resistant PCa (mCRPC). Inherited/germline mutations are associated with a hereditary predisposition to early PCa development and aggressive behavior. BRCA2, ATM and CHECK2 are the most frequently HRD-mutated genes. BRCA2-mutated tumors have unfavorable clinical and pathological characteristics, such as intraductal carcinoma. PARP inhibitors, due to the induction of synthetic lethality, have been therapeutically approved for mCRPC with HRD alterations. Mutations are detected in metastatic tissue, while a liquid biopsy is utilized during follow-up, recognizing acquired resistance mechanisms. The mismatch repair (MMR) pathway is another DNA repair mechanism implicated in carcinogenesis, although only 5% of metastatic PCa is affected. It is associated with aggressive disease. PD-1 inhibitors have been used in MMR-deficient tumors; thus, the MMR status should be tested in all metastatic PCa cases. A surrogate marker of defective DNA repair mechanisms is the tumor mutational burden. PDL-1 expression and intratumoral lymphocytes have ambivalent predictive value. Few experimental molecules have been so far proposed as potential biomarkers. Future research may further elucidate the role of DNA damage pathways in PCa, revealing new therapeutic targets and predictive biomarkers.
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Affiliation(s)
- Ioanna-Maria Grypari
- Cytology Department, Aretaieion University Hospital, National Kapodistrian University of Athens, 11528 Athens, Greece
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Kostis Gyftopoulos
- Department of Anatomy, School of Medicine, University of Patras, 26504 Patras, Greece
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9
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Powell CL, Saddoughi SA, Wigle DA. Progress in genome-inspired treatment decisions for multifocal lung adenocarcinoma. Expert Rev Respir Med 2023; 17:1009-1021. [PMID: 37982734 DOI: 10.1080/17476348.2023.2286277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
INTRODUCTION Multifocal lung adenocarcinoma (MFLA) is becoming increasingly recognized as a distinct subset of lung cancer, with unique biology, disease course, and treatment outcomes. While definitions remain controversial, MFLA is characterized by the development and concurrent presence of multiple independent (non-metastatic) lesions on the lung adenocarcinoma spectrum. Disease progression typically follows an indolent course measured in years, with a lower propensity for nodal and distant metastases than other more common forms of non-small cell lung cancer. AREAS COVERED Traditional imaging and histopathological analyses of tumor biopsies are frequently unable to fully characterize the disease, prompting interest in molecular diagnosis. We highlight some of the key questions in the field, including accurate definitions to identify and stage MLFA, molecular tests to stratify patients and treatment decisions, and the lack of clinical trial data to delineate best management for this poorly understood subset of lung cancer patients. We review the existing literature and progress toward a genomic diagnosis for this unique disease entity. EXPERT OPINION Multifocal lung adenocarcinoma behaves differently than other forms of non-small cell lung cancer. Progress in molecular diagnosis may enhance potential for accurate definition, diagnosis, and optimizing treatment approach.
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Affiliation(s)
- Chelsea L Powell
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Sahar A Saddoughi
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Dennis A Wigle
- Division of Thoracic Surgery, Department of Surgery, Mayo Clinic, Rochester, MN, USA
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10
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Pinheiro BG, Pôssa AP, Ricci G, Nishikaku AS, Hagen F, Hahn RC, de Camargo ZP, Rodrigues AM. Development of a Multiplex qPCR Assay for Fast Detection and Differentiation of Paracoccidioidomycosis Agents. J Fungi (Basel) 2023; 9:jof9030358. [PMID: 36983526 PMCID: PMC10057483 DOI: 10.3390/jof9030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Classic paracoccidioidomycosis (PCM) is a potentially deadly neglected tropical systemic mycosis caused by members of the Paracoccidioides brasiliensis complex (P. brasiliensis s. str., P. americana, P. restrepiensis, and P. venezuelensis) and P. lutzii. The laboratorial diagnosis of PCM relies on observing pathognomonic structures such as the “steering wheel” or “Mickey Mouse” shape in the direct mycological examination, fresh biopsied tissue in 10% KOH, histopathological analysis, and/or the isolation of the fungus in culture. However, these procedures are time-consuming and do not allow for the speciation of Paracoccidioides due to overlapping morphologies. Here, we propose a new one-tube multiplex probe-based qPCR assay to detect and recognize agents of the P. brasiliensis complex and P. lutzii. Primers (Paracoco-F and Paracoco-R) and TaqMan probes (PbraCx-Fam, Plu-Ned, and Paracoco-Vic) were developed to target the rDNA (ITS2/28S) in the Paracoccidioides genome. A panel of 77 Paracoccidioides isolates revealed a 100% specificity (AUC = 1.0, 95% CI 0.964–1.000, p < 0.0001) without cross-reacting with other medically relevant fungi or human and murine DNA. The lower limit of detection was 10 fg of gDNA and three copies of the partial rDNA amplicon. Speciation using qPCR was in perfect agreement with AFLP and TUB1-RFLP markers (kappa = 1.0). As a proof of concept, we assessed a panel of 16 formalin-fixed and paraffin-embedded specimens from histopathologically confirmed PCM patients to reveal a significant sensitivity of 81.25% and specificity of 100% (AUC = 0.906 ± 0.05, 95% CI = 0.756–0.979, p < 0.0001, Youden index J = 0.8125). Our assay achieved maximum sensitivity (100%) and specificity (100%) using fresh clinical samples (n = 9) such as sputum, bronchoalveolar lavage, and tissue fragments from PCM patients (AUC = 1.0, 95% CI 0.872–1.000, p < 0.0001, Youden index J = 1.0). Overall, our qPCR assay simplifies the molecular diagnosis of PCM and can be easily implemented in any routine laboratory, decreasing a critical bottleneck for the early treatment of PCM patients across a vast area of the Americas.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Ana Paula Pôssa
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Carlos 13561-020, Brazil
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060-900, Brazil
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048-902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023-062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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11
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Larson NB, Oberg AL, Adjei AA, Wang L. A Clinician's Guide to Bioinformatics for Next-Generation Sequencing. J Thorac Oncol 2023; 18:143-157. [PMID: 36379355 PMCID: PMC9870988 DOI: 10.1016/j.jtho.2022.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 11/15/2022]
Abstract
Next-generation sequencing (NGS) technologies are high-throughput methods for DNA sequencing and have become a widely adopted tool in cancer research. The sheer amount and variety of data generated by NGS assays require sophisticated computational methods and bioinformatics expertise. In this review, we provide background details of NGS technology and basic bioinformatics concepts for the clinician investigator interested in cancer research applications, with a focus on DNA-based approaches. We introduce the general principles of presequencing library preparation, postsequencing alignment, and variant calling. We also highlight the common variant annotations and NGS applications for other molecular data types. Finally, we briefly discuss the revealed utility of NGS methods in NSCLC research and study design considerations for research studies that aim to leverage NGS technologies for clinical care.
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Affiliation(s)
- Nicholas Bradley Larson
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
| | - Ann L Oberg
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Alex A Adjei
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Liguo Wang
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
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12
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Analytical Performance of Next-Generation Sequencing and RT-PCR on Formalin-Fixed Paraffin-Embedded Tumor Tissues for PIK3CA Testing in HR+/HER2- Breast Cancer. Cells 2022; 11:cells11223545. [PMID: 36428975 PMCID: PMC9688837 DOI: 10.3390/cells11223545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Somatic mutations in PIK3CA are present in ~40% breast cancers (BC); their detection in hormone receptor (HR)+/HER2- tumors allows for selecting patients with advanced disease eligible for PIK3CA targeting with alpelisib. The choice of what type of PIK3CA testing approach to adopt and which tissue sample to analyze is a new task in breast pathology. In this methodological study, we sought to assess the performance of next-generation sequencing (NGS) and RT-PCR for PIK3CA testing on archival formalin-fixed paraffin-embedded (FFPE) primary tumors and corresponding metastases. Sixteen HR+/HER2- BC with known PIK3CA-mutated status (ex. 7, 9, and 20) on metastatic samples by means of amplicon-based targeted NGS were selected, and n = 13 of these samples were re-tested with a commercially available CE-IVD RT-PCR assay. All available primary tumors (n = 8) were tested with both methods. NGS detected mutations in all samples, while RT-PCR in n = 2 sample-pairs and overall, in n = 5/8 (62.5%) primary tumors and 7/13 (53.8%) metastases (κ = 0.09; 95% CI, -0.69-0.87). Slight agreement (κ = 0; 95% CI, -0.59-0.59) was observed between NGS and RT-PCR, with the former being generally more sensitive in cases with low DNA quality and quantity. Post hoc visual inspection of the RT-PCR data increased the concordance to 76.9%. Targeted NGS offers reliable and robust PIK3CA testing on both tumor and metastasis FFPE samples; the accuracy of RT-PCR depends on the DNA quantity and quality. In HR+/HER2- BC, both the selection of the PIK3CA testing strategy of FFPE tissues and which sample to analyze should consider several technical parameters and should be tailored for each case.
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13
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Wong SJ, Wang HP, Shun CT, Chen CC, Han ML, Chen JH, Huang CT, Cheng TY. Tissue diagnosis necessary for small endoscopic ultrasound-suspected gastric gastrointestinal stromal tumors 2 cm or less in size: A prospective study focusing on the endoscopic incisional biopsy. J Gastroenterol Hepatol 2022; 37:1588-1595. [PMID: 35502128 DOI: 10.1111/jgh.15876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/05/2022] [Accepted: 04/22/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIM The small endoscopic ultrasound (EUS)-suspected gastric gastrointestinal stromal tumors (GISTs), gastric subepithelial tumors at the muscularis propria layer on EUS, are detected frequently. Bite-on-bite forceps biopsy and EUS-guided tissue sampling yield variable results. This study aimed to analyze clinicopathologic features of the small EUS-suspected gastric GISTs 2 cm or less in size and to evaluate the efficacy and safety of the endoscopic incisional biopsy (EIB) for these small tumors. METHODS This prospective study investigated 70 patients with small EUS-suspected gastric GISTs 2 cm or less in size in two stages. Firstly, 30 patients were recruited for the efficacy and safety evaluation of the EIB. Secondly, 40 patients were randomly assigned to receive either EIB or the bite-on-bite biopsy for comparison of the diagnostic yield, procedure time, and adverse event rate. RESULTS Combining two study stages, leiomyoma (74%) was diagnosed histologically to outnumber GIST (26%) with a diagnostic rate of 94% for patients receiving EIB. KIT exon 11 mutations (50%) and PDGFRA exon 12 mutations (16%) were detected in the small gastric GISTs. In the direct comparison, the diagnostic yield of EIB and the bite-on-bite biopsy was 85% and 50%, respectively (P = 0.018). There was no statistically significant difference of the mean procedure time or adverse event rate between these two groups. CONCLUSIONS Leiomyoma is more common than expected among these small tumors. Tissue diagnosis with an effective and safe sampling technique, such as EIB, is necessary for making further clinical decisions.
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Affiliation(s)
- Shenq-Jie Wong
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Division of Gastroenterology, Department of Internal Medicine, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Hsiu-Po Wang
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Tung Shun
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chien-Chuan Chen
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Lun Han
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jiann-Hwa Chen
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Division of Gastroenterology, Department of Internal Medicine, Taipei Tzu-Chi Hospital, New Taipei City, Taiwan
| | - Chung-Tsui Huang
- Division of Gastroenterology, Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Tsu-Yao Cheng
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Cancer Center and National Taiwan University College of Medicine, Taipei, Taiwan
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14
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Role of Image-Guided Percutaneous Needle Biopsy in the Age of Precision Medicine. Curr Oncol Rep 2022; 24:1035-1044. [PMID: 35362826 DOI: 10.1007/s11912-022-01271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW With the remarkable progress in cancer precision medicine, the demand for biopsy has been increasing, and the role of biopsy has been changing. In this review, we discuss the current state and recent advances in the role of image-guided percutaneous needle biopsy (PNB) in facilitating precision medicine. RECENT FINDINGS Biopsies are useful not only in the diagnosis of cancer and histological sub-type but also in the analysis of its molecular characteristics for targeted treatments. PNB specimens have been shown to provide high DNA yields for genomic analysis. Liquid biopsy is an emerging technology but is under development; therefore, PNB is the current standard of practice and is performed complimentarily with liquid biopsy. In the age of precision medicine, interventional oncologists play a key role in optimal tissue collection for adequate genomic analysis. Effective PNB may improve its diagnostic utility and help optimize precision medicine.
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15
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Cho MT, Gholami S, Gui D, Tejaswi SL, Fananapazir G, Abi-Jaoudeh N, Jutric Z, Samarasena JB, Li X, Valerin JB, Mercer J, Dayyani F. Optimizing the Diagnosis and Biomarker Testing for Patients with Intrahepatic Cholangiocarcinoma: A Multidisciplinary Approach. Cancers (Basel) 2022; 14:392. [PMID: 35053557 PMCID: PMC8773504 DOI: 10.3390/cancers14020392] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 01/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a heterogenous group of malignancies originating in the biliary tree, and associated with poor prognosis. Until recently, treatment options have been limited to surgical resection, liver-directed therapies, and chemotherapy. Identification of actionable genomic alterations with biomarker testing has revolutionized the treatment paradigm for these patients. However, several challenges exist to the seamless adoption of precision medicine in patients with CCA, relating to a lack of awareness of the importance of biomarker testing, hurdles in tissue acquisition, and ineffective collaboration among the multidisciplinary team (MDT). To identify gaps in standard practices and define best practices, multidisciplinary hepatobiliary teams from the University of California (UC) Davis and UC Irvine were convened; discussions of the meeting, including optimal approaches to tissue acquisition for diagnosis and biomarker testing, communication among academic and community healthcare teams, and physician education regarding biomarker testing, are summarized in this review.
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Affiliation(s)
- May T. Cho
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Sepideh Gholami
- University of California Davis Health, Sacramento, CA 95817, USA; (S.G.); (D.G.)
| | - Dorina Gui
- University of California Davis Health, Sacramento, CA 95817, USA; (S.G.); (D.G.)
| | | | | | - Nadine Abi-Jaoudeh
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Zeljka Jutric
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Jason B. Samarasena
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Xiaodong Li
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Jennifer B. Valerin
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
| | - Jacob Mercer
- Helsinn Therapeutics (U.S.), Inc., Iselin, NJ 08830, USA;
| | - Farshid Dayyani
- University of California Irvine Health, Orange, CA 92868, USA; (N.A.-J.); (Z.J.); (J.B.S.); (X.L.); (J.B.V.); (F.D.)
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16
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Marshall JL, Peshkin BN, Yoshino T, Vowinckel J, Danielsen HE, Melino G, Tsamardinos I, Haudenschild C, Kerr DJ, Sampaio C, Rha SY, FitzGerald KT, Holland EC, Gallagher D, Garcia-Foncillas J, Juhl H. OUP accepted manuscript. Oncologist 2022; 27:272-284. [PMID: 35380712 PMCID: PMC8982374 DOI: 10.1093/oncolo/oyab048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Corresponding author: John L. Marshall, MD, The Ruesch Center for the Cure of Gastrointestinal Cancers, Frederick P. Smith Endowed Chair, Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road, Washington, DC 20007, USA. Tel: +1 202 444 2223;
| | - Beth N Peshkin
- Georgetown University, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | | | - Håvard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Radiumhospitalet, Montebello, Oslo, Norway
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Ioannis Tsamardinos
- JADBio Gnosis DA, N. Plastira 100, Science and Technology Park of Crete and Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, Heraklion, GR, Greece
| | | | - David J Kerr
- Nuffield Division of Clinical and Laboratory Sciences, Level 4, Academic Block, John Radcliffe Infirmary, Headington, Oxford, UK
| | | | - Sun Young Rha
- Yonsei Cancer Center, Yonsei University College of Medicine, Seodaemun-Ku, Seoul, Korea
| | - Kevin T FitzGerald
- Department of Medical Humanities in the School of Medicine, Creighton University, Omaha, NE, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Gallagher
- St. James’s Hospital/Trinity College Dublin, St. Raphael’s House, Dublin, Ireland
| | - Jesus Garcia-Foncillas
- Cancer Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain
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17
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Yoon S, Kim M, Hong YS, Kim HS, Kim ST, Kim J, Yun H, Yoo C, Ahn HK, Kim HS, Lee IH, Kim IH, Park I, Jeong JH, Cheon J, Kim JW, Yun J, Lim SM, Cha Y, Jang SJ, Zang DY, Kim TW, Kang JH, Kim JH. Recommendations for the Use of Next-Generation Sequencing and the Molecular Tumor Board for Patients with Advanced Cancer: A Report from KSMO and KCSG Precision Medicine Networking Group. Cancer Res Treat 2021; 54:1-9. [PMID: 34902959 PMCID: PMC8756119 DOI: 10.4143/crt.2021.1115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/08/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is becoming essential in the fields of precision oncology. With implementation of NGS in daily clinic, the needs for continued education, facilitated interpretation of NGS results and optimal treatment delivery based on NGS results have been addressed. Molecular tumor board (MTB) is multidisciplinary approach to keep pace with the growing knowledge of complex molecular alterations in patients with advanced solid cancer. Although guidelines for NGS use and MTB have been developed in western countries, there is limitation for reflection of Korea’s public health environment and daily clinical practice. These recommendations provide a critical guidance from NGS panel testing to final treatment decision based on MTB discussion.
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Affiliation(s)
- Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Inkeun Park
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Jin Won Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jina Yun
- Division of Medical Oncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Research Institute and Hospital, Goyang, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dae Young Zang
- Department of Internal Medicine, Hallym University Medical Center, Hallym University, Anyang, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Hyoung Kang
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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18
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Jaliawala HA, Farooqui SM, Harris K, Abdo T, Keddissi JI, Youness HA. Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA): Technical Updates and Pathological Yield. Diagnostics (Basel) 2021; 11:diagnostics11122331. [PMID: 34943566 PMCID: PMC8699961 DOI: 10.3390/diagnostics11122331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Since the endobronchial ultrasound bronchoscope was introduced to clinical practice, endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has become the procedure of choice to sample hilar and mediastinal adenopathy. Multiple studies have been conducted in the last two decades to look at the different technical aspects of the procedure and their effects on the final cytopathological yield. In addition, newer modes of ultrasound scanning and newer tools with the potential to optimize the selection and sampling of the target lymph node have been introduced. These have the potential to reduce the number of passes, reduce the procedure time, and increase the diagnostic yield, especially in rare tumors and benign diseases. Herein, we review the latest updates related to the technical aspects of EBUS-TBNA and their effects on the final cytopathological yield in malignant and benign diseases.
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Affiliation(s)
- Huzaifa A. Jaliawala
- Interventional Pulmonary Program, Section of Pulmonary, Critical Care and Sleep Medicine, The Oklahoma City VA Health Care System, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.A.J.); (S.M.F.); (T.A.); (J.I.K.)
| | - Samid M. Farooqui
- Interventional Pulmonary Program, Section of Pulmonary, Critical Care and Sleep Medicine, The Oklahoma City VA Health Care System, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.A.J.); (S.M.F.); (T.A.); (J.I.K.)
| | - Kassem Harris
- Division of Pulmonary and Critical Care Medicine, Section of Interventional Pulmonology, Westchester Medical Center, Valhalla, NY 10595, USA;
| | - Tony Abdo
- Interventional Pulmonary Program, Section of Pulmonary, Critical Care and Sleep Medicine, The Oklahoma City VA Health Care System, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.A.J.); (S.M.F.); (T.A.); (J.I.K.)
| | - Jean I. Keddissi
- Interventional Pulmonary Program, Section of Pulmonary, Critical Care and Sleep Medicine, The Oklahoma City VA Health Care System, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.A.J.); (S.M.F.); (T.A.); (J.I.K.)
| | - Houssein A. Youness
- Interventional Pulmonary Program, Section of Pulmonary, Critical Care and Sleep Medicine, The Oklahoma City VA Health Care System, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (H.A.J.); (S.M.F.); (T.A.); (J.I.K.)
- Correspondence: ; Tel.: +1-405-271-6173
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19
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Auzanneau C, Bacq D, Bellera C, Blons H, Boland A, Boucheix M, Bourdon A, Chollet E, Chomienne C, Deleuze JF, Delmas C, Dinart D, Espérou H, Geillon F, Geneste D, Italiano A, Jean D, Khalifa E, Laizet Y, Laurent-Puig P, Lethimonnier F, Lévy-Marchal C, Lucchesi C, Malle C, Mancini P, Mathoulin-Pélissier S, Meyer V, Marie-Ange P, Perkins G, Sellan-Albert S, Soubeyran I, Wallet C. Feasibility of high-throughput sequencing in clinical routine cancer care: lessons from the cancer pilot project of the France Genomic Medicine 2025 plan. ESMO Open 2021; 5:S2059-7029(20)32644-2. [PMID: 32713836 PMCID: PMC7383956 DOI: 10.1136/esmoopen-2020-000744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/02/2022] Open
Abstract
Background Whole exome sequencing and RNA sequencing (WES/RNASeq) should now be implemented in the clinical practice in order to increase access to optimal care for cancer patients. Providing results to Tumour Boards in a relevant time frame—that is, compatible with the clinical pathway—is crucial. Assessing the feasibility of this implementation in the French care system is the primary objective of the Multipli study, as one of the four pilot projects of the national France Genomic Medicine 2025 (FGM 2025) plan. The Multipli study encompasses two innovative trials which will be driven in around 2400 patients suffering from a soft-tissue sarcoma (Multisarc) or a metastatic colorectal carcinoma (Acompli). Methods Prior to launching the FGM 2025 cancer pilot study itself, the performance of the Multipli genomic workflow has been evaluated through each step, from the samples collection to the Molecular Tumour Board (MTB) report. Two Multipli-assigned INCa-labelled molecular genetics centres, the CEA-CNRGH sequencing platform and the Institut Bergonié’s Bioinformatics Platform were involved in a multicentric study. The duration of each step of the genomic workflow was monitored and bottlenecks were identified. Results Thirty barriers which could affect the quality of the samples, sequencing results and the duration of each step of the genomic pathway were identified and mastered. The global turnaround time from the sample reception to the MTB report was of 44 calendar days. Conclusion Our results demonstrate the feasibility of tumour genomic analysis by WES/RNASeq within a time frame compatible with the current cancer patient care. Lessons learnt from the Multipli WES/RNASeq Platforms Workflow Study will constitute guidelines for the forthcoming Multipli study and more broadly for the future clinical routine practice in the first two France Genomic Medicine 2025 platforms.
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Affiliation(s)
| | - Céline Auzanneau
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Delphine Bacq
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Carine Bellera
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Hélène Blons
- Service de pharmacogénétique et d'oncologie moléculaire, Hopital Europeen Georges Pompidou, Paris, France.,U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France
| | - Anne Boland
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Marlène Boucheix
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France
| | - Aurélien Bourdon
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Emmanuelle Chollet
- ITMO Cancer, Alliance nationale pour les sciences de la vie et de la santé, Paris, France
| | - Christine Chomienne
- ITMO Cancer, Alliance nationale pour les sciences de la vie et de la santé, Paris, France .,Institut National du Cancer, Boulogne-Billancourt, France
| | - Jean-François Deleuze
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France.,Centre de référence, d'innovation et d'expertise, US39, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Christelle Delmas
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Derek Dinart
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Hélène Espérou
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Flore Geillon
- Fédération francophone de cancérologie digestive, Dijon, France
| | - Damien Geneste
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Antoine Italiano
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unités Essais cliniques de phase précoce et Sarcomes, Institut Bergonié, Bordeaux, France
| | - Delphine Jean
- CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Emmanuel Khalifa
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Yec'han Laizet
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Pierre Laurent-Puig
- U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France.,Service de génétique médicale et clinique, Hopital Europeen Georges Pompidou, Paris, France
| | - Franck Lethimonnier
- ITMO Technologies pour la santé, Alliance nationale pour les sciences de la vie et de la santé, Paris, France
| | - Claire Lévy-Marchal
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Carlo Lucchesi
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Carine Malle
- Institut de santé publique, Pôle recherche clinique, Institut national de la santé et de la recherche médicale, Paris, France
| | - Pierre Mancini
- U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France.,Unité de bioinformatique, Institut Bergonié, Bordeaux, France
| | - Simone Mathoulin-Pélissier
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Vincent Meyer
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Palomares Marie-Ange
- Centre national de recherche en génétique humaine, Institut de biologie François-Jacob, Commissariat à l'énergie atomique et aux énergies alternatives, Evry, France
| | - Géraldine Perkins
- U1147, Centre universitaire des Saint-Pères, Institut national de la santé et de la recherche médicale, Paris, France.,Service de génétique médicale et clinique, HEGP, Paris, Île-de-France, France
| | - Sabrina Sellan-Albert
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Isabelle Soubeyran
- Unité de pathologie moléculaire, Institut Bergonié, Bordeaux, France.,U1218, Institut Bergonié, Institut national de la santé et de la recherche médicale, Bordeaux, France
| | - Cédric Wallet
- Institut de santé publique, d'épidémiologie et de développement, Université de Bordeaux, Bordeaux, France.,CIC-EC1401/EUCLID, Institut national de la santé et de la recherche médicale, Bordeaux, France
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20
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Pasmans CTB, Tops BBJ, Steeghs EMP, Coupé VMH, Grünberg K, de Jong EK, Schuuring EMD, Willems SM, Ligtenberg MJL, Retèl VP, van Snellenberg H, de Bruijn E, Cuppen E, Frederix GWJ. Micro-costing diagnostics in oncology: from single-gene testing to whole- genome sequencing. Expert Rev Pharmacoecon Outcomes Res 2021; 21:413-414. [PMID: 33852815 DOI: 10.1080/14737167.2021.1917385] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Purpose: Predictive diagnostics play an increasingly important role in personalized medicine for cancer treatment. Whole-genome sequencing (WGS)-based treatment selection is expected to rapidly increase worldwide. This study aimed to calculate and compare the total cost of currently used diagnostic techniques and of WGS in treatment of non-small cell lung carcinoma (NSCLC), melanoma, colorectal cancer (CRC), and gastrointestinal stromal tumor (GIST) in the Netherlands.Methods: The activity-based costing (ABC) method was conducted to calculate total cost of included diagnostic techniques based on data provided by Dutch pathology laboratories and the Dutch-centralized cancer WGS facility. Costs were allocated to four categories: capital costs, maintenance costs, software costs, and operational costs.Results: The total cost per cancer patient per technique varied from € 58 (Sanger sequencing, three amplicons) to € 2925 (paired tumor-normal WGS). The operational costs accounted for the vast majority (over 90%) of the total per cancer patient technique costs.Conclusion: This study outlined in detail all costing aspects and cost prices of current and new diagnostic modalities used in treatment of NSCLC, melanoma, CRC, and GIST in the Netherlands. Detailed cost differences and value comparisons between these diagnostic techniques enable future economic evaluations to support decision-making.
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Affiliation(s)
- Clémence T B Pasmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Bilthoven, The Netherlands
| | - Elisabeth M P Steeghs
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, The Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eiko K de Jong
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ed M D Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,PALGA Foundation, Houten, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valesca P Retèl
- Department of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Health Technology and Services Research, University of Twente, Enschede, The Netherlands
| | | | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine and Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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21
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Pinheiro BG, Pôssa AP, Della Terra PP, de Carvalho JA, Ricci G, Nishikaku AS, Hahn RC, de Camargo ZP, Rodrigues AM. A New Duplex PCR-Assay for the Detection and Identification of Paracoccidioides Species. J Fungi (Basel) 2021; 7:169. [PMID: 33652623 PMCID: PMC7996757 DOI: 10.3390/jof7030169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/18/2022] Open
Abstract
Paracoccidioidomycosis (PCM) is a life-threatening systemic fungal infection caused by members of the Paracoccidioides brasiliensis complex and P. lutzii. Routine diagnoses of PCM down to the species level using classical mycological approaches are unspecific due to overlapping phenotypes. There is an urgent need for specific, sensitive, and cost-effective molecular tools to diagnose PCM. Variation among the exon-2 of the gp43 gene was exploited to design species-specific primer pairs to discriminate between members of the P. brasiliensis complex and P. lutzii in a duplex PCR assay. Primer-BLAST searches revealed highly species-specific primers, and no significant region of homology was found against DNA databases except for Paracoccidioides species. Primers PbraCx-F and PbraCx-R targeting P. brasiliensis DNA produced an amplicon of 308 bp, while primers Plu-F and Plu-R targeting P. lutzii DNA generated an amplicon of 142 bp. The lower limit of detection for our duplex PCR assay was 1 pg of gDNA. A panel of 62 Paracoccidioides revealed 100% specificity (AUC = 1.000, 95%CI 0.972-1.000, p < 0.0001) without cross-reacting with other medically relevant fungi or human DNA. As a proof of concept, we demonstrated the accurate identification of the P. brasiliensis complex (n = 7) or P. lutzii (n = 6) from a broad range of formalin-fixed, paraffin-embedded (FFPE) tissues of PCM patient's organs. In four cases, FFPE PCR results confirmed, for the first time, co-infection due to P. brasiliensis (S1) and P. lutzii in the same biopsy. Our duplex PCR assay is useful to detect and differentiate members of the P. brasiliensis complex and P. lutzii, providing clinical laboratories with an important tool to be applied routinely, especially in atypical cases such as those featuring negative serology and positive mycological examination of clinical specimens as well as for the investigation of putative co-infection cases. This will likely benefit thousands of infected patients every year in a wide area of the Americas.
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Affiliation(s)
- Breno Gonçalves Pinheiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
| | - Ana Paula Pôssa
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Paula Portella Della Terra
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
| | - Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Paulo 13561020, Brazil; (G.R.); (A.S.N.)
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr. Ivo Ricci, São Paulo 13561020, Brazil; (G.R.); (A.S.N.)
| | - Rosane Christine Hahn
- Laboratory of Mycology/Research, Faculty of Medicine, Federal University of Mato Grosso, Cuiabá 78060900, Brazil;
- Júlio Muller University Hospital, Federal University of Mato Grosso, Cuiabá 78048902, Brazil
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (B.G.P.); (A.P.P.); (P.P.D.T.); (J.A.d.C.); (Z.P.d.C.)
- Department of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
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22
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PD-L1 expression in paired biopsies and surgical specimens in gastric adenocarcinoma: A digital image analysis study. Pathol Res Pract 2021; 218:153338. [PMID: 33440275 DOI: 10.1016/j.prp.2020.153338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 01/13/2023]
Abstract
Programmed death-ligand 1 (PD-L1) expression in biopsies of gastric carcinoma may predict the results in corresponding surgical specimens. We compared PD-L1 immunohistochemistry (IHC) 22C3 pharmDx expression in paired biopsy and resection specimens. We also characterized the validity of a new PD-L1 assay using digital image analysis. PD-L1 IHC with 22C3 pharmDx and clone 73-10 was performed in 224 gastric cancer tissues (112 biopsies and paired surgical tissues) and the specimens were analyzed with the Leica Aperio Imagescope. For statistical analyses, the area under the receiver operating characteristic curve and R package were used. With 22C3 pharmDx, a PD-L1 combined positive score of ≥1 was found in 36 biopsied (32.14 %) and 53 surgical (47.32 %) samples. PD-L1 expression results were concordant in 71 cases (63.4 %) and discordant in 41 (36.6 %). The overall discordance rate was 36.61 % (95 % confidence interval 2.101-8.983) and the κ value was 0.254 with fair agreement. The sensitivity and specificity of biopsy PD-L1 to predict the results of the surgical specimen was 62 % and 73 %, respectively. The correlation of 22C3 pharmDx and clone 73-10 was high (correlation coefficient = 0.88). When only tumor cell staining was compared, this correlation was increased (correlation coefficient = 0.95). Our results indicated moderate association of PD-L1 expression between gastric biopsies and corresponding resected tumors. Results of PD-L1 assay with 73-10 are comparable to 22C3 pharmDx results.
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23
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Han LM, Khanafshar E, Afshar AR, Calkins SM. The diagnostic utility of next-generation sequencing on FNA biopsies of melanocytic uveal lesions. Cancer Cytopathol 2020; 128:499-505. [PMID: 32196967 DOI: 10.1002/cncy.22264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/04/2020] [Accepted: 02/27/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Uveal melanoma is highly aggressive, and overall prognosis depends on mutation status. Fine-needle aspiration biopsies (FNABs) play an important role in obtaining fresh tissue for cytologic diagnosis and molecular studies. It has been suggested that, although FNAB usually provides high diagnostic accuracy, there may be limited cellularity, which may compromise diagnostic potential for molecular studies. FNABs of uveal melanocytic lesions were evaluated to assess sample adequacy for both cytologic evaluation and next-generation sequencing (NGS). METHODS The authors retrospectively evaluated 36 cases of melanocytic uveal lesions from 2015 to 2018. Samples were obtained by ophthalmologist-performed FNAB and aliquoted for cytology and NGS. Various combinations of direct smears, liquid-based cytology slides, cell blocks, and immunohistochemical stains for melanocytic markers were performed. All samples were tested for molecular alterations using hybrid-capture-based NGS. RESULTS There was sufficient material for cytologic diagnosis in 33 of 36 cases (92%), for NGS testing in 30 of 36 cases (83%), and for both cytologic diagnosis and NGS testing in 28 of 36 cases (78%). Of 7 cases that were cytologically categorized as indeterminate or diagnosed as "atypical" or "nondiagnostic," NGS testing was sufficient and diagnostic for melanoma in 5 cases. Of the cases diagnosed as melanoma on pathology, 20 cases (87%) had concordant NGS testing results, 2 lacked molecular alterations, and 1 was insufficient for testing. CONCLUSIONS FNA sampling of melanocytic uveal lesions is adequate for both cytologic diagnosis and NGS testing. In a subset of cases in which pathologic findings were indeterminate, NGS testing results were clarifying for diagnosis. In addition, specific molecular alterations identified can aid in evaluating prognosis and guide further management.
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Affiliation(s)
- Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Elham Khanafshar
- Department of Pathology, University of California, San Francisco, San Francisco, California
| | - Armin R Afshar
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California
| | - Sarah M Calkins
- Department of Pathology, University of California, San Francisco, San Francisco, California
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24
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Fujii S, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shinozaki E, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K, Suzuki Y, Akagi K, Yamanaka T, Nomura S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A, Tsuchihara K. Histopathological factors affecting the extraction of high quality genomic DNA from tissue sections for next-generation sequencing. Biomed Rep 2019; 11:171-180. [PMID: 31565223 DOI: 10.3892/br.2019.1235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/28/2019] [Indexed: 01/03/2023] Open
Abstract
To enable the widespread application of genomic medicine, the extraction of genomic DNA from thin sections of archived formalin-fixed and paraffin-embedded (FFPE) tissue blocks for next-generation sequencing (NGS) is often necessary. However, there are currently no guidelines available on which specific regions of the microtome sections to use for macrodissection with respect to the histopathological factors observed under microscopic examination. The aim of this study was to clarify the relationship between histopathological factors and DNA quality, and to standardize the macrodissection method for more efficient implementation of NGS. FFPE tissue specimens of 218 patients from the Biomarker Research for Anti-EGFR Monoclonal Antibodies by Comprehensive Cancer Genomics study were used to investigate the relationship between 15 histopathological factors and the quantitative ratio of double-stranded DNA (dsDNA) to total nucleic acids, as well as the ∆ crossing point value of each tissue specimen. Multivariate logistic regression analysis revealed that specimen storage of ≥3 years was negatively associated with dsDNA quality (P=0.0007, OR: 4.30, 95% CI: 1.85-10.04). In contrast, the presence of a mucus pool was positively associated with dsDNA quality (P=0.0308, OR: 0.23, 95% CI: 0.06-0.87). Metastatic tumors and longer specimen storage periods were significantly associated with lower ∆Cp values (P=0.0007, OR: 4.43, 95% CI: 1.87-10.49; and P=0.0003, OR: 5.51, 95% CI: 2.18-13.95, respectively). Therefore, macrodissection should not be performed on specimens exhibiting histopathological factors associated with poor DNA quality. In particular, the use of tissue blocks with a storage period of <3 years allows the extraction of genomic DNA suitable for NGS.
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Affiliation(s)
- Satoshi Fujii
- Division of Pathology, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Kentaro Yamazaki
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center, Nagaizumi, Shizuoka 411-8777, Japan
| | - Kei Muro
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi 464-8681, Japan
| | - Kensei Yamaguchi
- Department of Gastrointestinal Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Tomohiro Nishina
- Department of Gastrointestinal Medical Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Ehime 791-0280, Japan
| | - Satoshi Yuki
- Department of Gastroenterology and Hepatology, Hokkaido University Hospital, Sapporo, Hokkaido 060-8648, Japan
| | - Eiji Shinozaki
- Department of Gastrointestinal Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Hideaki Bando
- Department of Clinical Oncology, Aichi Cancer Center Hospital, Nagoya, Aichi 464-8681, Japan
| | - Sachiyo Mimaki
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | | | | | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama 362-0806, Japan
| | - Takeharu Yamanaka
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Shogo Nomura
- Biostatistics Division, Center for Research and Administration and Support, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
| | - Hiroyasu Esumi
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Masaya Sugiyama
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Nao Nishida
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, National Center for Global Health and Medicine, Chiba 277-8516, Japan
| | - Yasuhiro Koh
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Yukiko Abe
- G&G Science Co. Ltd., Fukushima 960-1242, Japan
| | - Atsushi Ohtsu
- National Cancer Center Hospital East, Kashiwa, Chiba 277-8577, Japan
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277-8577, Japan
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25
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Ascierto PA, Bifulco C, Palmieri G, Peters S, Sidiropoulos N. Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis. J Mol Diagn 2019; 21:756-767. [PMID: 31251989 DOI: 10.1016/j.jmoldx.2019.05.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/23/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. Many preanalytic variables can influence the accuracy and reliability of NGS results. Standardization of preanalytic variables is, however, complicated by the plethora of specimen acquisition and processing methods. Variables across the tissue journey, including specimen acquisition, specimen fixation, and sectioning, as well as postfixation processing, such as nucleic acid extraction, library preparation, and choice of sequencing methods, are critical for the reliability of NGS analysis; thus, standardization would be beneficial. In this article, each step in the tissue journey is outlined, with specific focus on preanalytic variables that can influence NGS results. Practical considerations for standardization of these variables are provided to facilitate accurate, reliable, and reproducible NGS-based molecular characterization of tumors, ultimately informing diagnosis and guiding treatment.
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Affiliation(s)
- Paolo A Ascierto
- Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", Naples, Italy.
| | - Carlo Bifulco
- Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, Oregon
| | - Giuseppe Palmieri
- Institute of Biomolecular Chemistry - National Research Council, Sassari, Italy
| | - Solange Peters
- Department of Oncology, Lausanne University, Lausanne, Switzerland
| | - Nikoletta Sidiropoulos
- University of Vermont Health Network, Larner College of Medicine at the University of Vermont, Burlington, Vermont
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26
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Sone M, Arai Y, Sugawara S, Kubo T, Itou C, Hasegawa T, Umakoshi N, Yamamoto N, Sunami K, Hiraoka N, Kubo T. Feasibility of genomic profiling with next-generation sequencing using specimens obtained by image-guided percutaneous needle biopsy. Ups J Med Sci 2019; 124:119-124. [PMID: 31179853 PMCID: PMC6567228 DOI: 10.1080/03009734.2019.1607635] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aims: The demand for specimen collection for genomic profiling is rapidly increasing in the era of personalized medicine. Percutaneous needle biopsy is recognized as minimally invasive, but the feasibility of comprehensive genomic analysis using next-generation sequencing (NGS) is not yet clear. The purpose of this study was to evaluate the feasibility of genomic analysis using NGS with specimens obtained by image-guided percutaneous needle biopsy with 18-G needles. Patients and methods: Forty-eight patients who participated in a clinical study of genomic profiling with NGS with the specimen obtained by image-guided needle biopsy were included. All biopsies were performed under local anesthesia, with imaging guidance, using an 18-G cutting needle. A retrospective chart review was performed to determine the rate of successful genomic analysis, technical success rate of biopsy procedure, adverse events, rate of success in pathological diagnosis, and cause of failed genomic analysis. Results: The success rate of genomic analysis was 79.2% (38/48). The causes of failure were unprocessed for DNA extraction due to insufficient specimen volume (6/10), insufficient DNA volume (2/10), and deteriorated DNA quality (2/10). The rate of successful genomic analysis excluding NGS analysis that failed for reasons unrelated to the biopsy procedures was 95.2% (40/42). Technical success of biopsy was achieved in all patients without severe adverse events. The rate of success in the pathological diagnosis was 97.9% (47/48). Conclusions: Image-guided needle biopsy specimens using an 18-G cutting needle yielded a successful NGS genomic analysis rate with no severe adverse events and could be an adoptable method for tissue sampling for NGS.
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Affiliation(s)
- Miyuki Sone
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
- CONTACT Miyuki Sone Department of Diagnostic Radiology, National Cancer Center, 5-1-1, Tsukiji, Chuo-ku, Tokyo1040045, Japan
| | - Yasuaki Arai
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Shunsuke Sugawara
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Takatoshi Kubo
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Chihiro Itou
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Tetsuya Hasegawa
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Noriyuki Umakoshi
- Department of Diagnostic Radiology, National Cancer Center Hospital, Tokyo, Japan
| | - Noboru Yamamoto
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Kumiko Sunami
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Nobuyoshi Hiraoka
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kubo
- Division of Translational Genomics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Tokyo, Japan
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27
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Zhang X, Liang Z, Wang S, Lu S, Song Y, Cheng Y, Ying J, Liu W, Hou Y, Li Y, Liu Y, Hou J, Liu X, Shao J, Tai Y, Wang Z, Fu L, Li H, Zhou X, Bai H, Wang M, Lu Y, Yang J, Zhong W, Zhou Q, Yang X, Wang J, Huang C, Liu X, Zhou X, Zhang S, Tian H, Chen Y, Ren R, Liao N, Wu C, Zhu Z, Pan H, Gu Y, Wang L, Liu Y, Zhang S, Liu T, Chen G, Shao Z, Xu B, Zhang Q, Xu R, Shen L, Wu Y, Tumor Biomarker Committee OBOCSOCO(CSCO. Application of next-generation sequencing technology to precision medicine in cancer: joint consensus of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology. Cancer Biol Med 2019; 16:189-204. [PMID: 31119060 PMCID: PMC6528448 DOI: 10.20892/j.issn.2095-3941.2018.0142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 12/20/2018] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technology is capable of sequencing millions or billions of DNA molecules simultaneously. Therefore, it represents a promising tool for the analysis of molecular targets for the initial diagnosis of disease, monitoring of disease progression, and identifying the mechanism of drug resistance. On behalf of the Tumor Biomarker Committee of the Chinese Society of Clinical Oncology (CSCO) and the China Actionable Genome Consortium (CAGC), the present expert group hereby proposes advisory guidelines on clinical applications of NGS technology for the analysis of cancer driver genes for precision cancer therapy. This group comprises an assembly of laboratory cancer geneticists, clinical oncologists, bioinformaticians, pathologists, and other professionals. After multiple rounds of discussions and revisions, the expert group has reached a preliminary consensus on the need of NGS in clinical diagnosis, its regulation, and compliance standards in clinical sample collection. Moreover, it has prepared NGS criteria, the sequencing standard operation procedure (SOP), data analysis, report, and NGS platform certification and validation.
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Affiliation(s)
- Xuchao Zhang
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - Shengyue Wang
- National Research Center for Translational Medicine, Shanghai, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Shun Lu
- Lung Tumor Clinical Medical Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Song
- Division of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210029, China
| | - Ying Cheng
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yangqiu Li
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 519000, China
| | - Yi Liu
- Laboratory of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Hou
- Department of Oncology, First Clinical College of South China University of Technology/Guangdong Lung Cancer Institute, Guangzhou 510060, China
| | - Xiufeng Liu
- People's Liberation Army Cancer Center of Bayi Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Jianyong Shao
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Yanhong Tai
- Department of Pathology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Zheng Wang
- Department of Pathology, Beijing Hospital, Beijing 100071, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory of Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Oncology, Jilin Cancer Hospital, Changchun 132002, China
| | - Xiaojun Zhou
- Department of Pathology, Jinling Hospital Nanjing University School of Medicine, Nanjing 210029, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Mengzhao Wang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100006, China
| | - You Lu
- Department of Oncology, West China Hospital, Sichuan University, Chengdu 610065, China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenzhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xuening Yang
- Guangdong Lung Cancer Institute, Guangdong Provincical Prople's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Cheng Huang
- Department of Thoracic Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou 350001, China
| | - Xiaoqing Liu
- Department of Oncology, Affiliated Hospital of the Academy of Military Medical Sciences, Beijing 100071, China
| | - Xiaoyan Zhou
- Department of Pathology, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Shirong Zhang
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Hongxia Tian
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Yu Chen
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
| | - Ruibao Ren
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, RuiJin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Ning Liao
- Department of Breast Cancer, Cancer Center, Guangdong Provincial People's Hospital, Guangzhou 510080, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200240, China
| | - Zhongzheng Zhu
- Department of Oncology, No. 113 Hospital of People's Liberation Army, Ningbo 315040, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
| | - Liwei Wang
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang 110016, China
| | - Suzhan Zhang
- Department of Oncology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310020, China
| | - Tianshu Liu
- Department of Oncology, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Gong Chen
- Department of Colorectal, Sun Yat-sen University Cancer Center, Guangzhou 519000, China
| | - Zhimin Shao
- Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200433, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100006, China
| | - Qingyuan Zhang
- Department of Internal Medicine, The Third Affiliated Hospital of Harbin Medical University, Harbin 150030, China
| | - Ruihua Xu
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 519000, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yilong Wu
- Guangdong Lung Cancer Institute, Medical Research Center, Cancer Center of Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Affiliated Guangdong Provincial People's Hospital, South China University of Technology, Guangzhou 510630, China
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28
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Rosa-Rosa JM, Caniego-Casas T, Leskela S, Muñoz G, Del Castillo F, Garrido P, Palacios J. Modified SureSelect QXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples. Biol Proced Online 2018; 20:19. [PMID: 30337841 PMCID: PMC6182866 DOI: 10.1186/s12575-018-0084-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022] Open
Abstract
Background Personalised medicine is nowadays a major objective in oncology. Molecular characterization of tumours through NGS offers the possibility to find possible therapeutic targets in a time- and cost-effective way. However, the low quality and complexity of FFPE DNA samples bring a series of disadvantages for massive parallel sequencing techniques compared to high-quality DNA samples (from blood cells, cell cultures, etc.). Results We performed several experiments to understand the behaviour of FFPE DNA samples during the construction of SureSelectQXT libraries. First, we designed a quality checkpoint for FFPE DNA samples based on the quantification of their amplification capability (qcPCR). We observed that FFPE DNA samples can be classified according to DIN value and qcPCR concentration into unusable, or low-quality (LQ) and good-quality (GQ) DNA. For GQ samples, we increased the amount of input DNA to 150 ng and the digestion time to 30 min, whereas for LQ samples, we used 50 ng of DNA as input but we decreased the digestion time to 1 min. In all cases, we increased the cycles of the pre-hyb PCR to 10 but decreased the cycles of the post-hyb PCR to 8. In addition, we confirmed that using half of the volume of reagents can be beneficial. Finally, in order to obtain better results, we designed a decision flow-chart to achieve a seeding concentration of 12–14 pM for MiSeq Reagent Kit v2. Conclusions Our experiments allowed us to unveil the behaviour of low-quality FFPE DNA samples during the construction of SureSelectQXT libraries. Sequencing results showed that, using our modified SureSelectQXT protocol, the final percentage of usable reads for low-quality samples was increased more than three times allowing to reach median depth/million reads values of 76.35. This value is equivalent to ~ 0.9 and ~ 0.7 of the values obtained for good-quality FFPE and high-quality DNA respectively. Electronic supplementary material The online version of this article (10.1186/s12575-018-0084-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J M Rosa-Rosa
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain
| | - T Caniego-Casas
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - S Leskela
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain.,2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - G Muñoz
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - F Del Castillo
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,3Servicio de Genética, Hospital Universitario Ramón y Cajal, Madrid, Spain.,4CIBER-ER, Instituto de Salud Carlos III, Madrid, Spain
| | - P Garrido
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,5Medical Oncology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain.,6Facultad de Medicina, Universidad de Alcalá de Henares, Madrid, Spain
| | - J Palacios
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain.,2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,6Facultad de Medicina, Universidad de Alcalá de Henares, Madrid, Spain.,7Servicio de Anatomía Patológica, Hospital Ramón y Cajal, Ctra. Colmenar Viejo km 9,100, 28034 Madrid, Spain
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29
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Lee SH, Lee B, Shim JH, Lee KW, Yun JW, Kim SY, Kim TY, Kim YH, Ko YH, Chung HC, Yu CS, Lee J, Rha SY, Kim TW, Jung KH, Im SA, Moon HG, Cho S, Kang JH, Kim J, Kim SK, Ryu HS, Ha SY, Kim JI, Chung YJ, Kim C, Kim HL, Park WY, Noh DY, Park K. Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients. Cancer Res Treat 2018; 51:211-222. [PMID: 29690749 PMCID: PMC6333975 DOI: 10.4143/crt.2018.132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/19/2018] [Indexed: 12/15/2022] Open
Abstract
Purpose With the emergence of next-generation sequencing (NGS) technology, profiling a wide range of genomic alterations has become a possibility resulting in improved implementation of targeted cancer therapy. In Asian populations, the prevalence and spectrum of clinically actionable genetic alterations has not yet been determined because of a lack of studies examining high-throughput cancer genomic data. Materials and Methods To address this issue, 1,071 tumor samples were collected from five major cancer institutes in Korea and analyzed using targeted NGS at a centralized laboratory. Samples were either fresh frozen or formalin-fixed, paraffin embedded (FFPE) and the quality and yield of extracted genomic DNA was assessed. In order to estimate the effect of sample condition on the quality of sequencing results, tissue preparation method, specimen type (resected or biopsied) and tissue storage time were compared. Results We detected 7,360 non-synonymous point mutations, 1,164 small insertions and deletions, 3,173 copy number alterations, and 462 structural variants. Fifty-four percent of tumors had one or more clinically relevant genetic mutation. The distribution of actionable variants was variable among different genes. Fresh frozen tissues, surgically resected specimens, and recently obtained specimens generated superior sequencing results over FFPE tissues, biopsied specimens, and tissues with long storage duration. Conclusion In order to overcome, challenges involved in bringing NGS testing into routine clinical use, a centralized laboratory model was designed that could improve the NGS workflows, provide appropriate turnaround times and control costs with goal of enabling precision medicine.
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Affiliation(s)
- Se-Hoon Lee
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Boram Lee
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Ho Shim
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kwang Woo Lee
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Won Yun
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sook-Young Kim
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yeul Hong Kim
- Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Young Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyun Cheol Chung
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Chang Sik Yu
- Department of Colon & Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun Young Rha
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Hae Jung
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seock-Ah Im
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyeong-Gon Moon
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jin Hyoung Kang
- Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Kyum Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Yun Ha
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Cheolmin Kim
- Department of Medical Informatics, Pusan National University School of Medicine, Yangsan, Korea
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.,Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Kor
| | - Dong-Young Noh
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Keunchil Park
- Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Determining the Optimal Number of Core Needle Biopsy Passes for Molecular Diagnostics. Cardiovasc Intervent Radiol 2017; 41:489-495. [PMID: 29279975 DOI: 10.1007/s00270-017-1861-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 12/14/2017] [Indexed: 02/06/2023]
Abstract
PURPOSE The number of core biopsy passes required for adequate next-generation sequencing is impacted by needle cut, needle gauge, and the type of tissue involved. This study evaluates diagnostic adequacy of core needle lung biopsies based on number of passes and provides guidelines for other tissues based on simulated biopsies in ex vivo porcine organ tissues. METHODS The rate of diagnostic adequacy for pathology and molecular testing from lung biopsy procedures was measured for eight operators pre-implementation (September 2012-October 2013) and post-implementation (December 2013-April 2014) of a standard protocol using 20-gauge side-cut needles for ten core biopsy passes at a single academic hospital. Biopsy pass volume was then estimated in ex vivo porcine muscle, liver, and kidney using side-cut devices at 16, 18, and 20 gauge and end-cut devices at 16 and 18 gauge to estimate minimum number of passes required for adequate molecular testing. RESULTS Molecular diagnostic adequacy increased from 69% (pre-implementation period) to 92% (post-implementation period) (p < 0.001) for lung biopsies. In porcine models, both 16-gauge end-cut and side-cut devices require one pass to reach the validated volume threshold to ensure 99% adequacy for molecular characterization, while 18- and 20-gauge devices require 2-5 passes depending on needle cut and tissue type. CONCLUSION Use of 20-gauge side-cut core biopsy needles requires a significant number of passes to ensure diagnostic adequacy for molecular testing across all tissue types. To ensure diagnostic adequacy for molecular testing, 16- and 18-gauge needles require markedly fewer passes.
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