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Hatakeyama K, Muramatsu K, Nagashima T, Ichida H, Kawanishi Y, Fukumura R, Ohshima K, Shimoda Y, Ohnami S, Ohnami S, Maruyama K, Naruoka A, Kenmotsu H, Urakami K, Akiyama Y, Sugino T, Yamaguchi K. Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer with low tumor content. Sci Rep 2024; 14:13699. [PMID: 38871991 DOI: 10.1038/s41598-024-64541-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024] Open
Abstract
The detection of copy number variations (CNVs) and somatic mutations in cancer is important for the selection of specific drugs for patients with cancer. In cancers with sporadic tumor cells, low tumor content prevents the accurate detection of somatic alterations using targeted sequencing. To efficiently identify CNVs, we performed tumor cell enrichment using tissue suspensions of formalin-fixed paraffin-embedded (FFPE) tissue sections with low tumor cell content. Tumor-enriched and residual fractions were separated from FFPE tissue suspensions of intestinal and diffuse-type gastric cancers containing sporadic tumor cells, and targeted sequencing was performed on 225 cancer-related genes. Sequencing of a targeted panel of cancer-related genes using tumor-enriched fractions increased the number of detectable CNVs and the copy number of amplified genes. Furthermore, CNV analysis using the normal cell-enriched residual fraction as a reference for CNV scoring allowed targeted sequencing to detect CNV characteristics of diffuse-type gastric cancer with low tumor content. Our approach improves the CNV detection rate in targeted sequencing with tumor enrichment and the accuracy of CNV detection in archival samples without paired blood.
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Affiliation(s)
- Keiichi Hatakeyama
- Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Koji Muramatsu
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Hiroyuki Ichida
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuichi Kawanishi
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ryutaro Fukumura
- SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Akane Naruoka
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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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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Tamiya A, Kanaoka K, Inagaki Y, Taniguchi Y, Nakao K, Matsuda Y, Okishio K, Takeda M, Kasai T, Shigeki S. Enhancing tumour content and tumour cell count using microdissection contributes to higher detection rate of genetic mutations by next-generation sequencers. Heliyon 2023; 9:e22082. [PMID: 38027827 PMCID: PMC10658387 DOI: 10.1016/j.heliyon.2023.e22082] [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: 05/14/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Background Next-generation sequencing (NGS) analysis is becoming indispensable for the treatment of advanced lung cancer. NGS analysis requires a large number of cancer cell-containing tissues; however, it is often difficult for small biopsies to obtain the required quantities. In microdissection, only the tumour parts of a tissue specimen are obtained, which thereby increases the tumour content and tumour cell count of the tissue specimen. In this study, we investigated the extent to which the detection rate of genetic mutations changes by increasing the tumour content using microdissection. Patients and methods This is a retrospective study. In the genetic panel test using the Oncomine Dx Target Test (ODxTT), participants were divided into two groups: before (group A; April 2021-March 2022) and after (group B; April 2022-December 2022) the introduction of microdissection. The submission criteria for ODxTT were tumour content and tumour cell count >30 % and >2000 in group A, and >40 % and >5000 in group B, respectively. We compared the rate of genetic mutations detected using ODxTT between the two groups. Results This study included 214 consecutive ODxTT cases between April 2021 and December 2022. In group A (n = 112), 65 cases were adenocarcinoma, 84 involved lung tissue, and 64 underwent bronchoscopic sampling, whereas in group B (n = 102), 55 cases were adenocarcinoma, 91 cases involved lung tissue, and 79 cases underwent bronchoscopic sampling. Furthermore, genetic mutations were detected in 39 of 112 cases (35 %) in group A and 59 of 102 cases (58 %) in group B, which was statistically higher in group B (P = 0.0006). Genetic mutations were detected in 45 of 55 adenocarcinoma cases in group B. The genetic mutations detected in epidermal growth factor rescepor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS), and mesenchymal epithelial transition (MET) were higher in group B. Conclusion Increasing the number of tumour cells and tumour content can enhance the detection rate of genetic mutations using ODxTT.
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Affiliation(s)
- Akihiro Tamiya
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kensuke Kanaoka
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yuji Inagaki
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yoshihiko Taniguchi
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Keiko Nakao
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yoshinobu Matsuda
- Department of Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kyoichi Okishio
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Maiko Takeda
- Department of Laboratory Medicine and Pathology, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
- Department of Diagnostic Pathology, Nara Medical University, Nara, Japan
| | - Takahiko Kasai
- Department of Pathology, Tokushima Red Cross Hospital, Tokushima, Japan
| | - Shigeki Shigeki
- Department of Laboratory Medicine and Pathology, National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
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Pavlič A, Urh K, Boštjančič E, Zidar N. Analyzing the invasive front of colorectal cancer - By punching tissue block or laser capture microdissection? Pathol Res Pract 2023; 248:154727. [PMID: 37517168 DOI: 10.1016/j.prp.2023.154727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
The aim of this study was to determine the advantages and limitations of two commonly used sampling techniques, i.e., punching tissue block (PTB) and laser capture microdissection (LCM) when investigating tumor cell-derived gene expression patterns at the invasive front of colorectal cancer (CRC). We obtained samples from 20 surgically removed CRCs at locations crucial for tumor progression, i.e., the central part, the expansive front and the infiltrative front exhibiting tumor budding (TB), using both sampling techniques. At each location, we separately analyzed the expressions of miR-200 family (miR-141, miR-200a, miR-200b, miR-200c and miR-429), known as reliable markers of epithelial-mesenchymal transition (EMT). We found significant downregulation of all members of miR-200 family at the infiltrative front in comparison to the central part regardless of the used sampling technique. However, when comparing miR-200 expression between the expansive and the infiltrative front, we found significant downregulation of all tested miR-200 at the infiltrative front only in samples obtained by LCM. Our results suggest that, PTB is an adequate technique for studying the differences in tumor gene expression between the central part and the invasive front of CRC, but is insufficient to analyze and compare morphologically distinct patterns along the invasive front including TB. For this purpose, the use of LCM is essential.
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Affiliation(s)
- Ana Pavlič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Kristian Urh
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia
| | - Nina Zidar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000 Ljubljana, Slovenia.
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Jeroch J, Riedlinger T, Schmitt C, Ebner S, Winkelmann R, Wild PJ, Demes M. A Comparison of Two Different FFPE Tissue Dissection Methods for Routine Diagnostics in Molecular Pathology: Manual Macrodissection versus Automated Microdissection Using the Roche "AVENIO Millisect" System. Cancers (Basel) 2023; 15:3249. [PMID: 37370864 DOI: 10.3390/cancers15123249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/31/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Currently, in routine diagnostics, most molecular testing is performed on formalin-fixed, paraffin-embedded tissue after a histomorphological assessment. In order to find the best possible and targeted individual therapy, knowing the mutational status of the tumour is crucial. The "AVENIO Millisect" system Roche introduced an automation solution for the dissection of tissue on slides. This technology allows the precise and fully automated dissection of the tumour area without wasting limited and valuable patient material. In this study, the digitally guided microdissection was directly compared to the manual macrodissection regarding the precision and duration of the procedure, their DNA concentrations as well as DNA qualities, and the overall costs in 24 FFPE samples. In 21 of 24 cases (87.5%), the DNA yields of the manually dissected samples were higher in comparison to the automatically dissected samples. Shorter execution times and lower costs were also benefits of the manual scraping process. Nevertheless, the DNA quality achieved with both methods was comparable, which is essential for further molecular testing. Therefore, it could be used as an additional tool for precise tumour enrichment.
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Affiliation(s)
- Jan Jeroch
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Tobias Riedlinger
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Christina Schmitt
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Silvana Ebner
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Peter J Wild
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Melanie Demes
- Wildlab, University Hospital Frankfurt MVZ GmbH, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
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Kanesvaran R, Chia PL, Chiong E, Chua MLK, Ngo NT, Ow S, Sim HG, Tan MH, Tay KH, Wong ASC, Wong SW, Tan PH. An approach to genetic testing in patients with metastatic castration-resistant prostate cancer in Singapore. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2023; 52:135-148. [PMID: 38904491 DOI: 10.47102/annals-acadmedsg.2022372] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Introduction There has been a rapid evolution in the treatment strategies for metastatic castration-resistant prostate cancer (mCRPC) following the identification of targetable mutations, making genetic testing essential for patient selection. Although several international guidelines recommend genetic testing for patients with mCRPC, there is a lack of locally endorsed clinical practice guidelines in Singapore. Method A multidisciplinary specialist panel with representation from medical and radiation oncology, urology, pathology, interventional radiology, and medical genetics discussed the challenges associated with patient selection, genetic counselling and sample processing in mCRPC. Results A clinical model for incorporating genetic testing into routine clinical practice in Singapore was formulated. Tumour testing with an assay that is able to detect both somatic and germline mutations should be utilised. The panel also recommended the "mainstreaming" approach for genetic counselling in which pre-test counselling is conducted by the managing clinician and post-test discussion with a genetic counsellor, to alleviate the bottlenecks at genetic counselling stage in Singapore. The need for training of clinicians to provide pre-test genetic counselling and educating the laboratory personnel for appropriate sample processing that facilitates downstream genetic testing was recognised. Molecular tumour boards and multidisciplinary discussions are recommended to guide therapeutic decisions in mCRPC. The panel also highlighted the issue of reimbursement for genetic testing to reduce patient-borne costs and increase the reach of genetic testing among this patient population. Conclusion This article aims to provide strategic and implementable recommendations to overcome the challenges in genetic testing for patients with mCRPC in Singapore.
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Affiliation(s)
| | - Puey Ling Chia
- Department of Medical Oncology, Tan Tock Seng Hospital, Singapore
| | - Edmund Chiong
- Department of Urology, National University Hospital, Singapore
- Department of Surgery, National University of Singapore, Singapore
| | | | - Nye Thane Ngo
- Division of Pathology, Singapore General Hospital, Singapore
| | - Samuel Ow
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Hong Gee Sim
- Ravenna Urology Clinic, Gleneagles Medical Centre, Singapore
| | | | - Kiang Hiong Tay
- Department of Vascular and Interventional Radiation, Singapore General Hospital, Singapore
| | | | | | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
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Walsh EM, Halushka MK. A Comparison of Tissue Dissection Techniques for Diagnostic, Prognostic, and Theragnostic Analysis of Human Disease. Pathobiology 2022; 90:199-208. [PMID: 35952628 PMCID: PMC9918608 DOI: 10.1159/000525979] [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: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Histopathology has historically been the critical technique for the diagnosis and treatment of human disease. Today, genomics, transcriptomics, and proteomics from specific cells, rather than bulk tissue, have become key to understanding underlying disease mechanisms and rendering useful diagnostic information. Extraction of desired analytes, i.e., nucleic acids or proteins, from easily accessible formalin-fixed paraffin-embedded tissues allows for clinically relevant activities, such as sequencing biomarker mutations or typing amyloidogenic proteins. Genetic profiling has become routine for cancers as varied as non-small cell lung cancer and prostatic carcinoma. The five main tissue dissection techniques that have been developed thus far include: bulk scraping, manual macrodissection, manual microdissection, laser-capture microdissection, and expression microdissection. In this review, we discuss the importance of tissue dissection in clinical practice and research, the basic methods, applications, as well as some advantages and disadvantages for each modality.
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Affiliation(s)
- Elise M. Walsh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Wisner L, Larsen B, Maguire A. Enhancing Tumor Content through Tumor Macrodissection. J Vis Exp 2022:10.3791/62961. [PMID: 35225270 PMCID: PMC10448995 DOI: 10.3791/62961] [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] [Indexed: 08/26/2023] Open
Abstract
The presence of contaminating non-tumor tissues in formalin-fixed paraffin-embedded (FFPE) tissues can greatly undermine genomic studies. Herein we describe macrodissection, a method designed to augment the percentage tumor content of a tissue specimen by removing and eliminating unwanted tissue prior to performing downstream nucleic acid extractions. FFPE tissue blocks were sectioned to produce 4-5 µm slide-mounted tissue sections. A representative section was submitted for hematoxylin and eosin (H&E) staining and subsequently reviewed by a board-certified pathologist. During the review, the pathologist identified and marked the regions of tumor tissue in the H&E. Once complete, the demarked H&E was used to guide resection of the serial unstained sections from the same tissue block. To demonstrate the effects of macrodissection, RNA extracted from matched macrodissected and non-dissected Diffuse Large B-Cell Lymphomas (DLBCL) were run on a digital gene expression assay capable of determining DLBCL subtype and BCL2 translocation status. The results showed that macrodissection changed the subtype or BCL2 translocation status calls in 60% of the samples examined. In conclusion, macrodissection is a simple and effective method for performing tumor enrichment prior to nucleic acid extractions, the product of which can then be confidently used in downstream genomic studies.
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Affiliation(s)
| | - Brandon Larsen
- Department of Laboratory Medicine and Pathology, Mayo Clinic
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Relevance of gene mutations and methylation to the growth of pancreatic intraductal papillary mucinous neoplasms based on pyrosequencing. Sci Rep 2022; 12:419. [PMID: 35013462 PMCID: PMC8748617 DOI: 10.1038/s41598-021-04335-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
We aimed to assess some of the potential genetic pathways for cancer development from non-malignant intraductal papillary mucinous neoplasm (IPMN) by evaluating genetic mutations and methylation. In total, 46 dissected regions in 33 IPMN cases were analyzed and compared between malignant-potential and benign cases, or between malignant-potential and benign tissue dissected regions including low-grade IPMN dissected regions accompanied by malignant-potential regions. Several gene mutations, gene methylations, and proteins were assessed by pyrosequencing and immunohistochemical analysis. RASSF1A methylation was more frequent in malignant-potential dissected regions (p = 0.0329). LINE-1 methylation was inversely correlated with GNAS mutation (r = - 0.3739, p = 0.0105). In cases with malignant-potential dissected regions, GNAS mutation was associated with less frequent perivascular invasion (p = 0.0128), perineural invasion (p = 0.0377), and lymph node metastasis (p = 0.0377) but significantly longer overall survival, compared to malignant-potential cases without GNAS mutation (p = 0.0419). The presence of concordant KRAS and GNAS mutations in the malignant-potential and benign dissected regions were more frequent among branch-duct IPMN cases than among the other types (p = 0.0319). Methylation of RASSF1A, CDKN2A, and LINE-1 and GNAS mutation may be relevant to cancer development, IPMN subtypes, and cancer prognosis.
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Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides. Mod Pathol 2022; 35:1791-1803. [PMID: 36198869 PMCID: PMC9532237 DOI: 10.1038/s41379-022-01161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022]
Abstract
To achieve minimum DNA input requirements for next-generation sequencing (NGS), pathologists visually estimate macrodissection and slide count decisions. Unfortunately, misestimation may cause tissue waste and increased laboratory costs. We developed an artificial intelligence (AI)-augmented smart pathology review system (SmartPath) to empower pathologists with quantitative metrics for accurately determining tissue extraction parameters. SmartPath uses two deep learning architectures, a U-Net based network for cell segmentation and a multi-field-of-view convolutional network for tumor area segmentation, to extract features from digitized H&E-stained formalin-fixed paraffin-embedded slides. From the segmented tumor area, SmartPath suggests a macrodissection area. To predict DNA yield per slide, the extracted features from within the macrodissection area are correlated with known DNA yields to fit a regularized linear model (R = 0.85). Then, a pathologist-defined target yield divided by the predicted DNA yield per slide gives the number of slides to scrape. Following model development, an internal validation trial was conducted within the Tempus Labs molecular sequencing laboratory. We evaluated our system on 501 clinical colorectal cancer slides, where half received SmartPath-augmented review and half traditional pathologist review. The SmartPath cohort had 25% more DNA yields within a desired target range of 100-2000 ng. The number of extraction attempts was statistically unchanged between cohorts. The SmartPath system recommended fewer slides to scrape for large tissue sections, saving tissue in these cases. Conversely, SmartPath recommended more slides to scrape for samples with scant tissue sections, especially those with degraded DNA, helping prevent costly re-extraction due to insufficient extraction yield. A statistical analysis was performed to measure the impact of covariates on the results, offering insights on how to improve future applications of SmartPath. With these improvements, AI-augmented histopathologic review has the potential to decrease tissue waste, sequencing time, and laboratory costs by optimizing DNA yields, especially for samples with scant tissue and/or degraded DNA.
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12
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Hong YA, Park KC, Kim BK, Lee J, Sun WY, Sul HJ, Hwang KA, Choi WJ, Chang YK, Kim SY, Shin S, Park J. Analyzing Genetic Differences Between Sporadic Primary and Secondary/Tertiary Hyperparathyroidism by Targeted Next-Generation Panel Sequencing. Endocr Pathol 2021; 32:501-512. [PMID: 34215996 DOI: 10.1007/s12022-021-09686-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 12/25/2022]
Abstract
Secondary hyperparathyroidism (SHPT) is characterized by excessive serum parathyroid hormone levels in response to decreasing kidney function, and tertiary hyperparathyroidism (THPT) is often the result of a long-standing SHPT. To date, several genes have been associated with the pathogenesis of primary hyperparathyroidism (PHPT). However, the molecular genetic mechanisms of uremic hyperparathyroidism (HPT) remain uncharacterized. To elucidate the differences in genetic alterations between PHPT and SHPT/THPT, the targeted next-generation sequencing of genes associated with HPT was performed using DNA extracted from parathyroid tissues. As a result, 26 variants in 19 PHPT or SHPT/THPT appeared as candidate pathogenic mutations, which corresponded to 9 (35%) nonsense, 8 (31%) frameshift, 6 (23%) missense, and 3 (11%) splice site mutations. The MEN1 (23%, 6/26), ASXL3 (15%, 4/26), EZH2 (12%, 3/26), and MTOR (8%, 2/26) genes were frequently mutated. Sixteen of 25 patients with PHPT (64%) had one or more mutations, whereas 3 (21%) of 21 patients with SHPT/THPT had only 1 mutation (p = 0.001). Sixteen of 28 patients (57%) with parathyroid adenoma (PA) had one or more mutations, whereas 3 of 18 patients (17%) with parathyroid hyperplasia (PH) had just one mutation (p = 0.003). Known driver mutations associated with parathyroid tumorigenesis such as CCND1/PRAD1, CDC73/HRPT2, and MEN1 were identified only in PA (44%, 7/16 with mutations). Our results suggest that molecular genetic abnormalities in SHPT/THPT are distinct from those in PHPT. These findings may help in analyzing the molecular pathogenesis underlying uremic HPT development.
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Affiliation(s)
- Yu Ah Hong
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki Cheol Park
- Clinical Research Institute, Daejeon St. Mary's Hospital, Daejeon, Republic of Korea
| | - Bong Kyun Kim
- Division of Breast and Thyroid Surgery, Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jina Lee
- Division of Breast and Thyroid Surgery, Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woo Young Sun
- Division of Breast and Thyroid Surgery, Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hae Joung Sul
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung-Ah Hwang
- Department of Research and Development, SML Genetree, Seoul, Republic of Korea
| | - Won Jung Choi
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon-Kyung Chang
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Suk Young Kim
- Division of Nephrology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soyoung Shin
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Republic of Korea.
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea.
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13
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Javey M, Reinsch C, Feldkamp M, Siemann S, Blüher A, Woestmann C, Cai L, Tran I, May T, Havnar C, Lo AA, Hinzmann B, Heilek G, Palma JF. Innovative Tumor Tissue Dissection Tool for Molecular Oncology Diagnostics. J Mol Diagn 2021; 23:399-406. [PMID: 33497835 DOI: 10.1016/j.jmoldx.2021.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 01/04/2021] [Accepted: 01/12/2021] [Indexed: 11/30/2022] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissue is the most commonly used material for tumor molecular profiling, therapy selection, and prognostication. Tumor tissue enrichment by tissue dissection is highly recommended to generate quality data reproducibly for use in downstream assays, such as real-time PCR and next-generation sequencing. The aim of this study was to evaluate the performance of the automated tissue dissection tool AVENIO Millisect System compared with a manual dissection method using 18 FFPE tissue specimens. The study assessed performance of these two methods with paraffinized and deparaffinized sections at 5- and 10-μm thickness as well as at low (5% to 10%) and high (>50%) tumor content. In addition, compatibility with various nucleic acid and protein extraction methods was assessed. Overall, dissection by Millisect resulted in statistically significantly higher yields of nucleic acids and protein compared with manual dissection (P = 0.00524). In downstream analysis on a statistically nonpowered sample set, EGFR mutation testing by PCR led to highly concordant results, and next-generation sequencing testing yielded significantly higher allelic frequencies when tissue was dissected by Millisect compared with manual scraping, demonstrating noninferiority of the automated method. In summary, the AVENIO Millisect System may replace manual labor and support automation of FFPE tumor tissue workflows in clinical molecular laboratories with high testing volumes with adequate validation.
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Affiliation(s)
- Manana Javey
- Roche Sequencing Solutions, Pleasanton, California.
| | | | | | | | | | | | - Lingling Cai
- Roche Sequencing Solutions, Pleasanton, California
| | - Ian Tran
- Roche Sequencing Solutions, Pleasanton, California
| | - Theresa May
- Roche Sequencing Solutions, Pleasanton, California
| | | | - Amy A Lo
- Genentech Inc., South San Francisco, California
| | | | | | - John F Palma
- Roche Sequencing Solutions, Pleasanton, California
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14
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Qi P, Bai QM, Yao QL, Yang WT, Zhou XY. Performance of Automated Dissection on Formalin-Fixed Paraffin-Embedded Tissue Sections for the 21-Gene Recurrence Score Assay. Technol Cancer Res Treat 2020; 19:1533033820960760. [PMID: 33073677 PMCID: PMC7592317 DOI: 10.1177/1533033820960760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
This study aimed to compare the performance of MilliSect dissection and manual dissection. Twenty-five formalin-fixed paraffin-embedded (FFPE) breast cancer tissue blocks were selected for comparison. Specific areas of interest (AOIs) in invasive carcinoma on tissue sections were transferred to dissection slides by manual macrodissection or the MilliSect instrument. The comparison criteria were 1) the time required for dissection; 2) RNA concentration and purity; 3) RNA quantity of 5 housekeeping genes (by RT-qPCR); and 4) ER, PR, HER2, Ki-67 and recurrence score (RS) values (by the 21-gene assay). Then, tumor-adjacent tissues, including fibrocollagenous and epithelial tissues, from the same selected tissue blocks of 8 of 25 patients were scraped using the mesodissection method, and their RS values were assessed to evaluate the influence of tumor-adjacent tissues on the target AOIs. Ultimately, 4 AOIs of invasive ductal carcinoma (IDC) from 1 tissue block of another 4 patients with lymph node (LN) metastases each, LN tissue and a mixture of IDC and LN tissue from the other tissue block of the same 4 patients were mesodissected to evaluate the influence of infiltrating lymphocyte levels on the RS values of AOIs. In our experience, the MilliSect instrument, which provides process management documentation, required more time than manual macrodissection (on average, approximately 9.1 min per sample versus 5.8 min per sample, respectively). The RNA yield and quality of the dissected tissues were comparable for the 2 methods. However, the tumor-adjacent tissues of the AOIs may influence the RS to some extent. Tumor-infiltrating lymphocytes (TILs) can dramatically increase RSs, far exceeding the influence of tumor-adjacent fibrocollagenous and epithelial tissues. In conclusion, MilliSect mesodissection is comparable to manual dissection. This mesodissection tool may facilitate AOI alignment and the dissection process for the 21-gene RS assay. Samples whose adjacent tissues are intermixed with TILs warrant special attention.
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Affiliation(s)
- Peng Qi
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Qian-Ming Bai
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Qian-Lan Yao
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Wen-Tao Yang
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
| | - Xiao-Yan Zhou
- Department of Pathology, 89667Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, 89667Fudan University, Shanghai, China.,Institute of Pathology, 89667Fudan University, Shanghai, China
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Singh V, Nambirajan A, Malik PS, Thulkar S, Pandey RM, Luthra K, Arava S, Ray R, Mohan A, Jain D. Spectrum of uncommon and compound epidermal growth factor receptor mutations in non-small-cell lung carcinomas with treatment response and outcome analysis: A study from India. Lung Cancer 2020; 149:53-60. [PMID: 32971387 DOI: 10.1016/j.lungcan.2020.07.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/25/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Mutations in the tyrosine kinase domain of the epidermal growth factor receptor gene (EGFR) are key driver alterations in lung adenocarcinomas (ADCAs). Exon 19 deletions (exon19del) and exon 21 L858R (L858R) mutations account for 70-90 % of all such alterations and predict sensitivity to EGFR tyrosine kinase inhibitors (TKIs). However, the predictive value of uncommon and compound EGFR mutations for TKIs has not been clearly established. OBJECTIVE To assess the spectrum of EGFR mutations in non-small-cell lung carcinoma (NSCLC), and to compare the treatment responses and outcomes among single common, single uncommon, and compound mutations. METHOD The study was of combined retrospective (January 2010-December 2015) and prospective (January 2016-February 2020) design spanning 10 years. Tumor samples from TKI-naive NSCLC patients were tested for EGFR mutations by a qPCR-based method. Objective response rates (ORRs) and survival outcomes were analyzed. RESULT In total, 1227 tumor samples were tested. EGFR mutations were detected in 391 samples (31.8 %), and included 79.5 % (311/391) single common (exon19del/L858R), 6.6 % (26/391) single uncommon (non-exon19del/L858R), and 13.8 % (54/391) compound mutations. Exon 20 T790M mutations were most prevalent among uncommon/compound mutations (40/391, 10.2 %). Overall, patients with single uncommon/compound mutations responded poorly to both EGFRTKI (47 % ORR) and chemotherapy (43 % ORR), with significantly shorter time to progression (median 7 months) compared to those with exon19del/L858R mutations (median 14.7 months). Patients with baseline T790M mutations (single/compound) were least responsive to EGFR TKIs (11 % ORR) and chemotherapy (27 % ORR) and showed the shortest progression-free survival compared to other uncommon and compound mutations. CONCLUSION Approximately one fifth of EGFR-mutant patients harbor uncommon and compound mutations. Unlike those with exon19del/L858R, these patients-particularly those with baseline T790M mutations-show significantly inferior response rates to treatment (EGFR TKI or chemotherapy) and early disease progression.
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Affiliation(s)
- Varsha Singh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat Singh Malik
- Department of Medical Oncology, Dr B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Thulkar
- Department of Radiology, Dr B.R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ravindra Mohan Pandey
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sudheer Arava
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ruma Ray
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India.
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16
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Brown NA, Elenitoba-Johnson KSJ. Enabling Precision Oncology Through Precision Diagnostics. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:97-121. [PMID: 31977297 DOI: 10.1146/annurev-pathmechdis-012418-012735] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic testing enables clinical management to be tailored to individual cancer patients based on the molecular alterations present within cancer cells. Genomic sequencing results can be applied to detect and classify cancer, predict prognosis, and target therapies. Next-generation sequencing has revolutionized the field of cancer genomics by enabling rapid and cost-effective sequencing of large portions of the genome. With this technology, precision oncology is quickly becoming a realized paradigm for managing the treatment of cancer patients. However, many challenges must be overcome to efficiently implement the transition of next-generation sequencing from research applications to routine clinical practice, including using specimens commonly available in the clinical setting; determining how to process, store, and manage large amounts of sequencing data; determining how to interpret and prioritize molecular findings; and coordinating health professionals from multiple disciplines.
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Affiliation(s)
- Noah A Brown
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA;
| | - Kojo S J Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
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17
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Dufraing K, van Krieken JH, De Hertogh G, Hoefler G, Oniscu A, Kuhlmann TP, Weichert W, Marchiò C, Ristimäki A, Ryška A, Scoazec JY, Dequeker E. Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study. Histopathology 2019; 75:312-319. [PMID: 31054167 PMCID: PMC6851675 DOI: 10.1111/his.13891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
Abstract
AIMS Results from external quality assessment revealed considerable variation in neoplastic cell percentages (NCP) estimation in samples for biomarker testing. As molecular biology tests require a minimal NCP, overestimations may lead to false negative test results. We aimed to develop recommendations to improve the NCP determination in a prototypical entity - colorectal carcinoma - that can be adapted for other cancer types. METHODS AND RESULTS A modified Delphi study was conducted to reach consensus by 10 pathologists from 10 countries with experience in determining the NCP for colorectal adenocarcinoma. This study included two online surveys and a decision-making meeting. Consensus was defined a priori as an agreement of > 80%. All pathologists completed both surveys. Consensus was reached for 8 out of 19 and 2 out of 13 questions in the first and second surveys, respectively. Remaining issues were resolved during the meeting. Twenty-four recommendations were formulated. Major recommendations resulted as follows: only pathologists should conduct the morphological evaluation; nevertheless molecular biologists/technicians may estimate the NCP, if specific training has been performed and a pathologist is available for feedback. The estimation should be determined in the area with the highest density of viable neoplastic cells and lowest density of inflammatory cells. Other recommendations concerned: the determination protocol itself, needs for micro- and macro-dissection, reporting and interpreting, referral practices and applicability to other cancer types. CONCLUSION We believe these recommendations may lead to more accurate NCP estimates, ensuring the correct interpretation of test results, and might help in validating digital algorithms in the future.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Anca Oniscu
- Department of Molecular Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Tine P Kuhlmann
- Department of Pathology, Herlev Hospital, Copenhagen, Denmark
| | - Wilko Weichert
- Department of Pathology, Technical University Munich, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin and Pathology Unit, Torino, Italy.,FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aleš Ryška
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | | | - Elisabeth Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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18
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Goh F, Duhig EE, Clarke BE, McCaul E, Passmore L, Courtney D, Windsor M, Naidoo R, Franz L, Parsonson K, Yang IA, Bowman RV, Fong KM. Low tumour cell content in a lung tumour bank: implications for molecular characterisation. Pathology 2017; 49:611-617. [PMID: 28811084 DOI: 10.1016/j.pathol.2017.07.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/08/2017] [Indexed: 12/23/2022]
Abstract
Lung cancer encompasses multiple malignant epithelial tumour types, each with specific targetable, potentially actionable mutations, such that precision management mandates accurate tumour typing. Molecular characterisation studies require high tumour cell content and low necrosis content, yet lung cancers are frequently a heterogeneous mixture of tumour and stromal cells. We hypothesised that there may be systematic differences in tumour cell content according to histological subtype, and that this may have implications for tumour banks as a resource for comprehensive molecular characterisation studies in lung cancer. To investigate this, we estimated tumour cell and necrosis content of 4267 samples resected from 752 primary lung tumour specimens contributed to a lung tissue bank. We found that banked lung cancer samples had low tumour cell content (33%) generally, although it was higher in carcinoids (77.5%) than other lung cancer subtypes. Tumour cells comprise a variable and often small component of banked resected tumour samples, and are accompanied by stromal reaction, inflammation, fibrosis, and normal structures. This has implications for the adequacy of unselected tumour bank samples for diagnostic and molecular investigations, and further research is needed to determine whether tumour cell content has a significant impact on analytical results in studies using tissue from tumour bank resources.
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Affiliation(s)
- Felicia Goh
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia.
| | - Edwina E Duhig
- Sullivan Nicolaides Pathology, The John Flynn Hospital, Tugun, Qld, Australia
| | - Belinda E Clarke
- Pathology Queensland, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Elizabeth McCaul
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Linda Passmore
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Deborah Courtney
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Morgan Windsor
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rishendren Naidoo
- Cardiothoracic Surgery, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Louise Franz
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kylie Parsonson
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Ian A Yang
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Rayleen V Bowman
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, Qld, Australia
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Pyo JS, Kim NY, Kim RHJ, Kang G. Concordance analysis and diagnostic test accuracy review of IDH1 immunohistochemistry in glioblastoma. Brain Tumor Pathol 2016; 33:248-254. [PMID: 27638721 DOI: 10.1007/s10014-016-0272-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/08/2016] [Indexed: 12/12/2022]
Abstract
The study investigated isocitrate dehydrogenase (IDH) 1 immunohistochemistry (IHC) positive rate and concordance rate between IDH1 IHC and molecular test in glioblastoma. The current study included 1360 glioblastoma cases from sixteen eligible studies. Meta-analysis, including subgroup analysis by antibody clones and cut-off values, for IDH1 IHC positive rate was conducted. In addition, we performed a concordance analysis and diagnostic test accuracy review between IDH1 IHC and molecular tests. The estimated rates of IDH1 IHC were 0.106 [95 % confidence interval (CI) 0.085-0.132]. The IDH1 IHC positive rate of primary and secondary glioblastomas was 0.049 (95 % CI 0.023-0.99) and 0.729 (95 % CI 0.477-0.889), respectively. The overall concordance rate between IDH1 IHC and molecular test was 0.947 (95 % CI 0.878-0.978). In IDH1 IHC-positive and negative subgroups, the concordance rate was 0.842 (95 % CI 0.591-0.952) and 0.982 (95 % CI 0.941-0.995), respectively. The pooled sensitivity and specificity for IDH1 IHC were 1.00 (95 % CI 0.82-1.00) and 0.99 (95 % CI 0.96-1.00), respectively. IDH1 IHC is an accurate test for IDH1 mutation in glioblastoma patients. Further cumulative studies for evaluation criteria of IDH1 IHC will determine how to best apply this approach in daily practice.
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Affiliation(s)
- Jung-Soo Pyo
- Department of Pathology, Eulji University Hospital, Daejeon, Republic of Korea
| | - Nae Yu Kim
- Department of Internal Medicine, Eulji University Hospital, Daejeon, Republic of Korea
| | - Roy Hyun Jai Kim
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Guhyun Kang
- Department of Pathology, Inje University Sanggye Paik Hospital, 1342 Dongil-ro, Nowon-gu, Seoul, 139-707, Republic of Korea.
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