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Mukherjee T, Das T, Basak S, Mohanty S, Adhikary K, Chatterjee P, Maiti R, Karak P. Mucormycosis during COVID-19 era: A retrospective assessment. INFECTIOUS MEDICINE 2024; 3:100112. [PMID: 38948388 PMCID: PMC11214187 DOI: 10.1016/j.imj.2024.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/14/2024] [Accepted: 04/08/2024] [Indexed: 07/02/2024]
Abstract
In a retrospective view, this review examines the impact of mucormycosis on health workers and researchers during the COVID era. The diagnostic and treatment challenges arising from unestablished underlying pathology and limited case studies add strain to healthcare systems. Mucormycosis, caused by environmental molds, poses a significant threat to COVID-19 patients, particularly those with comorbidities and compromised immune systems. Due to a variety of infectious Mucorales causes and regionally related risk factors, the disease's incidence is rising globally. Data on mucormycosis remains scarce in many countries, highlighting the urgent need for more extensive research on its epidemiology and prevalence. This review explores the associations between COVID-19 disease and mucormycosis pathology, shedding light on potential future diagnostic techniques based on the fungal agent's biochemical components. Medications used in ICUs and for life support in ventilated patients have been reported, revealing the challenge of managing this dual onslaught. To develop more effective treatment strategies, it is crucial to identify novel pharmacological targets through "pragmatic" multicenter trials and registries. In the absence of positive mycology culture data, early clinical detection, prompt treatment, and tissue biopsy are essential to confirm the specific morphologic features of the fungal agent. This review delves into the history, pathogens, and pathogenesis of mucormycosis, its opportunistic nature in COVID or immunocompromised individuals, and the latest advancements in therapeutics. Additionally, it offers a forward-looking perspective on potential pharmacological targets for future drug development.
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Affiliation(s)
- Tuhin Mukherjee
- Department of Advanced Pharmacology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Tanisha Das
- School of Pharmaceutical Sciences (SPS), Siksha 'O' Anusandhan University, Bhubaneswar 751003, Odisha, India
| | - Sourav Basak
- Department of Pharmacy, Guru Ghasidas Central University, Bilaspur 495009, Chhattisgarh, India
| | - Satyajit Mohanty
- Department of Advanced Pharmacology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Krishnendu Adhikary
- Department of Interdisciplinary Science, Centurion University of Technology & Management, Odisha 761211, India
| | - Prity Chatterjee
- Department of Biotechnology, Paramedical College Durgapur, West Bengal 713212, India
| | - Rajkumar Maiti
- Department of Physiology, Bankura Christian College, Bankura, West Bengal 722101, India
| | - Prithviraj Karak
- Department of Physiology, Bankura Christian College, Bankura, West Bengal 722101, India
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Santucciu C, Peruzzu A, Fara AM, Cossu A, Kronenberg PA, Deplazes P, Masala G. Immunohistochemistry as a Reliable Tool for the Diagnosis of Cystic Echinococcosis in Patients from Sardinia, Italy-A Confirmatory Study. Diseases 2024; 12:84. [PMID: 38785739 PMCID: PMC11119186 DOI: 10.3390/diseases12050084] [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: 02/22/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Cystic Echinococcosis (CE) is a zoonotic disease caused by the larval stage of the tapeworm Echinococcus granulosus sensu lato (s.l.). This study aims to investigate the use of two monoclonal antibodies (mAbEmG3 and mAbEm2G11) by immunohistochemistry (IHC) to confirm the diagnosis of CE in human patients, in particular in those cases in which other techniques fail to provide a correct or conclusive diagnosis. For this purpose, a survey on 13 patients was performed. These subjects were referred to Sardinian hospitals (Italy) from 2017 to 2022 and were suspected to be affected by CE. Our findings from these 13 patients showed the detection of E. granulosus sensu stricto by IHC in 12 of 13 echinococcal cysts, as one sample was of a non-parasitological origin. The results confirmed that IHC, by means of the mAbEmG3 and mAbEm2G11, is a reliable diagnostic tool that showed a very high performances when tested on strain of E. granulosus s.l. from Sardinia.
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Affiliation(s)
- Cinzia Santucciu
- WOAH and National Reference Laboratory for Echinococcosis, Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.P.); (G.M.)
| | - Angela Peruzzu
- WOAH and National Reference Laboratory for Echinococcosis, Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.P.); (G.M.)
| | - Antonella Maria Fara
- Department of Biomedical Sciences, Institute of Pathology, University of Sassari, 07100 Sassari, Italy; (A.M.F.); (A.C.)
| | - Antonio Cossu
- Department of Biomedical Sciences, Institute of Pathology, University of Sassari, 07100 Sassari, Italy; (A.M.F.); (A.C.)
| | - Philipp A. Kronenberg
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; (P.A.K.); (P.D.)
- Medical Micro- and Molecular Biology, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland
| | - Peter Deplazes
- Institute of Parasitology, Vetsuisse and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; (P.A.K.); (P.D.)
- Clinics of Hepatology and Gastroenterology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Giovanna Masala
- WOAH and National Reference Laboratory for Echinococcosis, Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (A.P.); (G.M.)
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Youssef O, Loukola A, Zidi-Mouaffak YHS, Tamlander M, Ruotsalainen S, Kilpeläinen E, Mars N, Ripatti S, Palotie A, Donner K, Carpén O. High-Resolution Genotyping of Formalin-Fixed Tissue Accurately Estimates Polygenic Risk Scores in Human Diseases. J Transl Med 2024; 104:100325. [PMID: 38220043 DOI: 10.1016/j.labinv.2024.100325] [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: 08/10/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues stored in biobanks and pathology archives are a vast but underutilized source for molecular studies on different diseases. Beyond being the "gold standard" for preservation of diagnostic human tissues, FFPE samples retain similar genetic information as matching blood samples, which could make FFPE samples an ideal resource for genomic analysis. However, research on this resource has been hindered by the perception that DNA extracted from FFPE samples is of poor quality. Here, we show that germline disease-predisposing variants and polygenic risk scores (PRS) can be identified from FFPE normal tissue (FFPE-NT) DNA with high accuracy. We optimized the performance of FFPE-NT DNA on a genome-wide array containing 657,675 variants. Via a series of testing and validation phases, we established a protocol for FFPE-NT genotyping with results comparable with blood genotyping. The median call rate of FFPE-NT samples in the validation phase was 99.85% (range 98.26%-99.94%) and median concordance with matching blood samples was 99.79% (range 98.85%-99.9%). We also demonstrated that a rare pathogenic PALB2 genetic variant predisposing to cancer can be correctly identified in FFPE-NT samples. We further imputed the FFPE-NT genotype data and calculated the FFPE-NT genome-wide PRS in 3 diseases and 4 disease risk variables. In all cases, FFPE-NT and matching blood PRS were highly concordant (all Pearson's r > 0.95). The ability to precisely genotype FFPE-NT on a genome-wide array enables translational genomics applications of archived FFPE-NT samples with the possibility to link to corresponding phenotypes and longitudinal health data.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland; Clinical and Chemical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Anu Loukola
- Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Yossra H S Zidi-Mouaffak
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
| | - Max Tamlander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Clinicum, Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kati Donner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Helsinki Biobank, Helsinki University Hospital (HUS), Helsinki, Finland
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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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Linge A, Patil S, Grosser M, Lohaus F, Gurtner K, Kemper M, Gudziol V, Haim D, Nowak A, Tinhofer I, Zips D, Guberina M, Stuschke M, Balermpas P, Rödel C, Schäfer H, Grosu AL, Abdollahi A, Debus J, Ganswindt U, Belka C, Pigorsch S, Combs SE, Boeke S, Gani C, Jöhrens K, Baretton GB, Löck S, Baumann M, Krause M. The value of subcutaneous xenografts for individualised radiotherapy in HNSCC: Robust gene signature correlates with radiotherapy outcome in patients and xenografts. Radiother Oncol 2024; 191:110055. [PMID: 38109944 DOI: 10.1016/j.radonc.2023.110055] [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: 08/25/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023]
Abstract
PURPOSE To assess the robustness of prognostic biomarkers and molecular tumour subtypes developed for patients with head and neck squamous cell carcinoma (HNSCC) on cell-line derived HNSCC xenograft models, and to develop a novel biomarker signature by combining xenograft and patient datasets. MATERIALS AND METHODS Mice bearing xenografts (n = 59) of ten HNSCC cell lines and a retrospective, multicentre patient cohort (n = 242) of the German Cancer Consortium-Radiation Oncology Group (DKTK-ROG) were included. All patients received postoperative radiochemotherapy (PORT-C). Gene expression analysis was conducted using GeneChip Human Transcriptome Arrays. Xenografts were stratified based on their molecular subtypes and previously established gene classifiers. The dose to control 50 % of tumours (TCD50) was compared between these groups. Using differential gene expression analyses combining xenograft and patient data, a gene signature was developed to define risk groups for the primary endpoint loco-regional control (LRC). RESULTS Tumours of mesenchymal subtype were characterized by a higher TCD50 (xenografts, p < 0.001) and lower LRC (patients, p < 0.001) compared to the other subtypes. Similar to previously published patient data, hypoxia- and radioresistance-related gene signatures were associated with high TCD50 values. A 2-gene signature (FN1, SERPINE1) was developed that was prognostic for TCD50 (xenografts, p < 0.001) and for patient outcome in independent validation (LRC: p = 0.007). CONCLUSION Genetic prognosticators of outcome for patients after PORT-C and subcutaneous xenografts after primary clinically relevant irradiation show similarity. The identified robust 2-gene signature may help to guide patient stratification, after prospective validation. Thus, xenografts remain a valuable resource for translational research towards the development of individualized radiotherapy.
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Affiliation(s)
- Annett Linge
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany.
| | - Shivaprasad Patil
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany
| | - Marianne Grosser
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Fabian Lohaus
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Kristin Gurtner
- OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Max Kemper
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Department of Otorhinolaryngology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Volker Gudziol
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Department of Otorhinolaryngology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Dominik Haim
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Department of Oral and Maxillofacial Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Alexander Nowak
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Department of Oral and Maxillofacial Surgery, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Inge Tinhofer
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Berlin, Germany; Department of Radiooncology and Radiotherapy, Charité University Medicine Berlin, Germany
| | - Daniel Zips
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Berlin, Germany; Department of Radiooncology and Radiotherapy, Charité University Medicine Berlin, Germany
| | - Maja Guberina
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen, Germany; Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Martin Stuschke
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Essen, Germany; Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Panagiotis Balermpas
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Frankfurt, Germany; Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Germany
| | - Claus Rödel
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Frankfurt, Germany; Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Germany
| | - Henning Schäfer
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Freiburg, Germany; Department of Radiation Oncology, Medical Center, Medical Faculty, University of Freiburg, Germany
| | - Anca-Ligia Grosu
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Freiburg, Germany; Department of Radiation Oncology, Medical Center, Medical Faculty, University of Freiburg, Germany
| | - Amir Abdollahi
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany; Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Germany; National Center for Tumor Diseases (NCT), University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany; Translational Radiation Oncology, University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany
| | - Jürgen Debus
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany; Heidelberg Ion Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Germany; National Center for Tumor Diseases (NCT), University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany; Clinical Cooperation Unit Radiation Oncology, University of Heidelberg Medical School and German Cancer Research Center (DKFZ), Germany
| | - Ute Ganswindt
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany; Department of Radiotherapy and Radiation Oncology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Claus Belka
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany; Department of Radiotherapy and Radiation Oncology, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany; Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Steffi Pigorsch
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany; Department of RadioOncology, Technische Universität München, Germany
| | - Stephanie E Combs
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Munich, Germany; Department of RadioOncology, Technische Universität München, Germany; Department of Radiation Sciences (DRS), Institut für Innovative Radiotherapie (iRT), Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Simon Boeke
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Tübingen, Germany; Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls Universität Tübingen, Germany
| | - Cihan Gani
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Tübingen, Germany; Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls Universität Tübingen, Germany
| | - Korinna Jöhrens
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Gustavo B Baretton
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; Tumour- and Normal Tissue Bank, University Cancer Centre (UCC), University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany
| | - Steffen Löck
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Michael Baumann
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; German Cancer Research Center (DKFZ), Division of Radiooncology/Radiobiology, Heidelberg, Germany
| | - Mechthild Krause
- German Cancer Research Center (DKFZ), Heidelberg, Germany, and German Cancer Consortium (DKTK), partner site Dresden, Germany; OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Helmholtz-Zentrum Dresden - Rossendorf, Dresden, Germany; Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany: German Cancer Research Center (DKFZ), Heidelberg, Germany, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany, and Helmholtz Association/Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
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6
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Heo DH, Kim I, Seo H, Kim SG, Kim M, Park J, Park H, Kang S, Kim J, Paik S, Hong SE. DEEPOMICS FFPE, a deep neural network model, identifies DNA sequencing artifacts from formalin fixed paraffin embedded tissue with high accuracy. Sci Rep 2024; 14:2559. [PMID: 38297116 PMCID: PMC10831091 DOI: 10.1038/s41598-024-53167-0] [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: 06/27/2023] [Accepted: 01/29/2024] [Indexed: 02/02/2024] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissue specimens are routinely used in pathological diagnosis, but their large number of artifactual mutations complicate the evaluation of companion diagnostics and analysis of next-generation sequencing data. Identification of variants with low allele frequencies is challenging because existing FFPE filtering tools label all low-frequency variants as artifacts. To address this problem, we aimed to develop DEEPOMICS FFPE, an AI model that can classify a true variant from an artifact. Paired whole exome sequencing data from fresh frozen and FFPE samples from 24 tumors were obtained from public sources and used as training and validation sets at a ratio of 7:3. A deep neural network model with three hidden layers was trained with input features using outputs of the MuTect2 caller. Contributing features were identified using the SHapley Additive exPlanations algorithm and optimized based on training results. The performance of the final model (DEEPOMICS FFPE) was compared with those of existing models (MuTect filter, FFPolish, and SOBDetector) by using well-defined test datasets. We found 41 discriminating properties for FFPE artifacts. Optimization of property quantification improved the model performance. DEEPOMICS FFPE removed 99.6% of artifacts while maintaining 87.1% of true variants, with an F1-score of 88.3 in the entire dataset not used for training, which is significantly higher than those of existing tools. Its performance was maintained even for low-allele-fraction variants with a specificity of 0.995, suggesting that it can be used to identify subclonal variants. Different from existing methods, DEEPOMICS FFPE identified most of the sequencing artifacts in the FFPE samples while retaining more of true variants, including those of low allele frequencies. The newly developed tool DEEPOMICS FFPE may be useful in designing capture panels for personalized circulating tumor DNA assay and identifying candidate neoepitopes for personalized vaccine design. DEEPOMICS FFPE is freely available on the web ( http://deepomics.co.kr/ffpe ) for research.
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Affiliation(s)
- Dong-Hyuk Heo
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Inyoung Kim
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Heejae Seo
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Seong-Gwang Kim
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Minji Kim
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Jiin Park
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Hongsil Park
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Seungmo Kang
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Juhee Kim
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Soonmyung Paik
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea
| | - Seong-Eui Hong
- Theragen Bio Co., Ltd., Seongnam, Gyeonggi-do, 13488, Republic of Korea.
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7
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Hiramatsu K, Matsuda C, Masago K, Toriyama K, Sasaki E, Fujita Y, Haneda M, Ebi H, Shibata N, Hosoda W. Diagnostic utility of DNA integrity number as an indicator of sufficient DNA quality in next-generation sequencing-based genomic profiling. Am J Clin Pathol 2023; 160:261-267. [PMID: 37167067 DOI: 10.1093/ajcp/aqad046] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/29/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVES DNA integrity number (DIN) is a metric for assessing DNA degradation, calculated based on electrophoresis using the Agilent TapeStation System. The utility of DIN as a diagnostic indicator of sufficient DNA quality in clinical next-generation sequencing (NGS) has not been well described. METHODS We evaluated the DINs of 166 tumor formalin-fixed, paraffin-embedded (FFPE) tissue samples submitted for 124-gene panel sequencing. We also investigated a new metric on the electropherogram that could improve the predictive accuracy of the DIN. RESULTS A DIN cutoff of 2.5 discriminated samples with successful analysis (n = 143) from samples with failed analysis (n = 23), with a sensitivity of 0.84 and a specificity of 0.78 (area under the curve [AUC] = 0.88). The DIN was positively correlated with the mean coverage (r = 0.72, P < .0001) but could not discriminate success from failure when the DIN was below 2.5 (negative predictive value, 0.44). We introduced a new metric, the peak/base ratio, that distinguished success from failure with higher accuracy than the DIN (cutoff = 1.6; sensitivity = 0.98, specificity = 0.83, and AUC =0.96). CONCLUSIONS To predict successful NGS, the DNA quality of FFPE tissue can be easily and reliably assessed using the DIN and peak/base ratio.
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Affiliation(s)
- Kaho Hiramatsu
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Chiaki Matsuda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Kazuhiro Toriyama
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Yasuko Fujita
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Masataka Haneda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Hiromichi Ebi
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Noriko Shibata
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
| | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Aichi, Japan
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8
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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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9
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Vitošević K, Todorović D, Slović Ž, Varljen T, Radaković I, Radojević D, Čanović V, Todorović M. The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples. Mol Biol Rep 2023; 50:6323-6336. [PMID: 37310548 DOI: 10.1007/s11033-023-08491-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There are enormous formalin-fixed paraffin-embedded tissue archives and a constantly growing number of methods for molecular analyses but, the isolation of DNA from this tissue is still challenging due to the damaging effect of formalin on DNA. To determine the extent to which DNA purity, yield and integrity depend on the process of fixation in formalin, and to what extent on the process of tissue paraffin embedding, we compared the quality of DNA isolated from fixed tissues and DNA isolated from tissues embedded in paraffin blocks after fixation. METHODS AND RESULTS Heart, liver and brain tissues obtained from healthy people who suddenly died a violent death were fixed in 10% buffered formalin as well as in 4% unbuffered formalin for 6 h, 1-7 days (every 24 h), 10, 14, 28 days and 2 months. Additionally, the same tissues were fixed in 4% unbuffered formalin embedded in a paraffin block and stored from a few months to 30 years. The yield and purity of the DNA samples isolated from these tissues were measured using spectrophotometry. PCR amplification of the hTERT gene was performed to evaluate the degree of DNA fragmentation. Although the purity of the DNA isolated from almost all tissue samples was satisfactory, the DNA yields changed significantly. There was a decrease in successful PCR amplification of the hTERT gene in DNA samples isolated from tissue fixed in buffered and unbuffered formalin for up to 2 months from 100% to 8.3%. Archiving the tissue in paraffin blocks for up to 30 years also impacts the integrity of DNA, so there was a decrease in PCR amplification of the hTERT gene from 91% success to 3%. CONCLUSION The largest decrease in DNA yield was observed after tissue formalin fixation after 14 days of fixation in buffered and unbuffered formalin. DNA integrity depends on the time of tissue formalin fixation, especially after 6 days for tissue fixed in unbuffered formalin, while for tissue fixed in buffered formalin the time is prolonged up to 28 days. The age of paraffin blocks also impacted DNA integrity, after 1 year and 16 years of archiving the paraffin blocks of tissues, there was a decrease in the success of PCR amplification.
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Affiliation(s)
- Katarina Vitošević
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia.
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia.
| | - Danijela Todorović
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Živana Slović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
| | - Tatjana Varljen
- Institute of Legal Medicine, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivana Radaković
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Dušan Radojević
- Faculty of Medical Sciences, Department of Genetics, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Vanja Čanović
- Faculty of Medical Sciences, University of Kragujevac, Serbia, Kragujevac, Serbia
| | - Miloš Todorović
- Faculty of Medical Sciences, Department of Forensic Medicine, University of Kragujevac, Serbia, Kragujevac, Serbia
- Department of Forensic Medicine and Toxicology, University Clinical Center Kragujevac, Kragujevac, Serbia
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10
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Kleo K, Jovanovic VM, Arndold A, Lehmann A, Lammert H, Berg E, Harloff H, Treese C, Hummel M, Daum S. Response prediction in patients with gastric and esophagogastric adenocarcinoma under neoadjuvant chemotherapy using targeted gene expression analysis and next-generation sequencing in pre-therapeutic biopsies. J Cancer Res Clin Oncol 2023; 149:1049-1061. [PMID: 35246724 PMCID: PMC9984352 DOI: 10.1007/s00432-022-03944-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/02/2022] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Perioperative chemo-(radio-) therapy is the accepted standard in European patients with locally advanced adenocarcinoma of the esophagogastric junction or stomach (AEG/AS). However, 30-85% of patients do not respond to this treatment. The aim of our study was the identification of predictive biomarkers in pre-therapeutic endoscopic tumor biopsies from patients with histopathologic response (Becker-1) versus non-response (Becker-2/3) to preoperative chemotherapy. METHODS Formalin-fixed paraffin-embedded biopsies from 36 Caucasian patients (Becker-1 n = 11, Becker-2 n = 7, Becker-3 n = 18) with AEG/AS, taken prior to neoadjuvant chemotherapy were selected. For RNA expression analysis, we employed the NanoString nCounter System. To identify genomic alterations like single nucleotide variants (SNV), copy number variation (CNV) and fusion events, we used Illumina TST170 gene panel. For HER2 and FGFR2 protein expression, immunostaining was performed. Furthermore, we analyzed the microsatellite instability (MSI) and Epstein-Barr virus (EBV) infection status by EBER in situ hybridization. RESULTS Heat map and principal component analyses showed no clustering by means of gene expression according to regression grade. Concerning two recently proposed predictive markers, our data showed equal distribution for MSI (Becker-1: 2; Becker-2: 1; Becker-3: 3; out of 29 tested) and EBV infection was rare (1/32). We could not reveal discriminating target genes concerning SNV, but found a higher mutational burden in non-responders versus responders and fusion (in 6/14) and CNV events (in 5/14) exclusively in Becker-3. CONCLUSIONS Although we could not identify discriminating target genes, our data suggest that molecular alterations are in general more prevalent in patients with AEG/AS belonging to the non-responding Becker group 3.
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Affiliation(s)
- Karsten Kleo
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Vladimir M Jovanovic
- Institute of Informatics, Bioinformatics Solution Center, Freie Universität (FU), Takustr. 9, 14195, Berlin, Germany
| | - Alexander Arndold
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Hedwig Lammert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Erika Berg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Hannah Harloff
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
| | - Christoph Treese
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
- Experimental and Clinical Research Center, Charité University Medicine, Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Chariteplatz 1, 10117, Berlin, Germany
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Severin Daum
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany.
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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11
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Adolfsson E, Kling D, Gunnarsson C, Jonasson J, Gréen H, Gréen A. Whole exome sequencing of FFPE samples—expanding the horizon of forensic molecular autopsies. Int J Legal Med 2022:10.1007/s00414-022-02906-x. [PMID: 36346469 PMCID: PMC10247852 DOI: 10.1007/s00414-022-02906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/14/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Forensic molecular autopsies have emerged as a tool for medical examiners to establish the cause of death. It is particularly useful in sudden unexplained deaths where the cause of death cannot be determined with a regular medical autopsy. We provide the first study of exome data from formalin-fixed paraffin-embedded samples (FFPE) paired with data from high-quality blood samples in forensic applications. The approach allows exploration of the potential to use FFPE samples for molecular autopsies and identify variants in extensive exome data. We leverage the high uniformity of the hybridization capture approach provided by Twist Bioscience to target the complete exome and sequence the libraries on a NextSeq 550. Our findings suggest that exome sequencing is feasible for 24 out of a total of 35 included FFPE samples. When successful, the coverage across the exome is comparatively high (> 90% covered to 20X) and uniform (fold80 below 1.5). Detailed variant comparisons for matched FFPE and blood samples show high concordance with few false variants (positive predictive value of 0.98 and a sensitivity of 0.97) with no distinct FFPE artefacts. Ultimately, we apply carefully constructed forensic gene panels in a stepwise manner to find genetic variants associated with the clinical phenotype and with relevance to the sudden unexplained death.
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12
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Bapat PR, Epari S, Joshi PV, Dhanavade DS, Rumde RH, Gurav MY, Shetty OA, Desai SB. Comparative Assessment of DNA Extraction Techniques From Formalin-Fixed, Paraffin-Embedded Tumor Specimens and Their Impact on Downstream Analysis. Am J Clin Pathol 2022; 158:739-749. [PMID: 36197908 DOI: 10.1093/ajcp/aqac122] [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: 06/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Good-quality nucleic acid extraction from formalin-fixed, paraffin-embedded (FFPE) specimens remains a challenge in molecular-oncopathology practice. This study evaluates the efficacy of an in-house developed FFPE extraction buffer compared with other commercially available kits. METHODS Eighty FFPE specimens processed in different surgical pathology laboratories formed the study sample. DNA extraction was performed using three commercial kits and the in-house developed FFPE extraction buffer. DNA yield was quantified by a NanoDrop spectrophotometer and Qubit Fluorometer, and its purity was measured by the 260/280-nm ratio. A fragment analyzer system was used for accurate sizing of DNA fragments of FFPE DNA. The downstream effects of all extraction methods were evaluated by polymerase chain reaction (PCR) and Sanger sequencing. RESULTS In comparison with the commercial kits, the in-house buffer yielded higher DNA quantity and quality number (P < .0001). In addition, DNA integrity and fragment size were preserved in a significantly greater number of samples isolated with the in-house buffer (P < .05). The target PCR amplification rate with the in-house buffer extracted samples was also significantly higher, with 98% of the samples showing interpretable sequencing results. CONCLUSIONS The in-house developed FFPE extraction buffer performed superior to other methods in terms of suitability for downstream applications, time, cost-efficiency, and ease of performance.
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Affiliation(s)
- Prachi R Bapat
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Pradnya V Joshi
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Dipika S Dhanavade
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Rachna H Rumde
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Mamta Y Gurav
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree A Shetty
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sangeeta B Desai
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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13
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Ancient DNA analysis from epoxy resin Biodur ®-embedded bones. Biotechniques 2022; 73:113-122. [PMID: 36066013 DOI: 10.2144/btn-2022-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
For microscopic investigation, archaeological bone samples are often embedded in Biodur® epoxy resin. This study wants to test whether it is possible to extract DNA suitable for PCR amplification from this sample type. For eight individuals a set of samples - each consisting of a Biodur-embedded femur sample, a native femur sample and a control sample of different anatomical origin - were submitted to organic DNA extraction. The extraction success was tested by autosomal short tandem repeat amplification. Seven out of eight Biodur-embedded femur samples revealed successful amplification results. If Biodur-embedded bone material exists from earlier microscopic investigations, our results encourage the use of this sample type as a source for genetic research.
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14
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Ondracek RP, Chen J, Marosy B, Szewczyk S, Medico L, Mohan AS, Nair P, Pratt R, Roh JM, Khoury T, Carpten J, Kushi LH, Palmer JR, Doheny K, Davis W, Higgins MJ, Yao S, Ambrosone CB. Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study. BMC Genomics 2022; 23:614. [PMID: 36008758 PMCID: PMC9404650 DOI: 10.1186/s12864-022-08837-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of archived formalin-fixed paraffin-embedded (FFPE) tumor tissues has become a common practice in clinical and epidemiologic genetic research. Simultaneous extraction of DNA and RNA from FFPE tissues is appealing but can be practically challenging. Here we report our results and lessons learned from processing FFPE breast tumor tissues for a large epidemiologic study. METHODS Qiagen AllPrep DNA/RNA FFPE kit was adapted for dual extraction using tissue punches or sections from breast tumor tissues. The yield was quantified using Qubit and fragmentation analysis by Agilent Bioanalyzer. A subset of the DNA samples were used for genome-wide DNA methylation assays and RNA samples for sequencing. The QC metrices and performance of the assays were analyzed with pre-analytical variables. RESULTS A total of 1859 FFPE breast tumor tissues were processed. We found it critical to adjust proteinase K digestion time based on tissue volume to achieve balanced yields of DNA and RNA. Tissue punches taken from tumor-enriched regions provided the most reliable output. A median of 1475 ng DNA and 1786 ng RNA per sample was generated. The median DNA integrity number (DIN) was 3.8 and median DV200 for RNA was 33.2. Of 1294 DNA samples used in DNA methylation assays, 97% passed quality check by qPCR and 92% generated data deemed high quality. Of the 130 RNA samples with DV200 ≥ 20% used in RNA-sequencing, all but 5 generated usable transcriptomic data with a mapping rate ≥ 60%. CONCLUSIONS Dual DNA/RNA purification using Qiagen AllPrep FFPE extraction protocol is feasible for clinical and epidemiologic studies. We recommend tissue punches as a reliable source material and fine tuning of proteinase K digestion time based on tissue volume. IMPACT Our protocol and recommendations may be adapted by future studies for successful extraction of archived tumor tissues.
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Affiliation(s)
- Rochelle Payne Ondracek
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Jianhong Chen
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA.
| | - Beth Marosy
- Center for Inherited Disease Research, Johns Hopkins Genomics, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sirinapa Szewczyk
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Leonard Medico
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Amrutha Sherly Mohan
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Priya Nair
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Rachel Pratt
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Janise M Roh
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thaer Khoury
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - John Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Kim Doheny
- Center for Inherited Disease Research, Johns Hopkins Genomics, Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Michael J Higgins
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, 14263, USA
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Bleijenberg AGC, IJspeert JEG, Mulder JBG, Drillenburg P, Stel HV, Lodder EM, Carvalho B, Jansen J, Meijer G, van Eeden S, Dekker E, van Noesel CJM. The earliest events in BRAF-mutant colorectal cancer: exome sequencing of sessile serrated lesions with a tiny focus dysplasia or cancer reveals recurring mutations in two distinct progression pathways. J Pathol 2022; 257:239-249. [PMID: 35143042 PMCID: PMC9314978 DOI: 10.1002/path.5881] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/18/2022] [Accepted: 02/08/2022] [Indexed: 11/13/2022]
Abstract
Around 15–30% of colorectal cancers (CRC) develop from sessile serrated lesions (SSLs). After many years of indolent growth, SSLs can develop dysplasia and rapidly progress to CRC through events that are only partially understood. We studied molecular events at the very early stages of progression of SSLs via the MLH1‐proficient and deficient pathways to CRC. We collected a cohort of rare SSLs with a small focus (<10 mm) of dysplasia or cancer from the pathology archives of three hospitals. Whole‐exome sequencing was performed on DNA from nonprogressed and progressed components of each SSL. Putative somatic driver mutations were identified in known cancer genes that were differentially mutated in the progressed component. All analyses were stratified by MLH1 proficiency. Forty‐five lesions with a focus dysplasia or cancer were included, of which 22 (49%) were MLH1‐deficient. Lesions had a median diameter of 10 mm (interquartile range [IQR] 8–15), while the progressed component had a median diameter of 3.5 mm (IQR 1.75–4.75). Tumor mutational burden (TMB) was high in MLH1‐deficient lesions (23.9 mutations per MB) as compared to MLH1‐proficient lesions (6.3 mutations per MB). We identified 34 recurrently mutated genes in MLH1‐deficient lesions. Most prominently, ACVR2A and RNF43 were affected in 18/22 lesions, with mutations clustered in three hotspots. Most lesions with RNF43 mutations had concurrent mutations in ZNRF3. In MLH1‐proficient lesions APC (10/23 lesions) and TP53 (6/23 lesions) were recurrently mutated. Our results show that the mutational burden is exceptionally high even in the earliest MLH1‐deficient lesions. We demonstrate that hotspot mutations in ACVR2A and in the RNF43/ZNRF3 complex are extremely common in the early progression of SSLs along the MLH1‐deficient serrated pathway, while APC and TP53 mutations are early events in the the MLH1‐proficient pathway. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Arne G C Bleijenberg
- Amsterdam University Medical Centers, location AMC, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Joep E G IJspeert
- Amsterdam University Medical Centers, location AMC, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Jos B G Mulder
- Amsterdam University Medical Centers, location AMC, Department of Pathology, University of Amsterdam, the Netherlands
| | - Paul Drillenburg
- Onze Lieve Vrouwen Gasthuis (OLVG), Department of Pathology, Amsterdam, the Netherlands
| | - Herbert V Stel
- Tergooi Ziekenhuizen, Department of Pathology, Hilversum, the Netherlands
| | - Elisabeth M Lodder
- Amsterdam University Medical Centers, Core Facility Genomics, Department of Clinical Genetics, University of Amsterdam, Amsterdam, the Netherlands
| | - Beatriz Carvalho
- Netherlands Cancer Institute, Department of Pathology, Amsterdam, the Netherlands
| | - Jade Jansen
- Amsterdam University Medical Centers, location AMC, Department of Pathology, University of Amsterdam, the Netherlands
| | - Gerrit Meijer
- Netherlands Cancer Institute, Department of Pathology, Amsterdam, the Netherlands
| | - Susanne van Eeden
- Amsterdam University Medical Centers, location AMC, Department of Pathology, University of Amsterdam, the Netherlands
| | - Evelien Dekker
- Amsterdam University Medical Centers, location AMC, Department of Gastroenterology and Hepatology, Cancer Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Carel J M van Noesel
- Amsterdam University Medical Centers, location AMC, Department of Pathology, University of Amsterdam, the Netherlands
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16
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Mielonen OI, Pratas D, Hedman K, Sajantila A, Perdomo MF. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses 2022; 14:v14010133. [PMID: 35062338 PMCID: PMC8779449 DOI: 10.3390/v14010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023] Open
Abstract
Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.
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Affiliation(s)
- Outi I. Mielonen
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
| | - Diogo Pratas
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Klaus Hedman
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Maria F. Perdomo
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Correspondence:
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17
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Analyses of molecular subtypes and their association to mechanisms ofradioresistance in patients with HPV-negative HNSCC treated bypostoperative radiochemotherapy. Radiother Oncol 2022; 167:300-307. [PMID: 34999136 DOI: 10.1016/j.radonc.2021.12.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/05/2021] [Accepted: 12/31/2021] [Indexed: 11/23/2022]
Abstract
PURPOSE To assess the relation of the previously reported classification of molecular subtypes to the outcome of patients with HNSCC treated with postoperative radio(chemo)therapy (PORT-C), and to assess the association of these subtypes with gene expressions reflecting known mechanisms of radioresistance. MATERIAL AND METHODS Gene expression analyses were performed using the GeneChip Human Transcriptome Array 2.0 on a multicentre retrospective patient cohort (N=128) of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG) with locally advanced HNSCC treated with PORT-C. Tumours were assigned to four molecular subtypes, and correlation analyses between subtypes and clinical risk factors were performed. In addition, the classifications of eight genes or gene signatures related to mechanisms of radioresistance, which have previously shown an association with outcome of patients with HNSCC, were compared between the molecular subtypes. The endpoints loco-regional control (LRC) and overall survival (OS) were evaluated by log-rank tests and Cox regression. RESULTS Tumours were classified into the four subtypes basal (19.5%), mesenchymal (18.8%), atypical (15.6%) and classical (14.1%). The remaining tumours could not be classified (32.0%). Tumours of the mesenchymal subtype showed a lower LRC compared to the other subtypes (p=0.012). These tumours were associated with increased epithelial-mesenchymal transition (EMT) and overexpression of a gene signature enriched in DNA repair genes. The majority of the eight considered gene classifiers were significantly associated to LRC or OS in the whole cohort. CONCLUSION Molecular subtypes, previously identified on HNSCC patients treated with primary radio(chemo)therapy or surgery, were related to LRC for patients treated with PORT-C, where mesenchymal tumour presented with worse prognosis. After prospective validation, subtype-based patient stratification, potentially in combination with other molecular classifiers, may be considered in future interventional studies in the context of personalised radiotherapy and may guide the development of combined treatment approaches.
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18
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Mouttham L, Castelhano MG, Akey JM, Benton B, Borenstein E, Castelhano MG, Coleman AE, Creevy KE, Crowder K, Dunbar MD, Ernst HR, Fajt VR, Fitzpatrick AL, Garrison SJ, Herndon RS, Jaramilla D, Jeffery U, Jonlin EC, Kaeberlein M, Karlsson EK, Kerr KF, Levine JM, Ma J, McClelland RL, Prescott JO, Promislow DEL, Ruple A, Schwartz SM, Shrager S, Snyder-Mackler N, Tinkle AK, Tolbert MK, Urfer SR, Wilfond BS. Purpose, Partnership, and Possibilities: The Implementation of the Dog Aging Project Biobank. Biomark Insights 2022; 17:11772719221137217. [PMID: 36468152 PMCID: PMC9716607 DOI: 10.1177/11772719221137217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Biobanks have been supporting longitudinal prospective and retrospective studies by providing standardized services for the acquisition, transport, processing, storage, and distribution of high-quality biological material and associated data. Here, we describe how the Dog Aging Project (DAP), a large-scale longitudinal study of the domestic dog ( Canis familiaris) with translational applications for humans, developed a biobank of canine biospecimens and associated data. Design and methods: This was accomplished by working with the Cornell Veterinary Biobank, the first biobank in the world to receive accreditation to ISO 20387:2018—General Requirements for Biobanking. The biobank research team was involved in the early collection stages of the DAP, contributing to the development of appropriate workflows and processing fit-for-purpose biospecimens. In support of a dynamic strategy for real-time adjustment of processes, a pilot phase was implemented to develop, test, and optimize the biospecimen workflows, followed by an early phase of collection, processing, and banking of specimens from DAP participants. Results: During the pilot and early phases of collection, the DAP Biobank stored 164 aliquots of whole blood, 273 aliquots of peripheral blood mononuclear cells, 130 aliquots of plasma, and 70 aliquots of serum, and extracted high molecular weight genomic DNA suitable for whole-genome sequencing from 109 whole blood specimens. These specimens, along with their associated preanalytical data, have been made available for distribution to researchers. Conclusion: We discuss the challenges and opportunities encountered during the implementation of the DAP Biobank, along with novel strategies for promoting biobanking sustainability such as partnering with a DAP quality assurance manager and a DAP marketing and communication specialist and developing a pilot grant structure to fund small innovative research projects.
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Affiliation(s)
- Lara Mouttham
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Marta G Castelhano
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Joshua M Akey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Brooke Benton
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elhanan Borenstein
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- Santa Fe Institute, Santa Fe, NM, USA
| | - Marta G Castelhano
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Amanda E Coleman
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Kate E Creevy
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Kyle Crowder
- Department of Sociology, University of Washington, Seattle, WA, USA
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA
| | - Matthew D Dunbar
- Center for Studies in Demography and Ecology, University of Washington, Seattle, WA, USA
| | - Holley R Ernst
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Virginia R Fajt
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Annette L Fitzpatrick
- Department of Family Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Susan J Garrison
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Reba S Herndon
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Debra Jaramilla
- Cornell Veterinary Biobank, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Unity Jeffery
- Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Erica C Jonlin
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elinor K Karlsson
- Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jonathan M Levine
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Jing Ma
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Jena O Prescott
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Daniel EL Promislow
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Audrey Ruple
- Department of Population Health Sciences, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Stephen M Schwartz
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Epidemiology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sandi Shrager
- Collaborative Health Studies Coordinating Center, Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Noah Snyder-Mackler
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- School for Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Amanda K Tinkle
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - M Katherine Tolbert
- Department of Small Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Silvan R Urfer
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children’s Research Institute, Seattle, WA, USA
- Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington School of Medicine, Seattle, WA, USA
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Oba U, Kohashi K, Sangatsuda Y, Oda Y, Sonoda KH, Ohga S, Yoshimoto K, Arai Y, Yachida S, Shibata T, Ito T, Miura F. An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections. Biol Methods Protoc 2022; 7:bpac014. [PMID: 35937639 PMCID: PMC9351614 DOI: 10.1093/biomethods/bpac014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
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Affiliation(s)
- Utako Oba
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
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20
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Ricci G, Campanini EB, Nishikaku AS, Puccia R, Marques M, Bialek R, Rodrigues AM, Batista WL. PbGP43 Genotyping Using Paraffin-Embedded Biopsies of Human Paracoccidioidomycosis Reveals a Genetically Distinct Lineage in the Paracoccidioides brasiliensis Complex. Mycopathologia 2021; 187:157-168. [PMID: 34870754 DOI: 10.1007/s11046-021-00608-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Paracoccidioidomycosis (PCM) is a systemic mycosis caused by a group of cryptic species embedded in the Paracoccidioides brasiliensis complex and Paracoccidioides lutzii. Four species were recently inferred to belong to the P. brasiliensis complex, but the high genetic diversity found in both human and environmental samples have suggested that the number of lineages may be higher. This study aimed to assess the 43-kilodalton glycoprotein genotypes (PbGP43) in paraffin-embedded samples from PCM patients to infer the phylogenetic lineages of the P. brasiliensis complex responsible for causing the infection. Formalin-fixed, paraffin-embedded (FFPE) tissue samples from patients with histopathological diagnosis of PCM were analyzed. DNAs were extracted and amplified for a region of the second exon of the PbGP43 gene. Products were sequenced and aligned with other PbGP43 sequences available. A haplotype network and the phylogenetic relationships among sequences were inferred. Amino acid substitutions were investigated regarding the potential to modify physicochemical properties in the proteins. Six phylogenetic lineages were identified as belonging to the P. brasiliensis complex. Two lineages did not group with any of the four recognized species of the complex, and, interestingly, one of them comprised only FFPE samples. A coinfection involving two lineages was found. Five parsimony-informative sites were identified and three of them showed radical non-synonymous substitutions with the potential to promote changes in the protein. This study expands the knowledge regarding the genetic diversity existing in the P. brasiliensis complex and shows the potential of FFPE samples in species identification and in detecting coinfections.
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Affiliation(s)
- Giannina Ricci
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr Ivo Ricci, São Carlos, SP, Brazil.
- Departamento de Patologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Angela Satie Nishikaku
- Centro de Diagnóstico e Pesquisa em Biologia Molecular Dr Ivo Ricci, São Carlos, SP, Brazil
| | - Rosana Puccia
- Disciplina de Biologia Celular, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Mariângela Marques
- Faculdade de Medicina de Botucatu, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Ralf Bialek
- LADR GmbH MVZ Dr, Kramer & Kollegen, Lauenburger Straße 67, 21502, Geesthacht, Germany
| | - Anderson Messias Rodrigues
- Disciplina de Biologia Celular, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Wagner Luiz Batista
- Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo, Campus Diadema, São Paulo, SP, Brazil
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21
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Tellaetxe-Abete M, Calvo B, Lawrie C. Ideafix: a decision tree-based method for the refinement of variants in FFPE DNA sequencing data. NAR Genom Bioinform 2021; 3:lqab092. [PMID: 34729472 PMCID: PMC8557387 DOI: 10.1093/nargab/lqab092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/14/2021] [Accepted: 09/29/2021] [Indexed: 12/16/2022] Open
Abstract
Increasingly, treatment decisions for cancer patients are being made from next-generation sequencing results generated from formalin-fixed and paraffin-embedded (FFPE) biopsies. However, this material is prone to sequence artefacts that cannot be easily identified. In order to address this issue, we designed a machine learning-based algorithm to identify these artefacts using data from >1 600 000 variants from 27 paired FFPE and fresh-frozen breast cancer samples. Using these data, we assembled a series of variant features and evaluated the classification performance of five machine learning algorithms. Using leave-one-sample-out cross-validation, we found that XGBoost (extreme gradient boosting) and random forest obtained AUC (area under the receiver operating characteristic curve) values >0.86. Performance was further tested using two independent datasets that resulted in AUC values of 0.96, whereas a comparison with previously published tools resulted in a maximum AUC value of 0.92. The most discriminating features were read pair orientation bias, genomic context and variant allele frequency. In summary, our results show a promising future for the use of these samples in molecular testing. We built the algorithm into an R package called Ideafix (DEAmination FIXing) that is freely available at https://github.com/mmaitenat/ideafix.
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Affiliation(s)
| | - Borja Calvo
- Intelligent Systems Group, Computer Science Faculty, University of the Basque Country, Paseo Manuel Lardizabal, 20018 Donostia/San Sebastian, Spain
| | - Charles Lawrie
- Correspondence may also be addressed to Charles Lawrie. Tel: +34 943 006138;
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22
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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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23
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Wong K, Ludwig L, Krijgsman O, Adams DJ, Wood GA, van der Weyden L. Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma. Dis Model Mech 2021; 14:dmm049044. [PMID: 34296746 PMCID: PMC8319545 DOI: 10.1242/dmm.049044] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Angiosarcoma (AS) is a highly aggressive tumor of blood and lymphatic vessels in humans that shares many similarities with spontaneously occurring hemangiosarcoma (HSA) in dogs and cats. To investigate the genetic suitability of HSA as a model for AS, we sequenced ∼1000 cancer genes in 41 cases of HSA and matched germline tissue: 15 canine visceral HSAs, 13 canine skin HSAs and 13 feline skin HSAs. Analysis of visceral HSAs from dogs presenting with concurrent splenic and cardiac neoplasms showed that the tumors were not independent primaries, consistent with the highly metastatic nature of HSA. Comparison of HSA to AS revealed that several driver genes were recurrently mutated in both species, such as TP53, PIK3CA, ATRX, GRIN2A and LRP1B. Similar to AS, a UV mutational signature was found in a subset of canine cutaneous HSAs and both species show differing mutational profiles between tissue sites. Our characterization of canine and feline HSA demonstrates many important parallels to AS and provides hope that future studies on these cancers will benefit of all three species.
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Affiliation(s)
- Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Latasha Ludwig
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
| | - Oscar Krijgsman
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Geoffrey A. Wood
- Department of Pathobiology, University of Guelph, 50 Stone Road E., Guelph, ON N1G 2W1, Canada
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24
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Yuan Y, Van Dyke AL, Petkov VI, Hussey S, Moravec R, Altekruse SF, Sandoval M, Cress RD, Mueller LM, Mogi A, Hernandez BY, Selk FR, Lynch CF, Tucker TC, Lynch MA, Lefante C, Wu XC, Sweeney C, Doherty JA, Penberthy LS. Pathology Laboratory Policies and Procedures for Releasing Diagnostic Tissue for Cancer Research. Arch Pathol Lab Med 2021; 145:222-226. [PMID: 33501497 PMCID: PMC8135254 DOI: 10.5858/arpa.2019-0474-oa] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The Surveillance, Epidemiology, and End Results (SEER) cancer registry program is currently evaluating the use of archival, diagnostic, formalin-fixed, paraffin-embedded (FFPE) tissue obtained through SEER cancer registries, functioning as honest brokers for deidentified tissue and associated data. To determine the feasibility of this potential program, laboratory policies for sharing tissue for research needed to be assessed. OBJECTIVE.— To understand the willingness of pathology laboratories to share archival diagnostic tissue for cancer research and related policies. DESIGN.— Seven SEER registries administered a 27-item questionnaire to pathology laboratories within their respective registry catchment areas. Only laboratories that processed diagnostic FFPE specimens and completed the questionnaire were included in the analysis. RESULTS.— Of the 153 responding laboratories, 127 (83%) responded that they process FFPE specimens. Most (n = 88; 69%) were willing to share tissue specimens for research, which was not associated with the number of blocks processed per year by the laboratories. Most laboratories retained the specimens for at least 10 years. Institutional regulatory policies on sharing deidentified tissue varied considerably, ranging from requiring a full Institutional Review Board review to considering such use exempt from Institutional Review Board review, and 43% (55 of 127) of the laboratories did not know their terms for sharing tissue for research. CONCLUSIONS.— This project indicated a general willingness of pathology laboratories to participate in research by sharing FFPE tissue. Given the variability of research policies across laboratories, it is critical for each SEER registry to work with laboratories in their catchment area to understand such policies and state legislation regulating tissue retention and guardianship.
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Affiliation(s)
- Yao Yuan
- The Surveillance Research Program, Division of Cancer Control and Population Sciences (Yuan, Van Dyke, Petkov, Hussey, Penberthy), National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Alison L Van Dyke
- The Surveillance Research Program, Division of Cancer Control and Population Sciences (Yuan, Van Dyke, Petkov, Hussey, Penberthy), National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Valentina I Petkov
- The Surveillance Research Program, Division of Cancer Control and Population Sciences (Yuan, Van Dyke, Petkov, Hussey, Penberthy), National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Sarah Hussey
- The Surveillance Research Program, Division of Cancer Control and Population Sciences (Yuan, Van Dyke, Petkov, Hussey, Penberthy), National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Radim Moravec
- The Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis (Moravec), National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Sean F Altekruse
- The HIV/AIDS Program, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland (Altekruse)
| | - Mayra Sandoval
- The Cancer Registry of Greater California, Department of Public Health, Sacramento (Sandoval, Cress)
| | - Rosemary D Cress
- The Cancer Registry of Greater California, Department of Public Health, Sacramento (Sandoval, Cress)
| | - Lloyd M Mueller
- The Connecticut Tumor Registry, State Department of Public Health, Hartford (Mueller)
| | - Alan Mogi
- The Hawaii Tumor Registry, University of Hawaii Cancer Center, Honolulu (Mogi, Hernandez)
| | - Brenda Y Hernandez
- The Hawaii Tumor Registry, University of Hawaii Cancer Center, Honolulu (Mogi, Hernandez)
| | - Freda R Selk
- The Iowa Cancer Registry, The University of Iowa, Iowa City (Selk, Lynch)
| | - Charles F Lynch
- The Iowa Cancer Registry, The University of Iowa, Iowa City (Selk, Lynch)
| | - Thomas C Tucker
- The Kentucky Cancer Registry, University of Kentucky, Markey Cancer Center, Lexington (Tucker)
| | - Mary Anne Lynch
- The Louisiana Tumor Registry, Louisiana State University School of Public Health, New Orleans (Lynch, Lefante, Wu)
| | - Christina Lefante
- The Louisiana Tumor Registry, Louisiana State University School of Public Health, New Orleans (Lynch, Lefante, Wu)
| | - Xiao-Cheng Wu
- The Louisiana Tumor Registry, Louisiana State University School of Public Health, New Orleans (Lynch, Lefante, Wu)
| | | | - Jennifer A Doherty
- The Utah Cancer Registry (Sweeney, Doherty)
- Huntsman Cancer Institute (Doherty), University of Utah, Salt Lake City
| | - Lynne S Penberthy
- The Surveillance Research Program, Division of Cancer Control and Population Sciences (Yuan, Van Dyke, Petkov, Hussey, Penberthy), National Cancer Institute, National Institutes of Health, Rockville, Maryland
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25
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Major driver mutations are shared between sinonasal intestinal-type adenocarcinoma and the morphologically identical colorectal adenocarcinoma. J Cancer Res Clin Oncol 2020; 147:1019-1027. [PMID: 33051725 DOI: 10.1007/s00432-020-03421-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022]
Abstract
PURPOSE The purpose of our study was to compare genomic changes in sinonasal intestinal-type adenocarcinoma (sITAC) and colorectal adenocarcinoma (CRC), as they are histomorphologically indistinguishable. This can cause diagnostic difficulties as sinonasal tumours initially diagnosed as sITAC may represent metastasis from CRC, a frequent cancer. Previous studies have not uncovered the underlying mechanism behind the histomorphological resemblance. METHODS/PATIENTS Tissue samples from all consecutive patients with sITAC at our facility (20 patients) were compared to samples from 20 patients with CRC as well as samples from 2 patients with both CRC and sinonasal tumours. DNA sequencing was performed using Illumina TruSight Oncology 500 panel consisting of 523 cancer-associated genes. Frequent mutations were inspected manually using the Integrative Genomics Viewer. RESULTS Several well-known cancer-associated genes were mutated in the CRC group, but also in the sinonasal ITAC group. These genes included APC mutated in 65% of the CRC group and 37% of the sinonasal ITAC group, and TP53 mutated in 65% of CRC samples and 58% of ITAC samples. These shared mutations may explain the histomorphological similarities. Successful DNA sequencing was performed on the colorectal sample from one of the two patients with both CRC and sinonasal tumour. Comparing mutations in these samples from one patient we have shown that the sinonasal tumour in all probability was a CRC metastasis. CONCLUSION We have identified several genetic similarities between sITAC and CRC. This discovery brings us closer to understanding mechanisms behind the development of sITAC-and hopefully in the future targeted therapy.
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26
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Mathieson W, Thomas GA. Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion. J Histochem Cytochem 2020; 68:543-552. [PMID: 32697619 PMCID: PMC7400666 DOI: 10.1369/0022155420945050] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fresh-frozen tissue is the “gold standard” biospecimen type for next-generation sequencing (NGS). However, collecting frozen tissue is usually not feasible because clinical workflows deliver formalin-fixed, paraffin-embedded (FFPE) tissue blocks. Some clinicians and researchers are reticent to embrace the use of FFPE tissue for NGS because FFPE tissue can yield low quantities of degraded DNA, containing formalin-induced mutations. We describe the process by which formalin-induced deamination can lead to artifactual cytosine (C) to thymine (T) and guanine (G) to adenine (A) (C:G > T:A) mutation calls and perform a literature review of 17 publications that compare NGS data from patient-matched fresh-frozen and FFPE tissue blocks. We conclude that although it is indeed true that sequencing data from FFPE tissue can be poorer than those from frozen tissue, any differences occur at an inconsequential magnitude, and FFPE biospecimens can be used in genomic medicine with confidence:
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27
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Youssef O, Almangush A, Zidi YHS, Loukola A, Carpén O. Nonmalignant Formalin-Fixed Paraffin-Embedded Tissues as a Source to Study Germline Variants and Cancer Predisposition: A Systematic Review. Biopreserv Biobank 2020; 18:337-345. [PMID: 32551987 DOI: 10.1089/bio.2020.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Archived formalin-fixed paraffin-embedded (FFPE) specimens from nonmalignant tissues derived from cancer patients are a vast and potentially valuable resource for high-quality genotyping analyses and could have a role in establishing inherited cancer risk. Methods: We systematically searched PubMed, Ovid MEDLINE, and Scopus databases for all articles that compared genotyping performance of DNA from nonmalignant FFPE tissue with blood DNA derived from cancer patients irrespective of tumor type. Two independent researchers screened the retrieved studies, removed duplicates, excluded irrelevant studies, and extracted genotyping data from the eligible studies. These studies included, but were not limited to, genotyping technique, reported call rate, and concordance. Results: Thirteen studies were reviewed, in which DNA from nonmalignant FFPE tissues derived from cancer patients was successfully purified and genotyped. All these studies used different approaches for genotyping of DNA from nonmalignant FFPE tissues to amplify single nucleotide polymorphisms (SNPs) and to estimate of loss of heterozygosity. The concordance between genotypes from nonmalignant FFPE tissues and blood derived from cancer patients was observed to be high, whereas the call rate of the tested SNPs was not reported in all included studies. Conclusion: This review illustrates that DNA from nonmalignant FFPE tissues derived from cancer patients can serve as an alternative and reliable source for assessment of germline DNA for various purposes, including assessment of cancer predisposition.
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Affiliation(s)
- Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alhadi Almangush
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Pathology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Yossra H S Zidi
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Helsinki Biobank, HUS Helsinki University Hospital, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, University of Helsinki, Helsinki, Finland.,Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Helsinki Biobank, HUS Helsinki University Hospital, Helsinki, Finland
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28
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Frazer Z, Yoo C, Sroya M, Bellora C, DeWitt BL, Sanchez I, Thomas GA, Mathieson W. Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue. J Histochem Cytochem 2020; 68:171-184. [PMID: 32043912 DOI: 10.1369/0022155420906234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA extracted from formalin-fixed, paraffin-embedded tissue sections is often inadequate for sequencing, due to poor yield or degradation. We optimized the proteinase K digest by testing increased volume of enzyme and increased digest length from the manufacturer's protocol using 54 biospecimens, performing the digest in centrifuge tubes. Doubling the quantity of proteinase K resulted in a median increase in yield of 96%. Applying the optimized proteinase K protocol to sections deparaffinized on microscope slides generated a further increase in yield of 41%, but only at >50,000 epithelial tumor cells/section. DNA yield now correlated with (χ2 = 0.84) and could be predicted from the epithelial tumor cell number. DNA integrity was assayed using end point multiplex PCR (amplicons of 100-400 bp visualized on a gel), quantitative PCR (qPCR; Illumina FFPE QC Assay), and nanoelectrophoresis (DNA Integrity Numbers [DINs]). Generally, increases in yield were accompanied by increases in integrity, but sometimes qPCR and DIN results were conflicting. Amplicons of 400 bp were almost universally obtained. The process of optimization enabled us to reduce the percentage of samples that failed published quality control thresholds for determining amenability to whole genome sequencing from 33% to 7%.
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Affiliation(s)
- Zoe Frazer
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Changyoung Yoo
- Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Pathology, The Catholic University of Korea, St. Vincent's Hospital, Seoul, Korea
| | - Manveer Sroya
- Department of Surgery and Cancer, Imperial College London, London, UK
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29
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Muscarella LA, Fabrizio FP, De Bonis M, Mancini MT, Balsamo T, Graziano P, Centra F, Sparaneo A, Trombetta D, Bonfitto A, Scagliusi V, Larizza P, Capoluongo ED, Fazio VM. Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics. Cancers (Basel) 2019; 11:cancers11111691. [PMID: 31671666 PMCID: PMC6896097 DOI: 10.3390/cancers11111691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/27/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, timing and quality-control. We firstly evaluated DNA recovery from archived FFPE blocks from three different manual extraction methods and two automated extraction workstations. The workflow was then implemented to somatic (lung/colon panel) and germline (BRCA1/2) library preparation for NGS analysis exploiting two automated workstations. All commercial kits gave good results in terms of DNA yield and quality. On the other hand, the automated workstation workflow has been proven to be a valid automatic extraction system to obtain high quality DNA suitable for NGS analysis (lung/colon Ampli-seq panel). Moreover, it can be efficiently integrated with an open liquid handling platform to provide high-quality libraries from germline DNA with more reproducibility and high coverage for targeted sequences in less time (BRCA1/2). The introduction of automation in routine workflow leads to an improvement of NGS standardization and increased scale up of sample preparations, reducing labor and timing, with optimization of reagents and management.
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Affiliation(s)
- Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Maria De Bonis
- Department of Laboratory Medicine of the 'Agostino Gemelli' Foundation in Rome, 00168 Rome, Italy.
| | | | - Teresa Balsamo
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Flavia Centra
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | - Antonio Bonfitto
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
| | | | | | - Ettore Domenico Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II-CEINGE, 80145 Naples, Italy.
| | - Vito Michele Fazio
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, (FG), Italy.
- Department of Medicine, R.U. in Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy.
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Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, Davila JI, Vierkant RA, Hoskin TL, Frost M, Carter JM, Radisky DC, Cunningham JM, Degnim AC, Wang C. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Genomics 2019; 20:689. [PMID: 31477010 PMCID: PMC6720378 DOI: 10.1186/s12864-019-6056-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/22/2019] [Indexed: 01/20/2023] Open
Abstract
Background Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples. Results As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts. For FFPE samples, we tested two FFPE DNA extraction methods to determine impact of wet-lab procedures on variant calling: QIAGEN QIAamp DNA Mini Kit (“QA”), and QIAGEN GeneRead DNA FFPE Kit (“QGR”). We also used negative-control (NA12891) and positive control samples (Horizon Discovery Reference Standard FFPE). All DNA sample libraries were prepared for NGS according to the QIAseq Human Breast Cancer Targeted DNA Panel protocol and sequenced on the HiSeq 4000. Variant calling and filtering were performed using QIAGEN Gene Globe Data Portal. Detailed variant concordance comparisons and mutational signature analysis were performed to investigate effects of FFPE samples compared to paired fresh frozen samples, along with different DNA extraction methods. In this study, we found that five times or more variants were called with FFPE samples, compared to their paired fresh-frozen tissue samples even after applying molecular barcoding error-correction and default bioinformatics filtering recommended by the vendor. We also found that QGR as an optimized FFPE-DNA extraction approach leads to much fewer discordant variants between paired fresh frozen and FFPE samples. Approximately 92% of the uniquely called FFPE variants were of low allelic frequency range (< 5%), and collectively shared a “C > T|G > A” mutational signature known to be representative of FFPE artifacts resulting from cytosine deamination. Based on control samples and FFPE-frozen replicates, we derived an effective filtering strategy with associated empirical false-discovery estimates. Conclusions Through this study, we demonstrated feasibility of calling and filtering genetic variants from FFPE tissue samples using a combined strategy with molecular barcodes, optimized DNA extraction, and bioinformatics methods incorporating genomics context such as mutational signature and variant allelic frequency. Electronic supplementary material The online version of this article (10.1186/s12864-019-6056-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya Vijay Bhagwate
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Yuanhang Liu
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Stacey J Winham
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Samantha J McDonough
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | | | - Ethan P Heinzen
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jaime I Davila
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Robert A Vierkant
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Tanya L Hoskin
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Marlene Frost
- Departments of Medical Oncology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Jodi M Carter
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Derek C Radisky
- Departments of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Julie M Cunningham
- Departments of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Amy C Degnim
- Departments of Surgery, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA
| | - Chen Wang
- Departments of Health Science Research, Mayo Clinic, 200 1st Street SW, Rochester, MN, 55905, USA.
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Mombaerts I, Ramberg I, Coupland SE, Heegaard S. Diagnosis of orbital mass lesions: clinical, radiological, and pathological recommendations. Surv Ophthalmol 2019; 64:741-756. [PMID: 31276737 DOI: 10.1016/j.survophthal.2019.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023]
Abstract
The orbit can harbor mass lesions of various cellular origins. The symptoms vary considerably according to the nature, location, and extent of the disease and include common signs of proptosis, globe displacement, eyelid swelling, and restricted eye motility. Although radiological imaging tools are improving, with each imaging pattern having its own differential diagnosis, orbital mass lesions often pose a diagnostic challenge. To provide an accurate, specific, and sufficiently comprehensive diagnosis, to optimize clinical management and estimate prognosis, pathological examination of a tissue biopsy is essential. Diagnostic orbital tissue biopsy is obtained through a minimally invasive orbitotomy procedure or, in selected cases, fine needle aspiration. The outcome of successful biopsy, however, is centered on its representativeness, processing, and interpretation. Owing to the often small volume of the orbital biopsies, artifacts in the specimens should be limited by careful peroperative tissue handling, fixation, processing, and storage. Some orbital lesions can be characterized on the basis of cytomorphology alone, whereas others need ancillary molecular testing to render the most reliable diagnosis of therapeutic, prognostic, and predictive value. Herein, we review the diagnostic algorithm for orbital mass lesions, using clinical, radiological, and pathological recommendations, and discuss the methods and potential pitfalls in orbital tissue biopsy acquisition and analysis.
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Affiliation(s)
- Ilse Mombaerts
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium.
| | - Ingvild Ramberg
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sarah E Coupland
- Department of Cellular and Molecular Pathology, University of Liverpool, Liverpool, UK; Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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32
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Akahane T, Yamaguchi T, Kato Y, Yokoyama S, Hamada T, Nishida Y, Higashi M, Nishihara H, Suzuki S, Ueno S, Tanimoto A. Comprehensive validation of liquid-based cytology specimens for next-generation sequencing in cancer genome analysis. PLoS One 2019; 14:e0217724. [PMID: 31199826 PMCID: PMC6568385 DOI: 10.1371/journal.pone.0217724] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/07/2019] [Indexed: 12/20/2022] Open
Abstract
In addition to conventional cytology, liquid-based cytology (LBC) is also used for immunocytochemistry and gene analysis. However, an appropriate method to obtain high quality DNA for next-generation sequencing (NGS) using LBC specimens remains controversial. We determined the optimal conditions for fixation with an alcohol-based fixative for LBC and DNA extraction using cultured cancer cell lines and clinical specimens. The extracted DNA was processed for NGS after the DNA quality was confirmed based on the DNA concentration and degree of degradation. The optimal conditions for cultured cells to obtain high quality DNA were to fix the cells at a density of 6 × 103 or 2 × 104 cells/mL and to use the magnetic bead-based DNA extraction method. Even after storing the fixed cells for 90 days, DNA extracted using the above and other extraction kits, including membrane-based methods, did not undergo degradation. Furthermore, 5-year-old residual LBC samples demonstrated high DNA quality that was suitable for NGS. Furthermore, a cancer genome panel analysis was successfully performed with DNA extracted from cultured cells fixed at 6 × 103 cells/mL for 90 days, and with DNA from residual LBC samples even after 1 year of storage. Residual LBC samples may be a useful source of DNA for clinical NGS to promote genome-based cancer medicine.
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Affiliation(s)
- Toshiaki Akahane
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
| | - Tomomi Yamaguchi
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Yasutaka Kato
- Department of Pathology, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
| | - Seiya Yokoyama
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Taiji Hamada
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yukari Nishida
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Michiyo Higashi
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Japan
- Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Shinsuke Suzuki
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Shinichi Ueno
- Department of Clinical Cancer Research, Kagoshima University Graduate School of Medical and Dental Sciences, 890–8544 Kagoshima, Japan
- Kagoshima University Hospital Cancer Center, Kagoshima University Hospital, Kagoshima, Japan
| | - Akihide Tanimoto
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
- Center for Human Genome and Gene Analysis, Kagoshima University Hospital, Kagoshima, Japan
- Department Surgical Pathology, Kagoshima University Hospital, Kagoshima, Japan
- * E-mail:
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Zar G, Smith JG, Smith ML, Andersson B, Nilsson J. Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation. PLoS One 2019; 14:e0217747. [PMID: 31166960 PMCID: PMC6550412 DOI: 10.1371/journal.pone.0217747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) of heart transplant recipient- and donor-derived cardiac biopsies may facilitate organ matching, graft failure prediction, and immunotolerance research. The objective of this study was to determine the feasibility of WGS based on formalin-fixed paraffin-embedded endomyocardial biopsies. METHODS AND RESULTS The study included serial donor- and recipient samples from patients who had undergone heart transplantation at Skane University Hospital, Lund, Sweden, between 1988 and 2009. DNA extraction and WGS were conducted. Additional WGS sequencing quality metrics and coverage were obtained with the Genome Analysis Toolkit (GATK). 455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples. They were analyzed after 3-26 years of storage. DNA was extracted from 114 samples and WGS was run on 85 samples. DNA extraction yielded 313 ng (IQR 96-601) for all samples. A coverage of 11.3x (IQR 9.0-15.9) was recorded for all WGS samples. Three samples stored for > 25 years yielded a coverage of > 25x. Data were generated for 1.7 billion reads per sample (IQR 1.4-2.7). A Transition/Transversion (TiTv) ratio of 2.09 ± 0.05 was calculated for all WGS samples. No associations were found among storage time, DNA yield, or sequencing quality metrics. CONCLUSIONS The present study demonstrated the feasibility of whole-genome sequencing based on endomyocardial biopsies. This process could enable large-scale retrospective genomic studies using stored histopathological samples.
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Affiliation(s)
- Gustav Zar
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - J. Gustav Smith
- Department of Clinical Sciences, Cardiology, Lund University and Skane University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Maya Landenhed Smith
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Bodil Andersson
- Department of Clinical Sciences Lund, Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Johan Nilsson
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
- * E-mail:
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Mathieson W, Thomas G. Using FFPE Tissue in Genomic Analyses: Advantages, Disadvantages and the Role of Biospecimen Science. CURRENT PATHOBIOLOGY REPORTS 2019. [DOI: 10.1007/s40139-019-00194-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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McDonough SJ, Bhagwate A, Sun Z, Wang C, Zschunke M, Gorman JA, Kopp KJ, Cunningham JM. Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods. PLoS One 2019; 14:e0211400. [PMID: 30973937 PMCID: PMC6459541 DOI: 10.1371/journal.pone.0211400] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/20/2019] [Indexed: 12/25/2022] Open
Abstract
Archival tissues represent a rich resource for clinical genomic studies, particularly when coupled with comprehensive medical records. Use of these in next generation sequencing (NGS) is a priority. Nine formalin-fixed paraffin-embedded (FFPE) DNA extraction methods were evaluated using twelve FFPE samples of varying tissue types. Quality assessment included total yield, percent dsDNA, fragment analysis and multiplex PCR. After assessment, three tissue types from four FFPE DNA methods were selected for NGS downstream evaluation, targeted and whole exome sequencing. In addition, two low input library protocols were evaluated for WES. Analysis revealed average coverage across the target regions for WES was ~20-30X for all four FFPE DNA extraction methods. For the targeted panels, the highest molecular tag coverage was obtained with the Kingfisher FFPE extraction method. The genotype concordance was 99% for the commonly called variant positions between all four extraction methods with the targeted PCR NGS panel and 96% with WES. Assessing quality of extracted DNA aids in selecting the optimal NGS approach, and the choice of both DNA extraction and library preparation approaches can impact the performance of archival tissue in NGS.
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Affiliation(s)
- Samantha J. McDonough
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Aditya Bhagwate
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Zhifu Sun
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Chen Wang
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Michael Zschunke
- Pathology Research Core, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Joshua A. Gorman
- Pathology Research Core, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Karla J. Kopp
- Pathology Research Core, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Julie M. Cunningham
- Medical Genome Facility, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
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Bai Y, Wang G, Wei J, Dai C, Xu X, Cai X, Wu B, Sun W, Xu Q, Jiao S. Using clinical genomic sequencing to guide personalized cancer therapy in China. Per Med 2019; 16:287-299. [PMID: 30895868 DOI: 10.2217/pme-2018-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To evaluate whether clinical genomic sequencing may benefit Chinese patients with stage IV cancer. Patients & methods: Chinese patients with cancer and their oncologists were provided with genomic sequencing results and corresponding clinical treatment recommendations based on evidence-based medicine, defined as CWES (clinical whole-exome sequencing) analysis. Chinese patients with stage IV cancer who failed the previous treatment upon receiving the CWES reports were included for analyzing the impact of CWES on clinical outcomes in 1-year follow-ups. Results: A total of 88.6% of 953 Chinese patients with cancer had clinically actionable somatic genomic alterations. Eleven patients followed the CWES reports, and 11 patients did not follow the CWES suggestions. The median progression-free survival of two groups were 12 and 4 months, and 45 and 91% of patients failed this round of therapy, respectively. Conclusion: The current study suggested that CWES has the potential to increase clinical benefits for Chinese patients with stage IV cancer.
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Affiliation(s)
- Yuxian Bai
- Department of Digestive Internal Medicine & Photodynamic Therapy Center, Harbin Medical University Cancer Hospital
| | - Guan Wang
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Jinwang Wei
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Xiaoman Xu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Xin Cai
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Bing Wu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Wending Sun
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Qiang Xu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Shunchang Jiao
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing
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Hulsen T, Jamuar SS, Moody AR, Karnes JH, Varga O, Hedensted S, Spreafico R, Hafler DA, McKinney EF. From Big Data to Precision Medicine. Front Med (Lausanne) 2019; 6:34. [PMID: 30881956 PMCID: PMC6405506 DOI: 10.3389/fmed.2019.00034] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 02/04/2019] [Indexed: 02/05/2023] Open
Abstract
For over a decade the term "Big data" has been used to describe the rapid increase in volume, variety and velocity of information available, not just in medical research but in almost every aspect of our lives. As scientists, we now have the capacity to rapidly generate, store and analyse data that, only a few years ago, would have taken many years to compile. However, "Big data" no longer means what it once did. The term has expanded and now refers not to just large data volume, but to our increasing ability to analyse and interpret those data. Tautologies such as "data analytics" and "data science" have emerged to describe approaches to the volume of available information as it grows ever larger. New methods dedicated to improving data collection, storage, cleaning, processing and interpretation continue to be developed, although not always by, or for, medical researchers. Exploiting new tools to extract meaning from large volume information has the potential to drive real change in clinical practice, from personalized therapy and intelligent drug design to population screening and electronic health record mining. As ever, where new technology promises "Big Advances," significant challenges remain. Here we discuss both the opportunities and challenges posed to biomedical research by our increasing ability to tackle large datasets. Important challenges include the need for standardization of data content, format, and clinical definitions, a heightened need for collaborative networks with sharing of both data and expertise and, perhaps most importantly, a need to reconsider how and when analytic methodology is taught to medical researchers. We also set "Big data" analytics in context: recent advances may appear to promise a revolution, sweeping away conventional approaches to medical science. However, their real promise lies in their synergy with, not replacement of, classical hypothesis-driven methods. The generation of novel, data-driven hypotheses based on interpretable models will always require stringent validation and experimental testing. Thus, hypothesis-generating research founded on large datasets adds to, rather than replaces, traditional hypothesis driven science. Each can benefit from the other and it is through using both that we can improve clinical practice.
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Affiliation(s)
- Tim Hulsen
- Department of Professional Health Solutions and Services, Philips Research, Eindhoven, Netherlands
- *Correspondence: Tim Hulsen
| | - Saumya S. Jamuar
- Department of Paediatrics, KK Women's and Children's Hospital, and Paediatric Academic Clinical Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Alan R. Moody
- Department of Medical Imaging, University of Toronto, Toronto, ON, Canada
| | - Jason H. Karnes
- Pharmacy Practice and Science, College of Pharmacy, University of Arizona Health Sciences, Phoenix, AZ, United States
| | - Orsolya Varga
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Stine Hedensted
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - Eoin F. McKinney
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Eoin F. McKinney
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Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests. Biotechniques 2018; 65:79-85. [PMID: 30091391 DOI: 10.2144/btn-2018-0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parameters.
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