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Chierto E, Aneli S, Nocco N, Riem A, Onofri M, Carnevali E, Robino C. Assessing DNA Degradation through Differential Amplification Efficiency of Total Human and Human Male DNA in a Forensic qPCR Assay. Genes (Basel) 2024; 15:622. [PMID: 38790251 PMCID: PMC11120943 DOI: 10.3390/genes15050622] [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: 04/15/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
The assessment of degradation is crucial for the analysis of human DNA samples isolated from forensic specimens. Forensic quantitative PCR (qPCR) assays can include multiple targets of varying amplicon size that display differential amplification efficiency, and thus different concentrations, in the presence of degradation. The possibility of deriving information on DNA degradation was evaluated in a forensic qPCR assay not specifically designed to detect DNA fragmentation, the Plexor HY (Promega), by calculating the ratio between the estimated concentrations of autosomal (99 bp) and Y-chromosomal (133 bp) targets ("[Auto]/[Y]"). The [Auto]/[Y] ratio measured in 57 formalin-fixed, paraffin-embedded samples was compared to a quality score (QS) calculated for corresponding STR profiles using quantitative data (allele peak height). A statistically significant inverse correlation was observed between [Auto]/[Y] and QS (R = -0.65, p < 0.001). The [Auto]/[Y] values were highly correlated (R = 0.75, p < 0.001) with the "[Auto]/[D]" values obtained using the PowerQuant (Promega) assay, expressly designed to detect DNA degradation through simultaneous quantification of a short (Auto) and a long (D) autosomal target. These results indicate that it is possible to estimate DNA degradation in male samples through Plexor HY data and suggest an alternative strategy for laboratories lacking the equipment required for the assessment of DNA integrity through dedicated qPCR assays.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Nicola Nocco
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Alessia Riem
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Martina Onofri
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy (E.C.)
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy
| | - Eugenia Carnevali
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy (E.C.)
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy
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2
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Lim H, Gingras MC, Zhao J, Byun J, Castro PD, Tsavachidis S, Hu J, Doddapaneni H, Han Y, Muzny DM, Gibbs RA, Amos CI, Thrift AP. Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients. Sci Rep 2024; 14:8988. [PMID: 38637560 PMCID: PMC11026501 DOI: 10.1038/s41598-024-59257-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Esophageal adenocarcinoma is the most common histological subtype of esophageal cancer in Western countries and shows poor prognosis with rapid growth. EAC is characterized by a strong male predominance and racial disparity. EAC is up to fivefold more common among Whites than Blacks, yet Black patients with EAC have poorer survival rates. The racial disparity remains largely unknown, and there is limited knowledge of mutations in EAC regarding racial disparities. We used whole-exome sequencing to show somatic mutation profiles derived from tumor samples from 18 EAC male patients. We identified three molecular subgroups based on the pre-defined esophageal cancer-specific mutational signatures. Group 1 is associated with age and NTHL1 deficiency-related signatures. Group 2 occurs primarily in Black patients and is associated with signatures related to DNA damage from oxidative stress and NTHL1 deficiency-related signatures. Group 3 is associated with defective homologous recombination-based DNA often caused by BRCA mutation in White patients. We observed significantly mutated race related genes (LCE2B in Black, SDR39U1 in White) were (q-value < 0.1). Our findings underscore the possibility of distinct molecular mutation patterns in EAC among different races. Further studies are needed to validate our findings, which could contribute to precision medicine in EAC.
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Affiliation(s)
- Hyeyeun Lim
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jing Zhao
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Patricia D Castro
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Spiridon Tsavachidis
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, One Baylor Plaza, MS: BCM451, Suite 100D, Houston, TX, 77030, USA.
| | - Aaron P Thrift
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, MS: BCM307, Room 621D, Houston, TX, 77030, USA.
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3
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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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Meggendorfer M, Jobanputra V, Wrzeszczynski KO, Roepman P, de Bruijn E, Cuppen E, Buttner R, Caldas C, Grimmond S, Mullighan CG, Elemento O, Rosenquist R, Schuh A, Haferlach T. Analytical demands to use whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:16-22. [PMID: 34119643 DOI: 10.1016/j.semcancer.2021.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Interrogating the tumor genome in its entirety by whole-genome sequencing (WGS) offers an unprecedented insight into the biology and pathogenesis of cancer, with potential impact on diagnostics, prognostication and therapy selection. WGS is able to detect sequence as well as structural variants and thereby combines central domains of cytogenetics and molecular genetics. Given the potential of WGS in directing targeted therapeutics and clinical decision-making, we envision a gradual transition of the method from research to clinical routine. This review is one out of three within this issue aimed at facilitating this effort, by discussing in-depth analytical validation, clinical interpretation and clinical utility of WGS. The review highlights the requirements for implementing, validating and maintaining a clinical WGS pipeline to obtain high-quality patient-specific data in accordance with the local regulatory landscape. Every step of the WGS pipeline, which includes DNA extraction, library preparation, sequencing, bioinformatics analysis, and data storage, is considered with respect to its logistics, necessities, potential pitfalls, and the required quality management. WGS is likely to drive clinical diagnostics and patient care forward, if requirements and challenges of the technique are recognized and met.
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Affiliation(s)
| | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, USA; Columbia University Medical Center, 650 W 168th St, New York, USA
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, USA
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
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5
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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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6
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Zhao L, Polavarapu VK, Yadav RP, Xing P, Chen X. A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples. Bio Protoc 2022; 12:e4418. [PMID: 35865114 PMCID: PMC9257839 DOI: 10.21769/bioprotoc.4418] [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: 12/29/2021] [Accepted: 03/31/2022] [Indexed: 12/29/2022] Open
Abstract
The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. Nevertheless, it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissue of interest are limited. Here, we present F FPE tissue with a ntibody-guided c hromatin t agmentation with sequencing (FACT-seq), highly sensitive method to efficiently profile histone modifications in FFPE tissue by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We showed a very small piece of FFPE tissue section containing ~4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. In archived FFPE human colorectal and human glioblastoma cancer tissue, H3K27ac FACT-seq revealed disease specific super enhancers. In summary, FACT-seq allows researchers to decode histone modifications like H3K27ac and H3K27me3 in archival FFPE tissues with high sensitivity, thus allowing us to understand epigenetic regulation. Graphical abstract: ( i ) FFPE tissue section; ( ii ) Isolated nuclei; ( iii ) Primary antibody, secondary antibody and T7-pA-Tn5 bind to targets; ( iv ) DNA purification; ( v ) In vitro transcription and sequencing library preparation; ( vi ) Sequencing.
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Affiliation(s)
- Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Ram Prakash Yadav
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden;
,
*For correspondence:
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7
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Wang XQ, Goytain A, Dickson BC, Nielsen TO. Advances in Sarcoma Molecular Diagnostics. Genes Chromosomes Cancer 2022; 61:332-345. [DOI: 10.1002/gcc.23025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xue Qi Wang
- Faculty of Medicine University of British Columbia Vancouver Canada
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Angela Goytain
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Torsten Owen Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
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8
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MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples. Commun Biol 2021; 4:1396. [PMID: 34912045 PMCID: PMC8674242 DOI: 10.1038/s42003-021-02930-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022] Open
Abstract
The clinical sequencing of tumors is usually performed on formalin-fixed, paraffin-embedded samples and results in many sequencing errors. We identified that most of these errors are detected in chimeric reads caused by single-strand DNA molecules with microhomology. During the end-repair step of library preparation, mutations are introduced by the mis-annealing of two single-strand DNA molecules comprising homologous sequences. The mutated bases are distributed unevenly near the ends in the individual reads. Our filtering pipeline, MicroSEC, focuses on the uneven distribution of mutations in each read and removes the sequencing errors in formalin-fixed, paraffin-embedded samples without over-eliminating the mutations detected also in fresh frozen samples. Amplicon-based sequencing using 97 mutations confirmed that the sensitivity and specificity of MicroSEC were 97% (95% confidence interval: 82–100%) and 96% (95% confidence interval: 88–99%), respectively. Our pipeline will increase the reliability of the clinical sequencing and advance the cancer research using formalin-fixed, paraffin-embedded samples. Masachika Ikegami and Shinji Kohsaka et al. develop MicroSEC, a computational pipeline to filter sequencing artifacts from archival formalin-fixed and paraffin-embedded samples. Given that archival FFPE tissue is of great interest for genomic analysis, but difficult to reliably analyze, this tool may improve the ability of researchers to probe sequencing data from these samples.
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9
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Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Sahu A, Jiang P, Yan C, Duose DY, Cerami E, Chen L, Cohen D, Chen Q, Enos R, Huang X, Lee JJ, Liu Y, Neuberg DS, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirather JL, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal A, Karlovich C, Gabriel SB, Wistuba II, Liu XS, Wu CJ. Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network. Clin Cancer Res 2021; 27:5049-5061. [PMID: 33323402 PMCID: PMC8203757 DOI: 10.1158/1078-0432.ccr-20-3251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/24/2020] [Accepted: 12/08/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Whole-exome (WES) and RNA sequencing (RNA-seq) are key components of cancer immunogenomic analyses. To evaluate the consistency of tumor WES and RNA-seq profiling platforms across different centers, the Cancer Immune Monitoring and Analysis Centers (CIMAC) and the Cancer Immunologic Data Commons (CIDC) conducted a systematic harmonization study. EXPERIMENTAL DESIGN DNA and RNA were centrally extracted from fresh frozen and formalin-fixed paraffin-embedded non-small cell lung carcinoma tumors and distributed to three centers for WES and RNA-seq profiling. In addition, two 10-plex HapMap cell line pools with known mutations were used to evaluate the accuracy of the WES platforms. RESULTS The WES platforms achieved high precision (> 0.98) and recall (> 0.87) on the HapMap pools when evaluated on loci using > 50× common coverage. Nonsynonymous mutations clustered by tumor sample, achieving an index of specific agreement above 0.67 among replicates, centers, and sample processing. A DV200 > 24% for RNA, as a putative presequencing RNA quality control (QC) metric, was found to be a reliable threshold for generating consistent expression readouts in RNA-seq and NanoString data. MedTIN > 30 was likewise assessed as a reliable RNA-seq QC metric, above which samples from the same tumor across replicates, centers, and sample processing runs could be robustly clustered and HLA typing, immune infiltration, and immune repertoire inference could be performed. CONCLUSIONS The CIMAC collaborating laboratory platforms effectively generated consistent WES and RNA-seq data and enable robust cross-trial comparisons and meta-analyses of highly complex immuno-oncology biomarker data across the NCI CIMAC-CIDC Network.
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Affiliation(s)
- Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China
| | | | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Biswajit Das
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, China
| | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tomas Vilimas
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Peng Jiang
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Dzifa Yawa Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Li Chen
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Qingrong Chen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | | | - Xin Huang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jack J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Donna S Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | | | - Sharmistha Sarkar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sachet Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Junko Tsuji
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Mohamed Uduman
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xiaoman Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason L Weirather
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jijun Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Bethesda, Maryland
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chris Karlovich
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Ignacio Ivan Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine J Wu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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10
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Macioszek S, Dudzik D, Jacyna J, Wozniak A, Schöffski P, Markuszewski MJ. A Robust Method for Sample Preparation of Gastrointestinal Stromal Tumour for LC/MS Untargeted Metabolomics. Metabolites 2021; 11:metabo11080554. [PMID: 34436495 PMCID: PMC8400919 DOI: 10.3390/metabo11080554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal stromal tumour has already been well explored at the genome level; however, little is known about metabolic processes occurring in the sarcoma. Sample preparation is a crucial step in untargeted metabolomics workflow, highly affecting the metabolome coverage and the quality of the results. In this study, four liquid-liquid extraction methods for the isolation of endogenous compounds from gastrointestinal stromal tumours were compared and evaluated. The protocols covered two-step or stepwise extraction with methyl-tert-butyl ether (MTBE) or dichloromethane. The extracts were subjected to LC-MS analysis by the application of reversed-phase and hydrophilic interaction liquid chromatography to enable the separation and detection of both polar and nonpolar analytes. The extraction methods were compared in terms of efficiency (total number of detected metabolites) and reproducibility. The method was based on the stepwise extraction with MTBE, methanol, and water proved to be the most reproducible, and thus, its robustness to fluctuations in experimental conditions was assessed employing Plackett–Burman design and hierarchical modelling. While most studied factors had no effect on the metabolite abundance, the highest coefficient value was observed for the volume of MTBE added during extraction. Herein, we demonstrate the application and the feasibility of the selected protocol for the analysis of gastrointestinal stromal tumour samples. The method selected could be considered as a reference for the best characterization of underlying molecular changes associated with complex tissue extracts of GIST.
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Affiliation(s)
- Szymon Macioszek
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Danuta Dudzik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Julia Jacyna
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Agnieszka Wozniak
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (A.W.); (P.S.)
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Patrick Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (A.W.); (P.S.)
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
- Correspondence: ; Tel.: +48-58-349-1493
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11
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Multi-omics profiling of primary small cell carcinoma of the esophagus reveals RB1 disruption and additional molecular subtypes. Nat Commun 2021; 12:3785. [PMID: 34145257 PMCID: PMC8213753 DOI: 10.1038/s41467-021-24043-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/28/2021] [Indexed: 01/04/2023] Open
Abstract
Primary small cell carcinoma of the esophagus (PSCCE) is a lethal neuroendocrine carcinoma. Previous studies proposed a genetic similarity between PSCCE and esophageal squamous cell carcinoma (ESCC) but provided little evidence for differences in clinical course and neuroendocrine differentiation. We perform whole-exome sequencing, RNA sequencing and immunohistochemistry profiling on 46 PSCCE cases. Integrated analyses enable the discovery of multiple mechanisms of RB1 disruption in 98% (45/46) of cases. The transcriptomic landscape of PSCCE closely resembles small cell lung cancer (SCLC) but differs from ESCC or esophageal adenocarcinoma (EAC). Distinct gene expression patterns regulated by ASCL1 and NEUROD1 define two molecular subtypes, PSCCE-A and PSCCE-N, which are highly similar to SCLC subtypes. A T cell excluded phenotype is widely observed in PSCCE. In conclusion, PSCCE has genomic alterations, transcriptome features and molecular subtyping highly similar to SCLC but distinct from ESCC or EAC. These observations are relevant to oncogenesis mechanisms and therapeutic vulnerability. Primary small cell carcinoma of the oesophagus has a poor prognosis, and has not been fully characterised molecularly. Here, the authors study the disease using multi-omics technology and find frequent RB1 disruptions and similarities to small cell lung cancer, opening potential therapeutic avenues.
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12
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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13
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Ohmomo H, Komaki S, Ono K, Sutoh Y, Hachiya T, Arai E, Fujimoto H, Yoshida T, Kanai Y, Sasaki M, Shimizu A. Evaluation of clinical formalin-fixed paraffin-embedded tissue quality for targeted-bisulfite sequencing. Pathol Int 2020; 71:135-140. [PMID: 33333623 PMCID: PMC7898333 DOI: 10.1111/pin.13054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 11/16/2020] [Indexed: 11/29/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are promising biological resources for genetic research. Recent improvements in DNA extraction from FFPE samples allowed the use of these tissues for multiple sequencing methods. However, fundamental research addressing the application of FFPE-derived DNA for targeted-bisulfite sequencing (TB-seq) is lacking. Here, we evaluated the suitability of FFPE-derived DNA for TB-seq. We conducted TB-seq using FFPE-derived DNA and corresponding fresh frozen (FF) tissues of patients with kidney cancer and compared the quality of DNA, libraries, and TB-seq statistics between the two preservation methods. The approximately 600-bp average fragment size of the FFPE-derived DNA was significantly shorter than that of the FF-derived DNA. The sequencing libraries constructed using FFPE-derived DNA and the mapping ratio were approximately 10 times and 10% lower, respectively, than those constructed using FF-derived DNA. In the mapped data of FFPE-derived DNA, duplicated reads accounted for > 60% of the obtained sequence reads, with lower mean on-target coverage. Therefore, the standard TB-seq protocol is inadequate for obtaining high-quality data for epigenetic analysis from FFPE-derived DNA, and technical improvements are necessary for enabling the use of archived FFPE resources.
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Affiliation(s)
- Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Kanako Ono
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Teruhiko Yoshida
- Department of Clinical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1, Tsukiji, Chuo, Tokyo, 104-0045, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Shiwa, Iwate, 028-3694, Japan
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14
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Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. Mutational profiling of micro-dissected pre-malignant lesions from archived specimens. BMC Med Genomics 2020; 13:173. [PMID: 33208147 PMCID: PMC7672910 DOI: 10.1186/s12920-020-00820-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Systematic cancer screening has led to the increased detection of pre-malignant lesions (PMLs). The absence of reliable prognostic markers has led mostly to over treatment resulting in potentially unnecessary stress, or insufficient treatment and avoidable progression. Importantly, most mutational profiling studies have relied on PML synchronous to invasive cancer, or performed in patients without outcome information, hence limiting their utility for biomarker discovery. The limitations in comprehensive mutational profiling of PMLs are in large part due to the significant technical and methodological challenges: most PML specimens are small, fixed in formalin and paraffin embedded (FFPE) and lack matching normal DNA. METHODS Using test DNA from a highly degraded FFPE specimen, multiple targeted sequencing approaches were evaluated, varying DNA input amount (3-200 ng), library preparation strategy (BE: Blunt-End, SS: Single-Strand, AT: A-Tailing) and target size (whole exome vs. cancer gene panel). Variants in high-input DNA from FFPE and mirrored frozen specimens were used for PML-specific variant calling training and testing, respectively. The resulting approach was applied to profile and compare multiple regions micro-dissected (mean area 5 mm2) from 3 breast ductal carcinoma in situ (DCIS). RESULTS Using low-input FFPE DNA, BE and SS libraries resulted in 4.9 and 3.7 increase over AT libraries in the fraction of whole exome covered at 20x (BE:87%, SS:63%, AT:17%). Compared to high-confidence somatic mutations from frozen specimens, PML-specific variant filtering increased recall (BE:85%, SS:80%, AT:75%) and precision (BE:93%, SS:91%, AT:84%) to levels expected from sampling variation. Copy number alterations were consistent across all tested approaches and only impacted by the design of the capture probe-set. Applied to DNA extracted from 9 micro-dissected regions (8 PML, 1 normal epithelium), the approach achieved comparable performance, illustrated the data adequacy to identify candidate driver events (GATA3 mutations, ERBB2 or FGFR1 gains, TP53 loss) and measure intra-lesion genetic heterogeneity. CONCLUSION Alternate experimental and analytical strategies increased the accuracy of DNA sequencing from archived micro-dissected PML regions, supporting the deeper molecular characterization of early cancer lesions and achieving a critical milestone in the development of biology-informed prognostic markers and precision chemo-prevention strategies.
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Affiliation(s)
- Daniela Nachmanson
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Joseph Steward
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Huazhen Yao
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA.,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Eliza Jeong
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Thomas J O'Keefe
- Division of Breast Surgery and The Comprehensive Breast Health Center - UC San Diego School of Medicine, 3855 Health Sciences Dr., La Jolla, CA, 92093, USA
| | - Farnaz Hasteh
- Department of Pathology - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine - UC San Diego, 9500 Gilman Dr., La Jolla, CA, 92093, USA
| | - Gillian L Hirst
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Laura J Esserman
- Helen Diller Family Comprehensive Cancer Center - UC San Francisco School of Medicine, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine - UC Davis Comprehensive Cancer Center, UC Davis School of Medicine, 2279 45th Street, Sacramento, CA, 95817, USA
| | - Olivier Harismendy
- Moores Cancer Center - UC San Diego Health - 3855 Health Sciences Dr., La Jolla, CA, 92093, USA. .,Division of Biomedical Informatics, Department of Medicine - UC San Diego School of Medicine, 9500 Gilman Dr., La Jolla, CA, 92093, USA.
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15
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Modeling performance of sample collection sites using whole exome sequencing metrics. Biotechniques 2020; 69:420-426. [PMID: 33103912 DOI: 10.2144/btn-2020-0086] [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
Although next-generation sequencing assays are routinely carried out using samples from cancer trials, the sequencing data are not always of the required quality. There is a need to evaluate the performance of tissue collection sites and provide feedback about the quality of next-generation sequencing data. This study used a modeling approach based on whole exome sequencing quality control (QC) metrics to evaluate the relative performance of sites participating in the Bristol Myers Squibb Immuno-Oncology clinical trials sample collection. We identified several events for the sample swap. Overall, most sites performed well and few showed poor performance. These findings can increase awareness of sample failure and improve the quality of samples.
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16
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Wang Y, Call J. Mutational Testing in Gastrointestinal Stromal Tumor. Curr Cancer Drug Targets 2020; 19:688-697. [PMID: 30914028 DOI: 10.2174/1568009619666190326123945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 02/05/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022]
Abstract
Targeted treatment has become a major modality in cancer management. Such cancer drugs are generally designed to treat tumors with certain genetic/genomic makeups. Mutational testing prior to prescribing targeted therapy is crucial in identifying who can receive clinical benefit from specific cancer drugs. Over the last two decades, gastrointestinal stromal tumors (GISTs) have evolved from histogenetically obscure to being identified as distinct gastrointestinal mesenchymal tumors with well-defined clinical and molecular characteristics, for which multiple lines of targeted therapies are available. Although the National Comprehensive Cancer Network (NCCN) strongly recommends mutational testing for optimal management of GIST, many GIST patients still have neither a mutation test performed or any mutation-guided cancer management. Here, we review the mutation-guided landscape of GIST, mutational testing methods, and the recent development of new therapies targeting GIST with specific mutations.
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Affiliation(s)
- Yu Wang
- The Life Raft Group, 155 US-46 Wayne, NJ 07470, United States
| | - Jerry Call
- The Life Raft Group, 155 US-46 Wayne, NJ 07470, United States
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17
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Li R, Han D, Shi J, Han Y, Tan P, Zhang R, Li J. Choosing tumor mutational burden wisely for immunotherapy: A hard road to explore. Biochim Biophys Acta Rev Cancer 2020; 1874:188420. [PMID: 32828886 DOI: 10.1016/j.bbcan.2020.188420] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022]
Abstract
Immunotherapy has revolutionized the treatment of cancer due to its remarkable efficacy and extensive survival benefit in multiple tumor types. However, predictive biomarkers are required to identify patients who are likely to respond to immunotherapy. Recently, tumor mutational burden (TMB) has been shown to be associated with clinical outcomes in diverse cancers, such as melanoma, non-small-cell lung cancer and colorectal cancer. Several studies have demonstrated that high TMB can effectively predict the objective response rate and progression-free survival, but the ability of TMB to predict overall survival is limited. Thus, the clinical utility of TMB as a predictive and prognostic biomarker in immunotherapy is currently controversial. Importantly, multiple factors can affect the accurate assessment of TMB and further interfere with its prediction of clinical outcomes. These factors include preanalytical factors such as sample status, analytical factors such as differences in platforms and methods for determining TMB and variability of cutoff values, and postanalytical factors such as inconsistent interpretation and reporting of results. In addition, the optimal definition and quantification of TMB are unclear and require harmonization and standardization for reliable clinical application. This review elaborates on the factors affecting TMB status in primary tumors, summarizes the clinical utility of TMB as a biomarker in immunotherapy, and evaluates the impact of each analysis stage on the accurate estimation of TMB, especially its quantification, aiming to facilitate TMB assessment in routine clinical settings.
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Affiliation(s)
- Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Peking University Fifth School of Clinical Medicine, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - YanXi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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18
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Walsh HL, Sperry AJ, Blazer VS. The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu). PLoS One 2020; 15:e0236104. [PMID: 32776939 PMCID: PMC7416921 DOI: 10.1371/journal.pone.0236104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
There is an increasing emphasis on effects-based monitoring to document responses associated with exposure to complex mixtures of chemicals, climate change, pathogens, parasites and other environmental stressors in fish populations. For decades aquatic monitoring programs have included the collection of tissues preserved for microscopic pathology. Consequently, formalin-fixed, paraffin-embedded (FFPE) tissue can be an important reservoir of nucleic acids as technologies emerge that utilize molecular endpoints. Despite the cross-linking effects of formalin, its impact on nucleic acid quality and concentration, amplification, and sequencing are not well described. While fresh-frozen tissue is optimal for working with nucleic acids, FFPE samples have been shown to be conducive for molecular studies. Laser capture microdissection (LCM) is one technology which allows for collection of specific regions or cell populations from fresh or preserved specimens with pathological alterations, pathogens, or parasites. In this study, smallmouth bass (Micropterus dolomieu) liver was preserved in three different fixatives, including 10% neutral buffered formalin (NBF), Z-Fix® (ZF), and PAXgene® (PG) for four time periods (24 hr, 48 hr, seven days, and 14 days). Controls consisted of pieces of liver preserved in RNALater® or 95% ethanol. Smallmouth bass were chosen as they are an economically important sportfish and have been utilized as indicators of exposure to endocrine disruptors and other environmental stressors. Small liver sections were cut out with laser microdissection and DNA and RNA were purified and analyzed for nucleic acid concentration and quality. Sanger sequencing and the NanoString nCounter® technology were used to assess the suitability of these samples in downstream molecular techniques. The results revealed that of the formalin fixatives, NBF samples fixed for 24 and 48 hr were superior to ZF samples for both Sanger sequencing and the Nanostring nCounter®. The non-formalin PAXgene® samples were equally successful and they showed greater stability in nucleic acid quality and concentration over longer fixation times. This study demonstrated that small quantities of preserved tissue from smallmouth bass can be utilized in downstream molecular techniques; however, future studies will need to optimize the methods presented here for different tissue types, fish species, and pathological conditions.
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Affiliation(s)
- Heather L. Walsh
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
- * E-mail:
| | - Adam J. Sperry
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
| | - Vicki S. Blazer
- U.S. Geological Survey, National Fish Health Research Laboratory, Leetown Science Center, Kearneysville, West Virginia, United States of America
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19
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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: 18] [Impact Index Per Article: 4.5] [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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20
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Astolfi A, Indio V, Nannini M, Saponara M, Schipani A, De Leo A, Altimari A, Vincenzi B, Comandini D, Grignani G, Secchiero P, Urbini M, Pantaleo MA. Targeted Deep Sequencing Uncovers Cryptic KIT Mutations in KIT/PDGFRA/SDH/RAS-P Wild-Type GIST. Front Oncol 2020; 10:504. [PMID: 32391261 PMCID: PMC7188756 DOI: 10.3389/fonc.2020.00504] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Gastrointestinal stromal tumors (GIST) are known to carry oncogenic KIT or PDGFRA mutations, or less commonly SDH or NF1 gene inactivation, with very rare cases harboring mutant BRAF or RAS alleles. Approximately 10% of GISTs are devoid of any of such mutations and are characterized by very limited therapeutic opportunities and poor response to standard treatments. Methods: Twenty-six sporadic KIT/PDGFRA/SDH/RAS-pathway wild type GIST were profiled for the molecular status of genes frequently altered in GIST by a targeted next generation sequencing (NGS) approach. Molecular findings were validated by alternative amplicon-based targeted sequencing, immunohistochemistry, gene expression profiling and Sanger sequencing. Results: Three patients harboring NF1 inactivating mutations were identified and excluded from further analysis. Intriguingly, five patients carried cryptic KIT alterations, mainly represented by low-allele-fraction mutations (12–16% allele ratio). These mutations were confirmed by another targeted NGS approaches and supported by CD117 immuno-staining, gene expression profiling, Sanger sequencing, with peak signals at the level of background noise, and by the patients' clinical course assessment. Conclusion: This study indicates that ~20% patients diagnosed with a KIT/PDGFRA/SDH/RAS-pathway wild-type GIST are bona-fide carriers of pathogenic KIT mutations, thus expected to be eligible for and responsive to the various therapeutic lines of TK-inhibitors in use for KIT/PDGFRA-mutant GIST. The centralization for a second level molecular analysis of GIST samples diagnosed as wild-type for KIT and PDGFRA is once again strongly recommended.
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Affiliation(s)
- Annalisa Astolfi
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Valentina Indio
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Margherita Nannini
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy.,Medical Oncology Unit, S.Orsola-Malpighi University Hospital, Bologna, Italy
| | - Maristella Saponara
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Angela Schipani
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Antonio De Leo
- Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Annalisa Altimari
- Laboratory of Oncologic Molecular Pathology, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, University Campus Bio-Medico, Rome, Italy
| | - Danila Comandini
- Medical Oncology 1, Policlinico San Martino, University of Genova, Genova, Italy
| | - Giovanni Grignani
- Sarcoma Unit, Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Italy
| | - Paola Secchiero
- Department of Morphology, Surgery & Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Milena Urbini
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy
| | - Maria Abbondanza Pantaleo
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
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21
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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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22
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Wu P, Hou L, Zhang Y, Zhang L. Phylogenetic Tree Inference: A Top-Down Approach to Track Tumor Evolution. Front Genet 2020; 10:1371. [PMID: 32117420 PMCID: PMC7020887 DOI: 10.3389/fgene.2019.01371] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/16/2019] [Indexed: 12/21/2022] Open
Abstract
Recently, an increasing number of studies sequence multiple biopsies of primary tumors, and even paired metastatic tumors to understand heterogeneity and the evolutionary trajectory of cancer progression. Although several algorithms are available to infer the phylogeny, most tools rely on accurate measurements of mutation allele frequencies from deep sequencing, which is often hard to achieve for clinical samples (especially FFPE samples). In this study, we present a novel and easy-to-use method, PTI (Phylogenetic Tree Inference), which use an iterative top-down approach to infer the phylogenetic tree structure of multiple tumor biopsies from same patient using just the presence or absence of somatic mutations without their allele frequencies. Therefore PTI can be used in a wide range of cases even when allele frequency data is not available. Comparison with existing state-of-the-art methods, such as LICHeE, Treeomics, and BAMSE, shows that PTI achieves similar or slightly better performance within a short run time. Moreover, this method is generally applicable to infer phylogeny for any other data sets (such as epigenetics) with a similar zero and one feature-by-sample matrix.
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Affiliation(s)
- Pin Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linjun Hou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yingdong Zhang
- Library and Information Center, ShanghaiTech University, Shanghai, China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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23
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Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer. Sci Rep 2019; 9:15716. [PMID: 31673122 PMCID: PMC6823544 DOI: 10.1038/s41598-019-51951-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, influencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no significant difference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the first study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil.
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24
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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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25
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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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26
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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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27
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Lee MF, Lindo JF, Auer H, Walochnik J. Successful extraction and PCR amplification of Giardia DNA from formalin-fixed stool samples. Exp Parasitol 2019; 198:26-30. [PMID: 30710500 DOI: 10.1016/j.exppara.2019.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 12/14/2018] [Accepted: 01/20/2019] [Indexed: 01/31/2023]
Abstract
Extracting genomic DNA of pathogenic agents from formalin-fixed specimens is inherently difficult. Storage of samples in formalin results in nucleic acid cross-linking and DNA fragmentation. In this study, DNA was extracted from 45 Giardia-positive stool samples stored in formalin and subjected to PCR amplification targeting the triose phosphate isomerase (tpi), beta gardin (bg) and glutamate dehydrogenase (gdh) genes. Samples were rehydrated by using a descending alcohol series before DNA extraction using a commercial kit. This was followed by EDTA-mediated inhibition of DNase activity and prolonged treatment with proteinase K to digest contaminating proteins. DNA was amplified at rates of 64.4% (29/45) at the tpi, 40% (18/45) at the bg and 20% (9/45) at the gdh loci as seen on nested PCR. DNA quality was subsequently tested in a genotyping experiment which produced high-quality sequences at the tpi (41.2%; 12/29) bg (50%; 9/18), and gdh (22.2%; 2/9) loci and enabled differentiation of Giardia strains at the subtype level. The modified extraction protocol was effective at removing inhibitors and reversing cross-linking of DNA. However, PCR amplification was limited to short fragments of DNA which resulted in highest success rate on amplification of the shortest (334 bp) gene fragment tested.
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Affiliation(s)
- Mellesia F Lee
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria; Department of Microbiology, The University of the West Indies Mona, Kingston, Jamaica
| | - John F Lindo
- Department of Microbiology, The University of the West Indies Mona, Kingston, Jamaica.
| | - Herbert Auer
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria
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28
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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29
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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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30
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Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp Mol Pathol 2018; 104:161-169. [PMID: 29608913 PMCID: PMC5993858 DOI: 10.1016/j.yexmp.2018.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Affiliation(s)
- Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
| | - Angela Santonja
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Marta Grzelak
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Harry Clifford
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Michelle Pugh
- Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mae A Goldgraben
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Helen A Bardwell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eun Yoon Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea
| | - Elena Provenzano
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Emilio Alba
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
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31
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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32
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Bonnet E, Moutet ML, Baulard C, Bacq-Daian D, Sandron F, Mesrob L, Fin B, Delépine M, Palomares MA, Jubin C, Blanché H, Meyer V, Boland A, Olaso R, Deleuze JF. Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples. PLoS One 2018; 13:e0195471. [PMID: 29621323 PMCID: PMC5886566 DOI: 10.1371/journal.pone.0195471] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/25/2018] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (representing at least 86% of the total number of variants for SNVs). The concordance rate is very high between all matched FF / FFPE pairs, with equivalent values for the three kits we analyzed. On the other hand, when looking at the difference between the total number of variants in FF and FFPE, we find a significant variation for the three different FFPE DNA extraction kits. Coverage analysis shows that FFPE samples have less good indicators than FF samples, yet the coverage quality remains above accepted thresholds. We detect limited but statistically significant variations in coverage indicator values between the three FFPE extraction kits. Globally, the GeneRead and QIAamp kits have better variant calling and coverage indicators than the Maxwell kit on the samples used in this study, although this kit performs better on some indicators and has advantages in terms of practical usage. Taken together, our results confirm the potential of FFPE samples analysis for clinical genomic studies, but also indicate that the choice of a FFPE DNA extraction kit should be done with careful testing and analysis beforehand in order to maximize the accuracy of the results.
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Affiliation(s)
- Eric Bonnet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Laure Moutet
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Céline Baulard
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Delphine Bacq-Daian
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Florian Sandron
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Lilia Mesrob
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Bertrand Fin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marc Delépine
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Marie-Ange Palomares
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Claire Jubin
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Hélène Blanché
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, Direction de la Recherche Fondamentale, CEA, Evry, France
- LabEx GenMed, Evry, France
- Centre d’Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France
- Centre de REFérence, d’Innovation, d’eXpertise et de transfert (CREFIX), Evry, France
- * E-mail:
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Joung JG, Ha SY, Bae JS, Nam JY, Gwak GY, Lee HO, Son DS, Park CK, Park WY. Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma. Oncotarget 2018; 8:2076-2082. [PMID: 27409339 PMCID: PMC5356781 DOI: 10.18632/oncotarget.10502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 05/17/2016] [Indexed: 12/21/2022] Open
Abstract
Dysplastic nodules are premalignant neoplastic nodules found in explanted livers with cirrhosis. Genetic signatures of premalignant dysplastic nodules (DNs) with concurrent hepatocellular carcinoma (HCC) may provide an insight in the molecular evolution of hepatocellular carcinogenesis. We analyzed four patients with multifocal nodular lesions and cirrhotic background by whole-exome sequencing (WES). The genomic profiles of somatic single nucleotide variations (SNV) and copy number variations (CNV) in DNs were compared to those of HCCs. The number and variant allele frequency of somatic SNVs of DNs and HCCs in each patient was identical along the progression of pathological grade. The somatic SNVs in DNs showed little conservation in HCC. Additionally, CNVs showed no conservation. Phylogenetic analysis based on SNVs and copy number profiles indicated a nonlinear segregation pattern, implying independent development of DNs and HCC in each patient. Thus, somatic mutations in DNs may be developed separately from other malignant nodules in the same liver, suggesting a nonlinear model for hepatocarcinogenesis from DNs to HCC.
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Affiliation(s)
- Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Yun Ha
- Departments of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Seol Bae
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae-Yong Nam
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Geum-Youn Gwak
- Departments of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Departments of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dae-Soon Son
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Biomedical Research Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Cheol-Keun Park
- Departments of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Departments of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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34
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Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA. Oncotarget 2018; 7:59115-59128. [PMID: 27463017 PMCID: PMC5312299 DOI: 10.18632/oncotarget.10827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/30/2016] [Indexed: 12/23/2022] Open
Abstract
DNA derived from formalin-fixed and paraffin-embedded (FFPE) tissue has been a challenge to large-scale genomic sequencing, due to its low quality and quantities. Improved techniques enabling the genome-wide analysis of FFPE material would be of great value, both from a research and clinical perspective. Comparing a single-strand DNA library preparation method originally developed for ancient DNA to conventional protocols using double-stranded DNA derived from FFPE material we obtain on average 900-fold more library molecules and improved sequence complexity from as little as 5 ng input DNA. FFPE DNA is highly fragmented, usually below 100bp, and up to 60% of reads start after or end prior to adenine residues, suggesting that crosslinks predominate at adenine residues. Similar to ancient DNA, C > T substitutions are slightly increased with maximum rates up to 3% at the ends of molecules. In whole exome sequencing of single-strand libraries from lung, breast, colorectal, prostate and skin cancers we identify known cancer mutations. In summary, we show that single-strand library preparation enables genomic sequencing, even from low amounts of degraded FFPE DNA. This method provides a clear advantage both in research and clinical settings, where FFPE material (e.g. from biopsies) often is the only source of DNA available. Improving the genetic characterization that can be performed on conventional archived FFPE tissue, the single-strand library preparation allows scarce samples to be used in personalized medicine and enables larger sample sizes in future sequencing studies.
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35
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Bianconi D, Heller G, Spies D, Herac M, Gleiss A, Liebmann-Reindl S, Unseld M, Kieler M, Scheithauer W, Streubel B, Zielinski CC, Prager GW. Biochemical and genetic predictors of overall survival in patients with metastatic pancreatic cancer treated with capecitabine and nab-paclitaxel. Sci Rep 2017; 7:4851. [PMID: 28687745 PMCID: PMC5501799 DOI: 10.1038/s41598-017-04743-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/30/2017] [Indexed: 12/18/2022] Open
Abstract
Pancreatic cancer is a dismal disease with a mortality rate almost similar to its incidence rate. To date, there are neither validated predictive nor prognostic biomarkers for this lethal disease. Thus, the aim of the present study was to retrospectively investigate the capability of biochemical parameters and molecular profiles to predict survival of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) who participated in a phase II clinical trial to test the safety and efficacy of the combination treatment of capecitabine plus nab-paclitaxel. Herein, we investigated the association of 18 biochemical parameters obtained from routine diagnosis and the clinical outcome of the 30 patients enrolled in the clinical trial. Furthermore, we analysed formalin-fixed paraffin-embedded (FFPE) tumour tissue to identify molecular biomarkers via RNA seq and the Illumina TruSeq Amplicon Cancer panel which covers 48 hotspot genes. Our analysis identified SERPINB7 as a novel transcript and a DNA mutation signature that might predict a poor outcome of disease. Moreover, we identified the bilirubin basal level as an independent predictive factor for overall survival in our study cohort.
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Affiliation(s)
- Daniela Bianconi
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Daniel Spies
- Swiss Federal Institute of Technology Zurich, Department of Biology, Institute of Molecular Health Sciences, Otto-Stern Weg 7, 8093, Zurich, Switzerland.,Life Science Zurich Graduate School, Molecular Life Science Program, Institute of Molecular Life Science, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland, Austria
| | - Merima Herac
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Andreas Gleiss
- Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | | | - Matthias Unseld
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Markus Kieler
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Werner Scheithauer
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Berthold Streubel
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Christoph C Zielinski
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Gerald W Prager
- Department of Medicine I, Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria.
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36
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Einaga N, Yoshida A, Noda H, Suemitsu M, Nakayama Y, Sakurada A, Kawaji Y, Yamaguchi H, Sasaki Y, Tokino T, Esumi M. Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation. PLoS One 2017; 12:e0176280. [PMID: 28498833 PMCID: PMC5428915 DOI: 10.1371/journal.pone.0176280] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 04/07/2017] [Indexed: 01/09/2023] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues used for pathological diagnosis are valuable for studying cancer genomics. In particular, laser-capture microdissection of target cells determined by histopathology combined with FFPE tissue section immunohistochemistry (IHC) enables precise analysis by next-generation sequencing (NGS) of the genetic events occurring in cancer. The result is a new strategy for a pathological tool for cancer diagnosis: 'microgenomics'. To more conveniently and precisely perform microgenomics, we revealed by systematic analysis the following three details regarding FFPE DNA compared with paired frozen tissue DNA. 1) The best quality of FFPE DNA is obtained by tissue fixation with 10% neutral buffered formalin for 1 day and heat treatment of tissue lysates at 95°C for 30 minutes. 2) IHC staining of FFPE tissues decreases the quantity and quality of FFPE DNA to one-fourth, and antigen retrieval (at 120°C for 15 minutes, pH 6.0) is the major reason for this decrease. 3) FFPE DNA prepared as described herein is sufficient for NGS. For non-mutated tissue specimens, no artifactual mutation occurs during FFPE preparation, as shown by precise comparison of NGS of FFPE DNA and paired frozen tissue DNA followed by validation. These results demonstrate that even FFPE tissues used for routine clinical diagnosis can be utilized to obtain reliable NGS data if appropriate conditions of fixation and validation are applied.
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Affiliation(s)
- Naoki Einaga
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Akio Yoshida
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- Department of Orthopaedic Surgery, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiroko Noda
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Masaaki Suemitsu
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- Department of Oral Pathology, Nihon University School of Dentistry at Matsudo, Matsudo, Chiba, Japan
| | - Yuki Nakayama
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Akihisa Sakurada
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yoshiko Kawaji
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Hiromi Yamaguchi
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
| | - Yasushi Sasaki
- Department of Medical Genome Sciences, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Takashi Tokino
- Department of Medical Genome Sciences, Sapporo Medical University, Sapporo, Hokkaido, Japan
| | - Mariko Esumi
- Department of Pathology, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
- * E-mail:
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37
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Ericson-Lindquist K, Johansson A, Levéen P, Elmberger G, Jönsson G, Staaf J, Brunnström H. Targeted sequencing may facilitate differential diagnostics of pulmonary tumours: a case series. Diagn Pathol 2017; 12:31. [PMID: 28347348 PMCID: PMC5368924 DOI: 10.1186/s13000-017-0621-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 03/20/2017] [Indexed: 01/11/2023] Open
Abstract
Background Histopathological diagnosis is important for prognostication and choice of treatment in patients with cancer in the lung. Metastases to the lungs are common and need to be distinguished from primary lung cancer. Furthermore, cases with synchronous or metachronous primary lung cancers (although infrequent) are often handled differently than cases with lung cancer with intrapulmonary metastasis or relapse, respectively. In some cases, morphology and immunohistochemical staining is not sufficient for certain diagnosis. Methods The present study included six cases where molecular genetic analysis in form of pyrosequencing or targeted next-generation sequencing was of value for certain diagnosis of selected tumours in the lung. Results Two of the included cases were rare metastases to the lung; colorectal cancer with IHC profile consistent with primary lung cancer and malignant adenomyoepithelioma of the breast, respectively, where molecular genetic analysis was of aid for proving the relationship to the primary tumour. The other four cases were multiple lung adenocarcinomas where molecular genetic analysis was of aid to distinguish between intrapulmonary metastasis and synchronous tumour. Conclusions Comparison of molecular genetic profile may be an important tool for determination of relationship between tumours in some situations and should always be considered in unclear cases. Further studies on concordance and discordance of molecular genetic profiles between spatially or temporally different tumours with common origin may be helpful for improved diagnostics of pulmonary tumours.
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Affiliation(s)
| | - Anna Johansson
- Department of Pathology, Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
| | - Per Levéen
- Department of Pathology, Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
| | - Göran Elmberger
- Department of Pathology, Örebro University Hospital, SE-701 85, Örebro, Sweden
| | - Göran Jönsson
- Department of Clinical Sciences in Lund, Division of Oncology and Pathology, Lund University, SE-221 00, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences in Lund, Division of Oncology and Pathology, Lund University, SE-221 00, Lund, Sweden
| | - Hans Brunnström
- Department of Pathology, Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden. .,Department of Clinical Sciences in Lund, Division of Oncology and Pathology, Lund University, SE-221 00, Lund, Sweden.
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Non-reproducible sequence artifacts in FFPE tissue: an experience report. J Cancer Res Clin Oncol 2017; 143:1199-1207. [PMID: 28314930 DOI: 10.1007/s00432-017-2399-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Recent advances in sequencing technologies supported the development of molecularly targeted therapy in cancer patients. Thus, genomic analyses are becoming a routine part in clinical practice and accurate detection of actionable mutations is essential to assist diagnosis and therapy choice. However, this is often challenging due to major problems associated with DNA from formalin-fixed paraffin-embedded tissue which is usually the primary source for genetic testing. OBJECTIVES Here we want to share our experience regarding major problems associated with FFPE DNA used for PCR-based sequencing as illustrated by the mutational analysis of ERBB4 in melanoma. We want to focus on two major problems including extensive DNA fragmentation and hydrolytic deamination as source of non-reproducible sequence artifacts. Further, we provide potential explanations and possible strategies to minimize these difficulties and improve the detection of targetable mutations. METHODS Genomic DNA from formalin-fixed paraffin-embedded tumor samples was isolated followed by PCR amplification, Sanger sequencing and statistical analysis. RESULTS Analysis of Sanger sequencing data revealed a total of 46 ERBB4 mutations in 27 of 96 samples including the identification of 11 mutations at three previously unknown mutational hotspots. Unfortunately, we were not able to confirm any assumed hotspot mutation within repeated sequencing of relevant amplicons suggesting the detection of sequence artifacts most likely caused by DNA lesions associated with FFPE tissues. CONCLUSION Since DNA from FFPE tissue is usually the primary source for mutational analyses, appropriate measures must be implemented in the workflow to assess DNA damage in formalin-fixed tissue to ensure accurate detection of actionable mutations and minimize the occurrence of sequence artifacts.
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Performance Comparison of NextSeq and Ion Proton Platforms for Molecular Diagnosis of Clinical Oncology. TUMORI JOURNAL 2017; 103:223-230. [PMID: 28127742 DOI: 10.5301/tj.5000600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 11/20/2022]
Abstract
Purpose Next-generation sequencing is a powerful approach to detect genetic mutations with which cancer diagnosis and treatment can be tailored to the individual patient in the era of personalized and precision medicine. Ion Torrent Systems Ion Proton and Illumina NextSeq are 2 major targeted sequencing platforms; however, not much work has been done to compare these platforms’ performance for mutation detection in formalin-fixed paraffin-embedded (FFPE) materials. Methods We benchmarked the performance by using a collection of FFPE samples from 23 patients with different cancers for NextSeq and Ion Proton platforms. We report analysis of sequencing in terms of average coverage depth, read length, and variant detection. Results Sequencing results by NextSeq and Ion Proton displayed near perfect coverage behavior (>99%) on target region. We analyzed the ability to call variants from each platform and found that Ion Proton sequencing can identify 89% of single nucleotide variants (SNVs) whose mutant allele frequency (MAF) is greater than or equal to 5% detected by the NextSeq pipeline in common analytical regions. The correlation coefficient of MAF for those common SNVs was 1.0046 (R2 = 0.973) between the 2 platforms. To call lower mutant frequency (5%-10%) mutations for NextSeq sequencing, coverage depth should be improved. The concordance of small insertions and deletions between these 2 pipelines was up to 100%. Conclusions The 2 sequencing pipelines evaluated were able to generate usable sequence and had high concordance. They are proper for mutation detection in clinical application.
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Omolo B, Yang M, Lo FY, Schell MJ, Austin S, Howard K, Madan A, Yeatman TJ. Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer. BMC Med Genomics 2016; 9:65. [PMID: 27756306 PMCID: PMC5069826 DOI: 10.1186/s12920-016-0225-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 10/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60 % of patients with a wild type KRAS fail to respond to EGFRi combination therapies, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. METHODS In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter™ (NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq (t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA). RESULTS Using Affy_FF as the "gold" standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE (r = 0.233, p = 0.090); (2) NanoS_FFPE (r = 0.608, p < 0.0001); (3) RNA-Acc_FFPE (r = 0.175, p = 0.21); (4) t-RNA_FFPE (r = -0.237, p = 0.085); (5) and t-RNA (r = -0.012, p = 0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified "problematic" samples (n = 15) and genes (n = 2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r = 0.672, p < 0.0001); NanoS_FFPE (r = 0.738, p < 0.0001); and RNA-Acc_FFPE (r = 0.483, p = 0.002). CONCLUSIONS Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix GeneChip and multiple RNASeq technologies. Moreover, NanoString was the most forgiving technology in the analysis of samples with presumably poor RNA quality. Using this approach, the RAS signature score may now be reasonably applied to FFPE clinical samples.
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Affiliation(s)
- Bernard Omolo
- Division of Mathematics and Computer Science, University of South Carolina-Upstate, 800 University Way, Spartanburg, SC, 29303, USA
| | - Mingli Yang
- Gibbs Cancer Center and Research Institute, 101 E Wood Street, Spartanburg, SC 29303, USA
| | - Fang Yin Lo
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Sharon Austin
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Kellie Howard
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Anup Madan
- Genomic Services, Covance Genomics Lab, 9911 Willows Road, Suite 175, Redmond, WA, 98052, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center and Research Institute, 101 E Wood Street, Spartanburg, SC 29303, USA.
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Bonfiglio S, Vanni I, Rossella V, Truini A, Lazarevic D, Dal Bello MG, Alama A, Mora M, Rijavec E, Genova C, Cittaro D, Grossi F, Coco S. Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples. BMC Cancer 2016; 16:692. [PMID: 27578032 PMCID: PMC5004269 DOI: 10.1186/s12885-016-2720-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 03/01/2023] Open
Abstract
Background Next Generation Sequencing (NGS) has become a valuable tool for molecular landscape characterization of cancer genomes, leading to a better understanding of tumor onset and progression, and opening new avenues in translational oncology. Formalin-fixed paraffin-embedded (FFPE) tissue is the method of choice for storage of clinical samples, however low quality of FFPE genomic DNA (gDNA) can limit its use for downstream applications. Methods To investigate the FFPE specimen suitability for NGS analysis and to establish the performance of two solution-based exome capture technologies, we compared the whole-exome sequencing (WES) data of gDNA extracted from 5 fresh frozen (FF) and 5 matched FFPE lung adenocarcinoma tissues using: SeqCap EZ Human Exome v.3.0 (Roche NimbleGen) and SureSelect XT Human All Exon v.5 (Agilent Technologies). Results Sequencing metrics on Illumina HiSeq were optimal for both exome systems and comparable among FFPE and FF samples, with a slight increase of PCR duplicates in FFPE, mainly in Roche NimbleGen libraries. Comparison of single nucleotide variants (SNVs) between FFPE-FF pairs reached overlapping values >90 % in both systems. Both WES showed high concordance with target re-sequencing data by Ion PGM™ in 22 lung-cancer genes, regardless the source of samples. Exon coverage of 623 cancer-related genes revealed high coverage efficiency of both kits, proposing WES as a valid alternative to target re-sequencing. Conclusions High-quality and reliable data can be successfully obtained from WES of FFPE samples starting from a relatively low amount of input gDNA, suggesting the inclusion of NGS-based tests into clinical contest. In conclusion, our analysis suggests that the WES approach could be extended to a translational research context as well as to the clinic (e.g. to study rare malignancies), where the simultaneous analysis of the whole coding region of the genome may help in the detection of cancer-linked variants. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2720-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Bonfiglio
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy.
| | - Irene Vanni
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Valeria Rossella
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Anna Truini
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy.,Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Italy, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Dejan Lazarevic
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Maria Giovanna Dal Bello
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Angela Alama
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Marco Mora
- Department of Pathology, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Erika Rijavec
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Carlo Genova
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Francesco Grossi
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy.
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