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Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W. Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing. Nat Biotechnol 2021; 39:1151-1160. [PMID: 34504347 PMCID: PMC8532138 DOI: 10.1038/s41587-021-00993-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/18/2021] [Indexed: 02/08/2023]
Abstract
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.
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Affiliation(s)
- Li Tai Fang
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yongmei Zhao
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Wanqiu Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Zhaowei Yang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liz Kerrigan
- ATCC (American Type Culture Collection), Manassas, VA, USA
| | | | | | - Charles Lu
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Kenneth Idler
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Howard Jacob
- Computational Genomics, Genomics Research Center (GRC), AbbVie, North Chicago, IL, USA
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | | | | | | | - Keyur Talsania
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Justin Lack
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tsai-Wei Shen
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhong Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Seta Stanbouly
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yuliya Kriga
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD, USA
| | - Virginie Petitjean
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Sultan
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Margaret Cam
- CCR Collaborative Bioinformatics Resource (CCBR), Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA
| | - Monika Mehta
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tiffany Hung
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | - Eric Peters
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | - Rasika Kalamegham
- Genentech, a member of the Roche group, South San Francisco, CA, USA
| | | | - Marghoob Mohiyuddin
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Yunfei Guo
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Lijing Yao
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hugo Y K Lam
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Jiri Drabek
- IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Petr Vojta
- IMTM, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | - Roberta Maestro
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Daniela Gasparotto
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Sulev Kõks
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Reimann
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andreas Scherer
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Jessica Nordlund
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulrika Liljedahl
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhipan Li
- Sentieon Inc., Mountain View, CA, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Malcolm Moos
- Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Eric Donaldson
- Center for Drug Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Zivana Tezak
- Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA
| | - Baitang Ning
- National Center for Toxicological Research, FDA, Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research, FDA, Jefferson, AR, USA
| | - Jing Li
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | | | | | | | | | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Erica Tassone
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | - Jeffrey Trent
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Huixiao Hong
- National Center for Toxicological Research, FDA, Jefferson, AR, USA.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Charles Wang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA, USA.
| | - Wenming Xiao
- Center for Devices and Radiological Health, FDA, Silver Spring, MD, USA.
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Affiliation(s)
- Dana C. Crawford
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Scott M. Williams
- Departments of Population and Quantitative Health Sciences and Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America
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Larson KL, Huang B, Weiss HL, Hull P, Westgate PM, Miller RW, Arnold SM, Kolesar JM. Clinical Outcomes of Molecular Tumor Boards: A Systematic Review. JCO Precis Oncol 2021; 5:PO.20.00495. [PMID: 34632252 PMCID: PMC8277300 DOI: 10.1200/po.20.00495] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/18/2021] [Accepted: 06/09/2021] [Indexed: 01/12/2023] Open
Abstract
We conducted this systematic review to evaluate the clinical outcomes associated with molecular tumor board (MTB) review in patients with cancer. METHODS A systematic search of PubMed was performed to identify studies reporting clinical outcomes in patients with cancer who were reviewed by an MTB. To be included, studies had to report clinical outcomes, including clinical benefit, response, progression-free survival, or overall survival. Two reviewers independently selected studies and assessed quality with the Quality Assessment Tool for Before-After (Pre-Post) Studies with No Control Group or the Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies depending on the type of study being reviewed. RESULTS Fourteen studies were included with a total of 3,328 patients with cancer. All studies included patients without standard-of-care treatment options and usually with multiple prior lines of therapy. In studies reporting response rates, patients receiving MTB-recommended therapy had overall response rates ranging from 0% to 67%. In the only trial powered on clinical outcome and including a control group, the group receiving MTB-recommended therapy had significantly improved rate of progression-free survival compared with those receiving conventional therapy. CONCLUSION Although data quality is limited by a lack of prospective randomized controlled trials, MTBs appear to improve clinical outcomes for patients with cancer. Future research should concentrate on prospective trials and standardization of approach and outcomes.
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Affiliation(s)
- Kara L. Larson
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
| | - Bin Huang
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
- Kentucky Cancer Registry, University of
Kentucky, Lexington, Kentucky
| | - Heidi L. Weiss
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
| | - Pam Hull
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
| | - Philip M. Westgate
- Department of Biostatistics, University of
Kentucky, Lexington, Kentucky
| | - Rachel W. Miller
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
- Department of Obstetrics and Gynecology,
University of Kentucky, Lexington, Kentucky
| | - Susanne M. Arnold
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
- Department of Internal Medicine,
University of Kentucky, Lexington, Kentucky
| | - Jill M. Kolesar
- Markey Cancer Center, University of
Kentucky, Lexington, Kentucky
- Department of Pharmacy Practice and
Science, University of Kentucky, Lexington, Kentucky
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4
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Martin AR, Atkinson EG, Chapman SB, Stevenson A, Stroud RE, Abebe T, Akena D, Alemayehu M, Ashaba FK, Atwoli L, Bowers T, Chibnik LB, Daly MJ, DeSmet T, Dodge S, Fekadu A, Ferriera S, Gelaye B, Gichuru S, Injera WE, James R, Kariuki SM, Kigen G, Koenen KC, Kwobah E, Kyebuzibwa J, Majara L, Musinguzi H, Mwema RM, Neale BM, Newman CP, Newton CRJC, Pickrell JK, Ramesar R, Shiferaw W, Stein DJ, Teferra S, van der Merwe C, Zingela Z. Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. Am J Hum Genet 2021; 108:656-668. [PMID: 33770507 PMCID: PMC8059370 DOI: 10.1016/j.ajhg.2021.03.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/05/2021] [Indexed: 12/21/2022] Open
Abstract
Genetic studies in underrepresented populations identify disproportionate numbers of novel associations. However, most genetic studies use genotyping arrays and sequenced reference panels that best capture variation most common in European ancestry populations. To compare data generation strategies best suited for underrepresented populations, we sequenced the whole genomes of 91 individuals to high coverage as part of the Neuropsychiatric Genetics of African Population-Psychosis (NeuroGAP-Psychosis) study with participants from Ethiopia, Kenya, South Africa, and Uganda. We used a downsampling approach to evaluate the quality of two cost-effective data generation strategies, GWAS arrays versus low-coverage sequencing, by calculating the concordance of imputed variants from these technologies with those from deep whole-genome sequencing data. We show that low-coverage sequencing at a depth of ≥4× captures variants of all frequencies more accurately than all commonly used GWAS arrays investigated and at a comparable cost. Lower depths of sequencing (0.5-1×) performed comparably to commonly used low-density GWAS arrays. Low-coverage sequencing is also sensitive to novel variation; 4× sequencing detects 45% of singletons and 95% of common variants identified in high-coverage African whole genomes. Low-coverage sequencing approaches surmount the problems induced by the ascertainment of common genotyping arrays, effectively identify novel variation particularly in underrepresented populations, and present opportunities to enhance variant discovery at a cost similar to traditional approaches.
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Affiliation(s)
- Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
| | - Elizabeth G Atkinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sinéad B Chapman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Anne Stevenson
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rocky E Stroud
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dickens Akena
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Melkam Alemayehu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fred K Ashaba
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lukoye Atwoli
- Department of Mental Health, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Tera Bowers
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Lori B Chibnik
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Institute for Molecular Medicine Finland, Helsinki 00014, Finland
| | - Timothy DeSmet
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Sheila Dodge
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Abebaw Fekadu
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia; Centre for Innovative Drug Development & Therapeutic Trials for Africa, Addis Ababa University, Addis Ababa, Ethiopia
| | - Steven Ferriera
- Broad Genomics, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Stella Gichuru
- Department of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Wilfred E Injera
- Department of Immunology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Roxanne James
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Symon M Kariuki
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Gabriel Kigen
- Department of Pharmacology and Toxicology, School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Karestan C Koenen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Edith Kwobah
- Department of Mental Health, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Joseph Kyebuzibwa
- Department of Psychiatry, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lerato Majara
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; SA MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa
| | - Henry Musinguzi
- Department of Immunology & Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rehema M Mwema
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Carter P Newman
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Charles R J C Newton
- Neurosciences Unit, Clinical Department, KEMRI-Wellcome Trust Research Programme-Coast, Kilifi, Kenya; Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | | | - Raj Ramesar
- SA MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Welelta Shiferaw
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa; SA MRC Unit on Risk & Resilience in Mental Disorders, University of Cape Town and Neuroscience Institute, Cape Town, South Africa
| | - Solomon Teferra
- Department of Psychiatry, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Celia van der Merwe
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Zukiswa Zingela
- Department of Psychiatry and Human Behavioral Sciences, Walter Sisulu University, Mthatha, South Africa
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5
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Vanni I, Casula M, Pastorino L, Manca A, Dalmasso B, Andreotti V, Pisano M, Colombino M, Pfeffer U, Tanda ET, Rozzo C, Paliogiannis P, Cossu A, Ghiorzo P, Palmieri G. Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI). Diagn Pathol 2020; 15:143. [PMID: 33317587 PMCID: PMC7737361 DOI: 10.1186/s13000-020-01052-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identification of somatic mutations in key oncogenes in melanoma is important to lead the effective and efficient use of personalized anticancer treatment. Conventional methods focus on few genes per run and, therefore, are unable to screen for multiple genes simultaneously. The use of Next-Generation Sequencing (NGS) technologies enables sequencing of multiple cancer-driving genes in a single assay, with reduced costs and DNA quantity needed and increased mutation detection sensitivity. METHODS We designed a customized IMI somatic gene panel for targeted sequencing of actionable melanoma mutations; this panel was tested on three different NGS platforms using 11 metastatic melanoma tissue samples in blinded manner between two EMQN quality certificated laboratory. RESULTS The detection limit of our assay was set-up to a Variant Allele Frequency (VAF) of 10% with a coverage of at least 200x. All somatic variants detected by all NGS platforms with a VAF ≥ 10%, were also validated by an independent method. The IMI panel achieved a very good concordance among the three NGS platforms. CONCLUSION This study demonstrated that, using the main sequencing platforms currently available in the diagnostic setting, the IMI panel can be adopted among different centers providing comparable results.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Milena Casula
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Antonella Manca
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Bruna Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marina Pisano
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Ulrich Pfeffer
- Tumor Epigenetics, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Carla Rozzo
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, L.go R Benzi, 10, 16132, Genoa, Italy.
- Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy.
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, National Research Council (CNR), Sassari, Italy
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6
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Germetaki T, Nicholls C, Adams RA, Braun M, Rogan J, Moghadam S, Lenfert E, Lukas A, Edelstein DL, Jones FS, Saunders MP. Blood-based RAS mutation testing: concordance with tissue-based RAS testing and mutational changes on progression. Future Oncol 2020; 16:2177-2189. [PMID: 32716216 DOI: 10.2217/fon-2020-0523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: To determine the concordance between plasma and tissue RAS mutation status in metastatic colorectal cancer patients to gauge whether blood-based testing is a viable alternative. We also evaluated the change in mutation status on progression. Materials/methods: RAS testing was performed on plasma from patients commencing first-line therapy (OncoBEAM™ RAS CEIVD kit). Results were then compared with formalin-fixed paraffin embedded tumor samples. Results: The overall percentage agreement (concordance) was 86.0% (86/100), which demonstrates that blood-based testing is an alternative to tissue-based testing. Reproducibility was 100% between three laboratories and 20% showed changes in their RAS mutational status on progression. Conclusion: These results show good concordance between tissue and plasma samples and suggest the need for longitudinal plasma testing during treatment to guide management decisions.
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Affiliation(s)
- Theodora Germetaki
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Camille Nicholls
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Richard A Adams
- Department of Medical Oncology, Velindre Hospital, Velindre Road, Cardiff, Wales CF14 2TL, UK
| | - Michael Braun
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Jane Rogan
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Sharzad Moghadam
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
| | - Eva Lenfert
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | - Antje Lukas
- Sysmex Inostics GmbH, Falkenried 88, Hamburg 20251, Germany
| | | | | | - Mark P Saunders
- Department of Medical & Clinical Oncology, The Christie Hospital, 550 Wilmslow Road, Manchester M20 4BX, UK
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Mosaab A, El-Ayadi M, Khorshed EN, Amer N, Refaat A, El-Beltagy M, Hassan Z, Soror SH, Zaghloul MS, El-Naggar S. Histone H3K27M Mutation Overrides Histological Grading in Pediatric Gliomas. Sci Rep 2020; 10:8368. [PMID: 32433577 PMCID: PMC7239884 DOI: 10.1038/s41598-020-65272-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Pediatric high-grade gliomas (HGG) are rare aggressive tumors that present a prognostic and therapeutic challenge. Diffuse midline glioma, H3K27M-mutant is a new entity introduced to HGG in the latest WHO classification. In this study we evaluated the presence of H3K27M mutation in 105 tumor samples histologically classified into low-grade gliomas (LGG) (n = 45), and HGG (n = 60). Samples were screened for the mutation in histone H3.3 and H3.1 variants to examine its prevalence, prognostic impact, and assess its potential clinical value in limited resource settings. H3K27M mutation was detected in 28 of 105 (26.7%) samples, and its distribution was significantly associated with midline locations (p-value < 0.0001) and HGG (p-value = 0.003). Overall and event- free survival (OS and EFS, respectively) of patients with mutant tumors did not differ significantly, neither according to histologic grade (OS p-value = 0.736, EFS p-value = 0.75) nor across anatomical sites (OS p-value = 0.068, EFS p-value = 0.153). Detection of H3K27M mutation in pediatric gliomas provides more precise risk stratification compared to traditional histopathological techniques. Hence, mutation detection should be pursued in all pediatric gliomas. Meanwhile, focusing on midline LGG can be an alternative in lower-middle-income countries to maximally optimize patients' treatment options.
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Affiliation(s)
- Amal Mosaab
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Moatasem El-Ayadi
- Children's Cancer Hospital Egypt 57357, Department of Pediatric Oncology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Pediatric Oncology, Cairo, Egypt
| | - Eman N Khorshed
- Children's Cancer Hospital Egypt 57357, Department of Surgical Pathology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Surgical Pathology, Cairo, Egypt
| | - Nada Amer
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt
| | - Amal Refaat
- Children's Cancer Hospital Egypt 57357, Department of Radiology, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiology, Cairo, Egypt
| | - Mohamed El-Beltagy
- Children's Cancer Hospital Egypt 57357, Department of Neurosurgery, Cairo, Egypt
- Faculty of Medicine, Cairo University, Department of Neurosurgery, Cairo, Egypt
| | - Zeinab Hassan
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Sameh H Soror
- Faculty of Pharmacy, Helwan University, Department of Biochemistry and Molecular Biology, Cairo, Egypt
| | - Mohamed Saad Zaghloul
- Children's Cancer Hospital Egypt 57357, Department of Radiotherapy, Cairo, Egypt
- National Cancer Institute, Cairo University, Department of Radiotherapy, Cairo, Egypt
| | - Shahenda El-Naggar
- Children's Cancer Hospital Egypt 57357, Tumor Biology Research Program, Research Department, Cairo, Egypt.
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Flegr J, Tureček P. New approach and new permutation tests with R programs for analyses of false-negative-contaminated data in medicine and biology. Biol Open 2020; 9:bio045948. [PMID: 31953266 PMCID: PMC6994960 DOI: 10.1242/bio.045948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022] Open
Abstract
Statistically, the concentration of antibodies against parasites decreases with the duration of infection. This can result in false-negative outcomes of diagnostic tests for subjects with old infections. When a property of seronegative and seropositive subjects is compared under these circumstances, the statistical tests can detect no difference between these two groups of subjects, despite the fact that they differ. When the effect of the infection has a cumulative character and subjects with older infections are affected to a greater degree, we may even get paradoxical results of the comparison - the seropositive subjects have, on average, a higher value of certain traits despite the infection having a negative effect on those traits. A permutation test for the contaminated data implemented, e.g. in the program Treept or available as a comprehensibly commented R function at https://github.com/costlysignalling/Permutation_test_for_contaminated_data, can be used to reveal and to eliminate the effect of false negatives. A Monte Carlo simulation in the program R showed that our permutation test is a conservative test - it could provide false negative, but not false positive, results if the studied population contains no false-negative subjects. A new R version of the test was expanded by skewness analysis, which helps to estimate the proportion of false-negative subjects based on the assumption of equal data skewness in groups of healthy and infected subjects. Based on the results of simulations and our experience with empirical studies we recommend the usage of a permutation test for contaminated data whenever seronegative and seropositive individuals are compared.
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Affiliation(s)
- Jaroslav Flegr
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Viničná 7, Prague, 128 43, Czech Republic
- Department of Applied Neurosciences and Brain Imagination, National Institute of Mental Health, Topolová 748, Klecany, 250 67, Czech Republic
| | - Petr Tureček
- Department of Philosophy and History of Science, Faculty of Science, Charles University, Viničná 7, Prague, 128 43, Czech Republic
- Department of Applied Neurosciences and Brain Imagination, National Institute of Mental Health, Topolová 748, Klecany, 250 67, Czech Republic
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9
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Halk AB, Potjer TP, Kukutsch NA, Vasen HFA, Hes FJ, van Doorn R. Surveillance for familial melanoma: recommendations from a national centre of expertise. Br J Dermatol 2019; 181:594-596. [PMID: 30742720 DOI: 10.1111/bjd.17767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- A B Halk
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - T P Potjer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - N A Kukutsch
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - H F A Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - F J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - R van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
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Li D, Kim W, Wang L, Yoon KA, Park B, Park C, Kong SY, Hwang Y, Baek D, Lee ES, Won S. Comparison of INDEL Calling Tools with Simulation Data and Real Short-Read Data. IEEE/ACM Trans Comput Biol Bioinform 2019; 16:1635-1644. [PMID: 30004886 DOI: 10.1109/tcbb.2018.2854793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Insertions and deletions (INDELs) comprise a significant proportion of human genetic variation, and recent papers have revealed that many human diseases may be attributable to INDELs. With the development of next-generation sequencing (NGS) technology, many statistical/computational tools have been developed for calling INDELs. However, there are differences among those tools, and comparisons among them have been limited. In order to better understand these inter-tool differences, five popular and publicly available INDEL calling tools-GATK HaplotypeCaller, Platypus, VarScan2, Scalpel, and GotCloud-were evaluated using simulation data, 1000 Genomes Project data, and family-based sequencing data. The accuracy of INDEL calling by each tool was mainly evaluated by concordance rates. Family-based sequencing data, which consisted of 49 individuals from eight Korean families, were used to calculate Mendelian error rates. Our comparison results show that GATK HaplotypeCaller usually performs the best and that joint calling with Platypus can lead to additional improvements in accuracy. The result of this study provides important information regarding future directions for the variant detection and the algorithms development.
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Maura F, Degasperi A, Nadeu F, Leongamornlert D, Davies H, Moore L, Royo R, Ziccheddu B, Puente XS, Avet-Loiseau H, Campbell PJ, Nik-Zainal S, Campo E, Munshi N, Bolli N. A practical guide for mutational signature analysis in hematological malignancies. Nat Commun 2019; 10:2969. [PMID: 31278357 PMCID: PMC6611883 DOI: 10.1038/s41467-019-11037-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 06/10/2019] [Indexed: 02/08/2023] Open
Abstract
Analysis of mutational signatures is becoming routine in cancer genomics, with implications for pathogenesis, classification, prognosis, and even treatment decisions. However, the field lacks a consensus on analysis and result interpretation. Using whole-genome sequencing of multiple myeloma (MM), chronic lymphocytic leukemia (CLL) and acute myeloid leukemia, we compare the performance of public signature analysis tools. We describe caveats and pitfalls of de novo signature extraction and fitting approaches, reporting on common inaccuracies: erroneous signature assignment, identification of localized hyper-mutational processes, overcalling of signatures. We provide reproducible solutions to solve these issues and use orthogonal approaches to validate our results. We show how a comprehensive mutational signature analysis may provide relevant biological insights, reporting evidence of c-AID activity among unmutated CLL cases or the absence of BRCA1/BRCA2-mediated homologous recombination deficiency in a MM cohort. Finally, we propose a general analysis framework to ensure production of accurate and reproducible mutational signature data.
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Affiliation(s)
- Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy.
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Andrea Degasperi
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Ferran Nadeu
- Patologia Molecular de Neoplàsies Limfoides, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Daniel Leongamornlert
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Helen Davies
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Luiza Moore
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08036, Barcelona, Spain
| | - Bachisio Ziccheddu
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy
| | - Xose S Puente
- Unitat Hematopatologia, Hospital Clínic of Barcelona, Universitat de Barcelona, 08036, Barcelona, Spain
- Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de Oncologia (IUOPA), Universidad de Oviedo, Oviedo, 33003, Spain
| | | | - Peter J Campbell
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Serena Nik-Zainal
- Cancer, Ageing, and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Medical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Elias Campo
- Patologia Molecular de Neoplàsies Limfoides, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08036, Barcelona, Spain
| | - Nikhil Munshi
- Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, MA, USA
- Veterans Administration Boston Healthcare System, West Roxbury, 02130, MA, USA
| | - Niccolò Bolli
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, Milan, 20122, Italy.
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, 20133, Italy.
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Choi SY, Kim HW, Jeon SH, Kim BN, Kang N, Yeo CD, Park CK, Kim YK, Lee YH, Lee KY, Lee SH, Park JY, Park MS, Yim HW, Kim SJ. Comparison of PANAMutyper and PNAClamp for Detecting KRAS Mutations from Patients With Malignant Pleural Effusion. In Vivo 2019; 33:945-954. [PMID: 31028221 PMCID: PMC6559923 DOI: 10.21873/invivo.11563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 03/08/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND/AIM KRAS is one of the frequently mutated genes in human cancers and often relates with drug resistance and poor prognosis. PANAMutyper™ is a novel technology that integrates PNAClamp™ and PANA S-Melting™. In the present study, PANAMutyper™ and PNAClamp™ were compared for the detection of KRAS mutations using different samples of patients with malignant pleural effusion. PATIENTS AND METHODS A total of 103 patients (including 56 lung adenocarcinoma, 10 lung squamous carcinoma, 17 small cell lung cancer, 3 large cell lung cancer, 3 stomach cancer, 2 ovarian cancer, and others) with malignant pleural effusion were investigated using matched tumor tissue, cell block, and pleural effusion samples. The diagnostic performance of these two methods was compared. RESULTS KRAS mutations were detected in 18 (17.5%) of 103 patients using tissue, cell block, and pleural effusion samples. All 18 patients with KRAS mutations were detected by PANAMutyper™ using any sample type, however, only 7 cases were detected by PNAClamp™. Among the subtypes of KRAS mutations, substitution in codon 12, 35G>T was the most frequent, followed by substitution in codon 12, 35G>A and codon 12, 34G>A. In pleural effusion specimens, PANAMutyper™ showed a better diagnostic performance compared to PNAClamp™. CONCLUSION PANAMutyper™ had a diagnostic superiority for the detection of KRAS mutations in patients with malignant pleural effusion compared to PNAClamp™, although there was a concordance between PANAMutyper™ and PNAClamp™ results. Therefore, PANAMutyper™ can be used for a more sensitive and accurate detection of KRAS mutations.
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Affiliation(s)
- Su Yeon Choi
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyung Woo Kim
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang Hoon Jeon
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bit Na Kim
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nahyeon Kang
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chang Dong Yeo
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chan Kwon Park
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Kyoon Kim
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoon Ho Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyo Young Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sug Hyung Lee
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, U.S.A
| | - Mi Sun Park
- Department of Biostatistics, Clinical Research Coordinating Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyeon Woo Yim
- Department of Biostatistics, Clinical Research Coordinating Center, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Joon Kim
- Division of Pulmonology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- The Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Pasello G, Vicario G, Zustovich F, Oniga F, Gori S, Rosetti F, Bonetti A, Favaretto A, Toso S, Redelotti R, Santo A, Bernardi D, Giovanis P, Oliani C, Calvetti L, Gatti C, Palazzolo G, Baretta Z, Bortolami A, Bonanno L, Basso M, Menis J, Corte DD, Frega S, Guarneri V, Conte P. From Diagnostic-Therapeutic Pathways to Real-World Data: A Multicenter Prospective Study on Upfront Treatment for EGFR-Positive Non-Small Cell Lung Cancer (MOST Study). Oncologist 2019; 24:e318-e326. [PMID: 30846513 DOI: 10.1634/theoncologist.2018-0712] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/25/2019] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Gefitinib, erlotinib, and afatinib represent the approved first-line options for epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC). Because pivotal trials frequently lack external validity, real-world data may help to depict the diagnostic-therapeutic pathway and treatment outcome in clinical practice. METHODS MOST is a multicenter observational study promoted by the Veneto Oncology Network, aiming at monitoring the diagnostic-therapeutic pathway of patients with nonsquamous EGFR-mutant NSCLC. We reported treatment outcome in terms of median time to treatment failure (mTTF) and assessed the impact of each agent on the expense of the regional health system, comparing it with a prediction based on the pivotal trials. RESULTS An EGFR mutation test was performed in 447 enrolled patients, of whom 124 had EGFR mutation and who received gefitinib (n = 69, 55%), erlotinib (n = 33, 27%), or afatinib (n = 22, 18%) as first-line treatment. Because erlotinib was administered within a clinical trial to 15 patients, final analysis was limited to 109 patients. mTTF was 15.3 months, regardless of the type of tyrosine kinase inhibitor (TKI) used. In the MOST study, the budget impact analysis showed a total expense of €3,238,602.17, whereas the cost estimation according to median progression-free survival from pivotal phase III trials was €1,813,557.88. CONCLUSION Good regional adherence and compliance to the diagnostic-therapeutic pathway defined for patients with nonsquamous NSCLC was shown. mTTF did not significantly differ among the three targeted TKIs. Our budget impact analysis suggests the potential application of real-world data in the process of drug price negotiation. IMPLICATIONS FOR PRACTICE The MOST study is a real-world data collection reporting a multicenter adherence and compliance to diagnostic-therapeutic pathways defined for patients with epidermal growth factor receptor-mutant non-small cell lung cancer. This represents an essential element of evidence-based medicine, providing information on patients and situations that may be challenging to assess using only data from randomized controlled trials, e.g., turn-around time of diagnostic tests, treatment compliance and persistence, guideline adherence, challenging-to-treat populations, drug safety, comparative effectiveness, and cost effectiveness. This study may be of interest to various stakeholders (patients, clinicians, and payers), providing a meaningful picture of the value of a given therapy in routine clinical practice.
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Affiliation(s)
- Giulia Pasello
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
| | - Giovanni Vicario
- Medical Oncology, Azienda Unità Locale Socio Sanitaria (AULSS) 2 Marca Trevigiana, San Giacomo Hospital, Castelfranco Veneto, Italy
| | - Fable Zustovich
- Clinical Oncology Department, AULSS 1 Dolomiti, San Martino Hospital, Belluno, Italy
| | - Francesco Oniga
- Medical Oncology, AULSS 3 Serenissima, Angelo Hospital, Venezia-Mestre, Italy
| | - Stefania Gori
- Medical Oncology, Sacro Cuore-Don Calabria Hospital, Cancer Care Center, Negrar, Italy
| | - Francesco Rosetti
- Oncology and Oncological Hematology, AULSS 3 Serenissima, Mirano-Dolo Hospital, Venezia, Italy
| | - Andrea Bonetti
- Department of Oncology, AULSS 9 Scaligera, Mater Salutis Hospital, Legnago, Italy
| | - Adolfo Favaretto
- Department of Medical Oncology, AULSS 2 Marca Trevigiana, Ca'Foncello Hospital, Treviso, Italy
| | - Silvia Toso
- Medical Oncology, AULSS 5 Polesana, Adria Hospital, Adria, Italy
| | - Roberta Redelotti
- Medical Oncology, AULSS 6 Euganea, South Padova Hospital, Padova, Italy
| | - Antonio Santo
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integra (AOUI) Verona, Verona, Italy
| | - Daniele Bernardi
- Medical Oncology, AULSS 4, San Donà Hospital, San Donà di Piave, Italy
| | - Petros Giovanis
- Medical Oncology, AULSS 1 Dolomiti, Santa Maria del Prato Hospital, Feltre, Italy
| | - Cristina Oliani
- Oncology Unit, AULSS 8, Montecchio Maggiore Hospital, Monteccio Maggiore, Italy
| | - Lorenzo Calvetti
- Department of Oncology, San Bortolo General Hospital, AULSS 8 Berica, Vicenza, Italy
| | - Carlo Gatti
- Medical Oncology, AULSS 3 Serenissima, Chioggia Hospital, Chioggia, Italy
| | - Giovanni Palazzolo
- Medical Oncology, AULSS 6 Euganea, Cittadella Camposampiero Hospital, Camposampiero, Italy
| | - Zora Baretta
- Oncology Unit, AULSS 8, Montecchio Maggiore Hospital, Monteccio Maggiore, Italy
| | - Alberto Bortolami
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
| | - Laura Bonanno
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
| | - Marco Basso
- Medical Oncology, Azienda Unità Locale Socio Sanitaria (AULSS) 2 Marca Trevigiana, San Giacomo Hospital, Castelfranco Veneto, Italy
| | - Jessica Menis
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Oncological, Surgical, and Gastroenterological Sciences Department, University of Padova, Padova, Italy
| | - Donatella Da Corte
- Clinical Oncology Department, AULSS 1 Dolomiti, San Martino Hospital, Belluno, Italy
| | - Stefano Frega
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Oncological, Surgical, and Gastroenterological Sciences Department, University of Padova, Padova, Italy
| | - PierFranco Conte
- Medical Oncology 2, Istituto Oncologico Veneto (IOV) Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Oncological, Surgical, and Gastroenterological Sciences Department, University of Padova, Padova, Italy
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Normanno N, Denis MG, Thress KS, Ratcliffe M, Reck M. Guide to detecting epidermal growth factor receptor (EGFR) mutations in ctDNA of patients with advanced non-small-cell lung cancer. Oncotarget 2017; 8:12501-12516. [PMID: 27980215 PMCID: PMC5355360 DOI: 10.18632/oncotarget.13915] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 11/24/2016] [Indexed: 12/31/2022] Open
Abstract
Cancer treatment is evolving towards therapies targeted at specific molecular abnormalities that drive tumor growth. Consequently, to determine which patients are eligible, accurate assessment of molecular aberrations within tumors is required. Obtaining sufficient tumor tissue for molecular testing can present challenges; therefore, circulating free tumor-derived DNA (ctDNA) found in blood plasma has been proposed as an alternative source of tumor DNA. The diagnostic utility of ctDNA for the detection of epidermal growth factor receptor (EGFR) mutations harbored in tumors of patients with advanced non-small-cell lung cancer (NSCLC) is supported by the results of several large studies/meta-analyses. However, recent real-world studies suggest that the performance of ctDNA testing varies between geographic regions/laboratories, demonstrating the need for standardized guidance. In this review, we outline recommendations for obtaining an accurate result using ctDNA, relating to pre-analytical plasma processing, ctDNA extraction, and appropriate EGFR mutation detection methods, based on clinical trial results. We conclude that there are several advantages associated with ctDNA, including the potential for repeated sampling - particularly following progression after first-line tyrosine kinase inhibitor (TKI) therapy, as TKIs targeting resistance mutations (eg T790M) are now approved for use in the USA/EU/Japan (at time of writing). However, evidence suggests that ctDNA does not allow detection of EGFR mutations in all patients with known mutation-positive NSCLC. Therefore, although tumor tissue should be the first sample choice for EGFR testing at diagnosis, ctDNA is a promising alternative diagnostic approach.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori Fondazione Giovanni Pascale, IRCCS, Napoli, Italy
| | - Marc G. Denis
- Department of Biochemistry, Nantes University Hospital, Nantes, France
| | | | | | - Martin Reck
- Department of Thoracic Oncology, LungenClinic Grosshansdorf, Grosshansdorf, Airway Research Center North (ARCN), Member of the German Centre for Lung Research (DZL), Germany
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Kugelman JR, Wiley MR, Nagle ER, Reyes D, Pfeffer BP, Kuhn JH, Sanchez-Lockhart M, Palacios GF. Error baseline rates of five sample preparation methods used to characterize RNA virus populations. PLoS One 2017; 12:e0171333. [PMID: 28182717 PMCID: PMC5300104 DOI: 10.1371/journal.pone.0171333] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/18/2017] [Indexed: 11/19/2022] Open
Abstract
Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic “no amplification” method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a “targeted” amplification method, sequence-independent single-primer amplification (SISPA) as a “random” amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced “no amplification” method, and Illumina TruSeq RNA Access as a “targeted” enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4−5) of all compared methods.
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Affiliation(s)
- Jeffrey R. Kugelman
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Michael R. Wiley
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Elyse R. Nagle
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Daniel Reyes
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Brad P. Pfeffer
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
| | - Gustavo F. Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, Maryland, United States of America
- * E-mail:
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16
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Song C, Liu Y, Fontana R, Makrigiorgos A, Mamon H, Kulke MH, Makrigiorgos GM. Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment. Nucleic Acids Res 2016; 44:e146. [PMID: 27431322 PMCID: PMC5100565 DOI: 10.1093/nar/gkw650] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/27/2016] [Accepted: 07/10/2016] [Indexed: 12/13/2022] Open
Abstract
Presence of excess unaltered, wild-type (WT) DNA providing no information of biological or clinical value often masks rare alterations containing diagnostic or therapeutic clues in cancer, prenatal diagnosis, infectious diseases or organ transplantation. With the surge of high-throughput technologies there is a growing demand for removing unaltered DNA over large pools-of-sequences. Here we present nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO), a single-step approach with broad genome coverage that can remove WT-DNA from numerous sequences simultaneously, prior to genomic analysis. NaME-PrO employs a double-strand-DNA-specific nuclease and overlapping oligonucleotide-probes interrogating WT-DNA targets and guiding nuclease digestion to these sites. Mutation-containing DNA creates probe-DNA mismatches that inhibit digestion, thus subsequent DNA-amplification magnifies DNA-alterations at all selected targets. We demonstrate several-hundred-fold mutation enrichment in diverse human samples on multiple clinically relevant targets including tumor samples and circulating DNA in 50-plex reactions. Enrichment enables routine mutation detection at 0.01% abundance while by adjusting conditions it is possible to sequence mutations down to 0.00003% abundance, or to scan tumor-suppressor genes for rare mutations. NaME-PrO introduces a simple and highly parallel process to remove un-informative DNA sequences and unmask clinically and biologically useful alterations.
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Affiliation(s)
- Chen Song
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yibin Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Fontana
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harvey Mamon
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew H Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - G Mike Makrigiorgos
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Kakavand H, Walker E, Lum T, Wilmott JS, Selinger CI, Smith E, Saw RPM, Yu B, Cooper WA, Long GV, O'Toole SA, Scolyer RA. BRAF(V600E) and NRAS(Q61L/Q61R) mutation analysis in metastatic melanoma using immunohistochemistry: a study of 754 cases highlighting potential pitfalls and guidelines for interpretation and reporting. Histopathology 2016; 69:680-6. [PMID: 27151331 DOI: 10.1111/his.12992] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/04/2016] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS BRAF or NRAS mutations occur in approximately 60% of cutaneous melanomas, and the identification of such mutations underpins the appropriate selection of patients who may benefit from BRAF and MEK inhibitor targeted therapies. The utility of immunohistochemistry (IHC) to detect NRAS(Q61L) mutations is currently unknown. This study sought to assess the sensitivity and specificity of anti-BRAF(V600E) (VE1), anti-NRAS(Q61R) (SP174) and anti-NRAS(Q61L) (26193) antibodies for mutation detection in a large series of cases. METHODS AND RESULTS Mutation status was determined using the OncoCarta assay in 754 cutaneous melanomas. IHC with the anti-BRAF(V600E) antibody was performed in all cases, and the anti-NRAS(Q61R) and anti-NRAS(Q61L) antibodies were assessed in a subset of 302 samples utilizing tissue microarrays. The staining with the anti-BRAF(V600E) and anti-NRAS(Q61R) antibodies was diffuse, homogeneous and cytoplasmic. The anti-NRAS(Q61L) antibody displayed variable intensity staining, ranging from weak to strong in NRAS(Q61L) mutant tumours. The sensitivity and specificity for anti-BRAF(V600E) was 100 and 99.3%, anti-NRAS(Q61R) was 100 and 100% and anti-NRAS(Q61L) was 82.6 and 96.2%, respectively. CONCLUSIONS The use of IHC is a fast, efficient and cost-effective method to identify single specific mutations in melanoma patients. BRAF(V600E) and NRAS(Q61R) antibodies have high sensitivity and specificity; however, the NRAS(Q61L) antibody appears less sensitive. IHC can help to facilitate the timely, appropriate selection and treatment of metastatic melanoma patients with targeted therapies. Detection of melanoma-associated mutations by IHC may also provide evidence for a diagnosis of melanoma in metastatic undifferentiated neoplasms lacking expression of melanoma antigens.
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Affiliation(s)
- Hojabr Kakavand
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Emily Walker
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Trina Lum
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Elizabeth Smith
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Bing Yu
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Wendy A Cooper
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, North Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Melanoma Oncology, Royal North Shore and Mater Hospital, Sydney, NSW, Australia
| | - Sandra A O'Toole
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, North Sydney, NSW, Australia.
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia.
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.
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18
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Abstract
The plasma enzyme butyrylcholinesterase (BChE) is of clinical interest because of the occurrence of genetic variants with decreased ability to hydrolyse, and therefore inactivate, muscle-relaxant drugs such as suxamethonium. Analysis of BChE involves the determination of both enzyme activity and biochemical phenotypes which are used to determine the risk of so-called 'scoline apnoea'. Problems in analysis arise from both the lack of a universally accepted reference method and the variety of substrates and conditions employed for the determination of activity and phenotypes. Phenotype is determined by the use of specific enzyme inhibitors that produce phenotype-specific patterns of 'inhibitor numbers'. DNA analysis is now possible, and true genotypes can be obtained. The nomenclature in use for cholinesterase studies can cause problems in interpretation and reporting as there is poor understanding of the difference between phenotype and genotype, and terms are often, inappropriately, transposed. Techniques for both biochemical and molecular analysis of the enzyme are discussed.
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Affiliation(s)
- Roberta Goodall
- The Cholinesterase Investigation Unit, Department of Clinical Biochemistry, North Bristol NHS Trust, Southmead Hospital, Bristol BS10 5NB, UK.
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19
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Richman SD, Adams R, Quirke P, Butler R, Hemmings G, Chambers P, Roberts H, James MD, Wozniak S, Bathia R, Pugh C, Maughan T, Jasani B. Pre-trial inter-laboratory analytical validation of the FOCUS4 personalised therapy trial. J Clin Pathol 2016; 69:35-41. [PMID: 26350752 PMCID: PMC4717430 DOI: 10.1136/jclinpath-2015-203097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/03/2015] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Molecular characterisation of tumours is increasing personalisation of cancer therapy, tailored to an individual and their cancer. FOCUS4 is a molecularly stratified clinical trial for patients with advanced colorectal cancer. During an initial 16-week period of standard first-line chemotherapy, tumour tissue will undergo several molecular assays, with the results used for cohort allocation, then randomisation. Laboratories in Leeds and Cardiff will perform the molecular testing. The results of a rigorous pre-trial inter-laboratory analytical validation are presented and discussed. METHODS Wales Cancer Bank supplied FFPE tumour blocks from 97 mCRC patients with consent for use in further research. Both laboratories processed each sample according to an agreed definitive FOCUS4 laboratory protocol, reporting results directly to the MRC Trial Management Group for independent cross-referencing. RESULTS Pyrosequencing analysis of mutation status at KRAS codons12/13/61/146, NRAS codons12/13/61, BRAF codon600 and PIK3CA codons542/545/546/1047, generated highly concordant results. Two samples gave discrepant results; in one a PIK3CA mutation was detected only in Leeds, and in the other, a PIK3CA mutation was only detected in Cardiff. pTEN and mismatch repair (MMR) protein expression was assessed by immunohistochemistry (IHC) resulting in 6/97 discordant results for pTEN and 5/388 for MMR, resolved upon joint review. Tumour heterogeneity was likely responsible for pyrosequencing discrepancies. The presence of signet-ring cells, necrosis, mucin, edge-effects and over-counterstaining influenced IHC discrepancies. CONCLUSIONS Pre-trial assay analytical validation is essential to ensure appropriate selection of patients for targeted therapies. This is feasible for both mutation testing and immunohistochemical assays and must be built into the workup of such trials. TRIAL REGISTRATION NUMBER ISRCTN90061564.
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Affiliation(s)
- Susan D Richman
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, St James Hospital, Leeds, UK
| | - Richard Adams
- Institute of Cancer & Genetics, Cardiff University School of Medicine, Velindre Hospital, Cardiff, UK
| | - Phil Quirke
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, St James Hospital, Leeds, UK
| | - Rachel Butler
- Cardiff and Vale UHB-Medical Genetics University Hospital of Wales, Heath Park, Cardiff, UK
| | - Gemma Hemmings
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, St James Hospital, Leeds, UK
| | - Phil Chambers
- Department of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, St James Hospital, Leeds, UK
| | - Helen Roberts
- Cardiff and Vale UHB-Medical Genetics University Hospital of Wales, Heath Park, Cardiff, UK
| | - Michelle D James
- Cardiff and Vale UHB- Histopathology University Hospital of Wales, Heath Park, Cardiff, UK
| | - Sue Wozniak
- Cardiff and Vale UHB- Histopathology University Hospital of Wales, Heath Park, Cardiff, UK
| | | | | | - Timothy Maughan
- Gray Laboratories, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Bharat Jasani
- Institute of Cancer and Genetics, Heath Park, Cardiff, UK
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20
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Araujo LH, Timmers C, Shilo K, Zhao W, Zhang J, Yu L, Natarajan TG, Miller CJ, Yilmaz AS, Liu T, Amann J, Lapa e Silva JR, Ferreira CG, Carbone DP. Impact of Pre-Analytical Variables on Cancer Targeted Gene Sequencing Efficiency. PLoS One 2015; 10:e0143092. [PMID: 26605948 PMCID: PMC4659597 DOI: 10.1371/journal.pone.0143092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/26/2015] [Indexed: 01/19/2023] Open
Abstract
Tumor specimens are often preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks, the most common clinical source for DNA sequencing. Herein, we evaluated the effect of pre-sequencing parameters to guide proper sample selection for targeted gene sequencing. Data from 113 FFPE lung tumor specimens were collected, and targeted gene sequencing was performed. Libraries were constructed using custom probes and were paired-end sequenced on a next generation sequencing platform. A PCR-based quality control (QC) assay was utilized to determine DNA quality, and a ratio was generated in comparison to control DNA. We observed that FFPE storage time, PCR/QC ratio, and DNA input in the library preparation were significantly correlated to most parameters of sequencing efficiency including depth of coverage, alignment rate, insert size, and read quality. A combined score using the three parameters was generated and proved highly accurate to predict sequencing metrics. We also showed wide read count variability within the genome, with worse coverage in regions of low GC content like in KRAS. Sample quality and GC content had independent effects on sequencing depth, and the worst results were observed in regions of low GC content in samples with poor quality. Our data confirm that FFPE samples are a reliable source for targeted gene sequencing in cancer, provided adequate sample quality controls are exercised. Tissue quality should be routinely assessed for pre-analytical factors, and sequencing depth may be limited in genomic regions of low GC content if suboptimal samples are utilized.
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Affiliation(s)
- Luiz H. Araujo
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Cynthia Timmers
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Konstantin Shilo
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Weiqiang Zhao
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Jianying Zhang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | | | | | - Ayse Selen Yilmaz
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, 43210, United States of America
- Biomedical Informatics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Tom Liu
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | - Joseph Amann
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
| | | | | | - David P. Carbone
- James Thoracic Center, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, 43210, United States of America
- * E-mail:
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Dumur CI, Almenara JA, Powers CN, Ferreira-Gonzalez A. Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing. Diagn Pathol 2015; 10:169. [PMID: 26376646 PMCID: PMC4573924 DOI: 10.1186/s13000-015-0403-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHP2) assay. METHODS The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC material was prepared from a mixture of cell lines derived from different cancers, comprising single nucleotide variants and small deletions on actionable genes at different allelic frequencies. RESULTS The CHP2 assay performed with high precision and sensitivity when custom variant calling pipeline parameters where established. In addition, all expected somatic variants in the QC material were consistently called at variant frequencies ranging from 9.1 % (CV = 11.1 %) to 37.9 % (CV = 2.8 %). CONCLUSIONS The availability of a reliable and cost-effective QC material is instrumental in assessing the performance of this or any targeted NGS assay that detects somatic variants in fixed solid tumor specimens.
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Affiliation(s)
- Catherine I Dumur
- Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA, 23298, USA.
| | - Jorge A Almenara
- Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA, 23298, USA.
| | - Celeste N Powers
- Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA, 23298, USA.
| | - Andrea Ferreira-Gonzalez
- Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA, 23298, USA.
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Jurkowska M, Gos A, Ptaszyński K, Michej W, Tysarowski A, Zub R, Siedlecki JA, Rutkowski P. Comparison between two widely used laboratory methods in BRAF V600 mutation detection in a large cohort of clinical samples of cutaneous melanoma metastases to the lymph nodes. Int J Clin Exp Pathol 2015; 8:8487-8493. [PMID: 26339422 PMCID: PMC4555750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/25/2015] [Indexed: 06/05/2023]
Abstract
AIMS The study compares detection rates of oncogenic BRAF mutations in a homogenous group of 236 FFPE cutaneous melanoma lymph node metastases, collected in one cancer center. BRAF mutational status was verified by two independent in-house PCR/Sanger sequencing tests, and the Cobas® 4800 BRAF V600 Mutation Test. RESULTS The best of two sequencing approaches returned results for 230/236 samples. In 140 (60.9%), the mutation in codon 600 of BRAF was found. 91.4% of all mutated cases (128 samples) represented p.V600E. Both Sanger-based tests gave reproducible results although they differed significantly in the percentage of amplifiable samples: 230/236 to 109/143. Cobas generated results in all 236 cases, mutations changing codon V600 were detected in 144 of them (61.0%), including 5 not amplifiable and 5 negative in the standard sequencing. However, 6 cases positive in sequencing turned out to be negative in Cobas. Both tests provided us with the same BRAF V600 mutational status in 219 out of 230 cases with valid results (95.2%). CONCLUSIONS The total BRAF V600 mutation detection rate didn't differ significantly between the two methodological approaches (60.9% vs. 61.0%). Sequencing was a reproducible method of V600 mutation detection and more powerful to detect mutations other than p.V600E, while Cobas test proved to be less susceptible to the poor DNA quality or investigator's bias. The study underlined an important role of pathologists in quality assurance of molecular diagnostics.
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Affiliation(s)
| | - Aleksandra Gos
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Konrad Ptaszyński
- Department of Pathology, Center of Postgraduate Medical EducationMarymoncka 99/103, Warsaw 01-809, Poland
| | - Wanda Michej
- Department of Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Andrzej Tysarowski
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Renata Zub
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
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23
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Zhang R, Han Y, Huang J, Ma L, Li Y, Li J. Results of first proficiency test for KRAS testing with formalin-fixed, paraffin-embedded cell lines in China. Clin Chem Lab Med 2015; 52:1851-7. [PMID: 24945428 DOI: 10.1515/cclm-2014-0227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/28/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND Laboratory testing for KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) mutations in metastatic colorectal cancer (mCRC) is performed by various methods in China, but there is no standardized system for proficiency testing or assay performance evaluations. The aim of this study was to evaluate assay and laboratory performance with artificial samples derived from formalin-fixed, paraffin-embedded (FFPE) cell lines. METHODS Artificial FFPE samples were prepared from cultured cell lines to construct a proficiency panel of 10 samples covering eight KRAS mutations and two wild-type samples. The samples were validated by Sanger sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The panel was distributed to participating laboratories and their reported results were compared to the reference sequences. RESULTS The percentages of mutant KRAS alleles in each mutant sample were more than 50% by MALDI-TOF-MS. Sixty-three laboratories reported results, including 41 hospital laboratories and 22 commercial laboratories and reagent manufacturers. Only 55.6% (35/63) of the laboratories correctly identified the mutations in all samples and 33.3% (21/63) reported at least one false-positive result. The false-positive ratio was 7.1% (45/630) and the false-negative ratio was 3.0% (15/504). CONCLUSIONS KRAS mutations can be missed even by the most sensitive methods if the procedures are not performed correctly. False-positive results are a substantial problem in KRAS testing; laboratories must use sufficient negative controls to identify cross-contamination from PCR-amplified products or between samples during handling and DNA extraction.
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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Yan L, Liu Y, Liu X, Xu F, Zhang K, Xu J, Li L. [Implementation of standard operation procedures for KRAS andBRAF gene mutation detection in colorectal cancer]. Zhonghua Bing Li Xue Za Zhi 2015; 44:55-58. [PMID: 25765033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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26
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Panka DJ, Buchbinder E, Giobbie-Hurder A, Schalck AP, Montaser-Kouhsari L, Sepehr A, Lawrence DP, McDermott DF, Cohen R, Carlson A, Wargo JA, Merritt R, Seery VJ, Hodi FS, Gunturi A, Fredrick D, Atkins MB, Iafrate AJ, Flaherty KT, Mier JW, Sullivan RJ. Clinical utility of a blood-based BRAF(V600E) mutation assay in melanoma. Mol Cancer Ther 2014; 13:3210-8. [PMID: 25319388 PMCID: PMC4258469 DOI: 10.1158/1535-7163.mct-14-0349] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BRAF inhibitors (BRAFi) have led to clinical benefit in patients with melanoma. The development of a blood-based assay to detect and quantify BRAF levels in these patients has diagnostic, prognostic, and predictive capabilities that could guide treatment decisions. Blood BRAF(V600E) detection and quantification were performed on samples from 128 patients with stage II (19), III (67), and IV (42) melanoma. Tissue BRAF analysis was performed in all patients with stage IV disease and in selected patients with stage II and III disease. Clinical outcomes were correlated to initial BRAF levels as well as BRAF level dynamics. Serial analysis was performed on 17 stage IV melanoma patients treated with BRAFi and compared with tumor measurements by RECIST. The assay was highly sensitive (96%) and specific (95%) in the stage IV setting, using a blood level of 4.8 pg as "positive." BRAF levels typically decreased following BRAFi. A subset of these patients (5) had an increase in BRAF(V600E) values 42 to 112 days before clinical or radiographic disease progression (PD). From 86 patients with resected, stage II or III melanoma, 39 had evidence of disease relapse (45.3%). Furthermore, BRAF mutation in the blood after surgical resection in these patients was not associated with a difference in relapse risk, although tissue BRAF status was only available for a subset of patients. In summary, we have developed a highly sensitive and specific, blood-based assay to detect BRAF(V600) mutation in patients with melanoma.
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Affiliation(s)
- David J Panka
- Beth Israel Deaconess Medical Center, Boston, Massachusetts.
| | | | | | | | | | - Alireza Sepehr
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | - Rachel Cohen
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | - Ryan Merritt
- Massachusetts General Hospital, Boston, Massachusetts
| | | | | | | | | | - Michael B Atkins
- Georgetown-Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | | | | | - James W Mier
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
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Beaudenon-Huibregtse S, Alexander EK, Guttler RB, Hershman JM, Babu V, Blevins TC, Moore P, Andruss B, Labourier E. Centralized molecular testing for oncogenic gene mutations complements the local cytopathologic diagnosis of thyroid nodules. Thyroid 2014; 24:1479-87. [PMID: 24811481 DOI: 10.1089/thy.2013.0640] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Molecular testing for oncogenic gene mutations and chromosomal rearrangements plays a growing role in the optimal management of thyroid nodules, yet lacks standardized testing modalities and systematic validation data. Our objective was to assess the performance of molecular cytology on preoperative thyroid nodule fine-needle aspirates (FNAs) across a broad range of variables, including independent collection sites, clinical practices, and anatomic pathology interpretations. METHODS Single-pass FNAs were prospectively collected from 806 nodules 1 cm or larger by ultrasonography at five independent sites across the United States. Specimens were shipped in a nucleic acid stabilization solution and tested at a centralized clinical laboratory. Seventeen genetic alterations (BRAF, KRAS, HRAS, and NRAS mutations, PAX8-PPARG and RET-PTC rearrangements) were evaluated by multiplex polymerase chain reaction and liquid bead array cytometry in 769 FNAs that met inclusion criteria. Cytology, histology, and clinical care followed local procedures and practices. All results were double-blinded. RESULTS Thirty-two specimens (4.2%) failed to yield sufficient nucleic acid to generate molecular data. A single genetic alteration was detected in 80% of cytology malignant cases, 21% of indeterminate, 7.8% of nondiagnostic, and 3.5% of benign cases. Among 109 nodules with surgical histology reference standard, oncogenic mutations were present in 50% of malignant nodules missed by cytology. There were 14 cancers not identified by cytology or molecular tests, including 5 carcinomas with histologic sizes less than 1 cm (3 multifocal) and 8 noninvasive follicular variants of papillary carcinoma (4 encapsulated). No mutations were detected in 89% of the nodules benign by histopathology with 6 false-positive molecular results in 5 adenomas (2-5.5 cm) and 1 cystic nodule with an incidental papillary microcarcinoma (0.15 cm). The posttest probability of thyroid cancer was 100% for nodules positive for BRAF or RET-PTC, 70% for RAS or PAX8-PPARG, and 88% for molecular cytology overall. CONCLUSIONS Centralized and standardized molecular testing for genetic alterations associated with a high risk of malignancy efficiently complements the local cytopathologic diagnosis of thyroid nodule aspirates in the clinical setting. Actionable molecular cytology can improve the personalized surgical and medical management of patients with thyroid cancers, facilitating one-stage total thyroidectomy and reducing the number of unnecessary diagnostic surgeries.
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Wong NACS, Gonzalez D, Salto-Tellez M, Butler R, Diaz-Cano SJ, Ilyas M, Newman W, Shaw E, Taniere P, Walsh SV. RAS testing of colorectal carcinoma—a guidance document from the Association of Clinical Pathologists Molecular Pathology and Diagnostics Group. J Clin Pathol 2014; 67:751-7. [PMID: 24996433 DOI: 10.1136/jclinpath-2014-202467] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Analysis of colorectal carcinoma (CRC) tissue for KRAS codon 12 or 13 mutations to guide use of anti-epidermal growth factor receptor (EGFR) therapy is now considered mandatory in the UK. The scope of this practice has been recently extended because of data indicating that NRAS mutations and additional KRAS mutations also predict for poor response to anti-EGFR therapy. The following document provides guidance on RAS (i.e., KRAS and NRAS) testing of CRC tissue in the setting of personalised medicine within the UK and particularly within the NHS. This guidance covers issues related to case selection, preanalytical aspects, analysis and interpretation of such RAS testing.
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Gentilini F, Turba ME. Optimization of the Divergent method for genotyping single nucleotide variations using SYBR Green-based single-tube real-time PCR. Mutat Res 2014; 766-767:14-18. [PMID: 25847266 DOI: 10.1016/j.mrfmmm.2014.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/10/2014] [Accepted: 05/21/2014] [Indexed: 06/04/2023]
Abstract
A novel technique, called Divergent, for single-tube real-time PCR genotyping of point mutations without the use of fluorescently labeled probes has recently been reported. This novel PCR technique utilizes a set of four primers and a particular denaturation temperature for simultaneously amplifying two different amplicons which extend in opposite directions from the point mutation. The two amplicons can readily be detected using the melt curve analysis downstream to a closed-tube real-time PCR. In the present study, some critical aspects of the original method were specifically addressed to further implement the technique for genotyping the DNM1 c.G767T mutation responsible for exercise-induced collapse in Labrador retriever dogs. The improved Divergent assay was easily set up using a standard two-step real-time PCR protocol. The melting temperature difference between the mutated and the wild-type amplicons was approximately 5°C which could be promptly detected by all the thermal cyclers. The upgraded assay yielded accurate results with 157pg of genomic DNA per reaction. This optimized technique represents a flexible and inexpensive alternative to the minor grove binder fluorescently labeled method and to high resolution melt analysis for high-throughput, robust and cheap genotyping of single nucleotide variations.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, via Tolara di Sopra 50, 40064 Ozzano dell'Emilia, Bologna, Italy.
| | - Maria E Turba
- Genefast srl, Via Castelfranco 17/d, 40053 Bazzano, Bologna, Italy.
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Canu L, Rapizzi E, Zampetti B, Fucci R, Nesi G, Richter S, Qin N, Giachè V, Bergamini C, Parenti G, Valeri A, Ercolino T, Eisenhofer G, Mannelli M. Pitfalls in genetic analysis of pheochromocytomas/paragangliomas-case report. J Clin Endocrinol Metab 2014; 99:2321-6. [PMID: 24758185 DOI: 10.1210/jc.2013-4453] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
CONTEXT About 35% of patients with pheochromocytoma/paraganglioma carry a germline mutation in one of the 10 main susceptibility genes. The recent introduction of next-generation sequencing will allow the analysis of all these genes in one run. When positive, the analysis is generally unequivocal due to the association between a germline mutation and a concordant clinical presentation or positive family history. When genetic analysis reveals a novel mutation with no clinical correlates, particularly in the presence of a missense variant, the question arises whether the mutation is pathogenic or a rare polymorphism. OBJECTIVE We report the case of a 35-year-old patient operated for a pheochromocytoma who turned out to be a carrier of a novel SDHD (succinate dehydrogenase subunit D) missense mutation. With no positive family history or clinical correlates, we decided to perform additional analyses to test the clinical significance of the mutation. METHODS We performed in silico analysis, tissue loss of heterozygosity analysis, immunohistochemistry, Western blot analysis, SDH enzymatic assay, and measurement of the succinate/fumarate concentration ratio in the tumor tissue by tandem mass spectrometry. RESULTS Although the in silico analysis gave contradictory results according to the different methods, all the other tests demonstrated that the SDH complex was conserved and normally active. We therefore came to the conclusion that the variant was a nonpathogenic polymorphism. CONCLUSIONS Advancements in technology facilitate genetic analysis of patients with pheochromocytoma but also offer new challenges to the clinician who, in some cases, needs clinical correlates and/or functional tests to give significance to the results of the genetic assay.
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Affiliation(s)
- Letizia Canu
- Department of Experimental and Clinical Biomedical Sciences (L.C., E.R., B.Z., R.F., V.G., M.M.), and Department of Human Pathology and Oncology (G.N.), University of Florence, 50134 Florence, Italy; General and Surgical Unit (C.B., A.V.), and Endocrinology Unit, Careggi Hospital (G.P., T.E.), Azienda Ospedaliera Universitaria Careggi, 50134 Florence, Italy; Division of Clinical Neurochemistry (S.R., N.Q., G.E.), Institute of Clinical Chemistry and Laboratory Medicine and Department of Medicine, Dresden University of Technology, 01069 Dresden, Germany; and Istituto Toscano Tumori (M.M.), 50139 Florence, Italy
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de Biase D, Visani M, Baccarini P, Polifemo AM, Maimone A, Fornelli A, Giuliani A, Zanini N, Fabbri C, Pession A, Tallini G. Next generation sequencing improves the accuracy of KRAS mutation analysis in endoscopic ultrasound fine needle aspiration pancreatic lesions. PLoS One 2014; 9:e87651. [PMID: 24504548 PMCID: PMC3913642 DOI: 10.1371/journal.pone.0087651] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/27/2013] [Indexed: 02/05/2023] Open
Abstract
The use of endoscopic ultrasonography has allowed for improved detection and pathologic analysis of fine needle aspirate material for pancreatic lesion diagnosis. The molecular analysis of KRAS has further improved the clinical sensitivity of preoperative analysis. For this reason, the use of highly analytical sensitive and specific molecular tests in the analysis of material from fine needle aspirate specimens has become of great importance. In the present study, 60 specimens from endoscopic ultrasonography fine needle aspirate were analyzed for KRAS exon 2 and exon 3 mutations, using three different techniques: Sanger sequencing, allele specific locked nucleic acid PCR and Next Generation sequencing (454 GS-Junior, Roche). Moreover, KRAS was also tested in wild-type samples, starting from DNA obtained from cytological smears after pathological evaluation. Sanger sequencing showed a clinical sensitivity for the detection of the KRAS mutation of 42.1%, allele specific locked nucleic acid of 52.8% and Next Generation of 73.7%. In two wild-type cases the re-sequencing starting from selected material allowed to detect a KRAS mutation, increasing the clinical sensitivity of next generation sequencing to 78.95%. The present study demonstrated that the performance of molecular analysis could be improved by using highly analytical sensitive techniques. The Next Generation Sequencing allowed to increase the clinical sensitivity of the test without decreasing the specificity of the analysis. Moreover we observed that it could be useful to repeat the analysis starting from selectable material, such as cytological smears to avoid false negative results.
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Affiliation(s)
- Dario de Biase
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
- * E-mail:
| | - Michela Visani
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Paola Baccarini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
| | - Anna Maria Polifemo
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | | | - Adele Fornelli
- Anatomic Pathology Unit, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Adriana Giuliani
- Indiana University, Bloomington, Indiana, United States of America
| | - Nicola Zanini
- Unit of General Surgery, Azienda Unità Sanitaria Locale di Bologna - Maggiore Hospital, Bologna, Italy
| | - Carlo Fabbri
- Unit of Gastroenterology, Azienda Unità Sanitaria Locale di Bologna - Bellaria Hospital, Bologna, Italy
| | - Annalisa Pession
- Department of Pharmacology and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Department of Medicine (DIMES) – Anatomic Pathology Unit, Bellaria Hospital, University of Bologna, Bologna, Italy
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Lee ST, Kim SW, Ki CS, Jang JH, Shin JH, Oh YL, Kim JW, Chung JH. Clinical implication of highly sensitive detection of the BRAF V600E mutation in fine-needle aspirations of thyroid nodules: a comparative analysis of three molecular assays in 4585 consecutive cases in a BRAF V600E mutation-prevalent area. J Clin Endocrinol Metab 2012; 97:2299-306. [PMID: 22500044 DOI: 10.1210/jc.2011-3135] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Detection of the BRAF V600E mutation in fine-needle aspiration cytology (FNAC) specimens may increase the value of FNAC. OBJECTIVE The objectives of the study was to compare the diagnostic performance of BRAF assays that differ in sensitivity and to examine the associations between the BRAF V600E mutation status and the clinicopathological features in papillary thyroid carcinoma (PTC). DESIGN AND SETTING Three molecular assays were performed in all subjects and compared with regard to FNAC and histology results. PARTICIPANTS We evaluated 4585 consecutive patients who were found to have malignant or indeterminate thyroid nodules by ultrasonography. OUTCOME MEASURES All FNAC samples were tested for the BRAF V600E mutation using conventional Sanger sequencing, dual-priming oligonucleotide-PCR, and mutant enrichment with 3'-modified oligonucleotide (MEMO) sequencing. RESULTS The detection sensitivities of the three molecular assays for the BRAF V600E mutation were 20, 2, and 0.1%, respectively. Compared with conventional Sanger sequencing (n = 673), dual-priming oligonucleotide-PCR and MEMO sequencing detected more tumors with the BRAF V600E mutation (n = 919 and n = 1044, respectively), especially tumors with a benign, indeterminate, or nondiagnostic cytology. All BRAF-positive tumors that were histologically examined were shown to be PTC, regardless of cytology results. The clinical sensitivities of the three assays for detecting PTC were 54.8, 74.4, and 79.7%, respectively. BRAF V600E mutations in microcarcinomas (≤ 10 mm) were detected more efficiently as the detection sensitivity of the assay increased (P < 0.001). Tumor size correlated significantly with multifocality, extrathyroidal extension, and lymph node metastasis (P = 0.003, P < 0.001 and P < 0.001, respectively), but the BRAF V600E mutation status was not associated with any of those features. CONCLUSION Highly sensitive and specific molecular assays such as MEMO sequencing are optimal for detecting the BRAF mutations in thyroid FNAC because these techniques can detect PTC that might be missed by cytology or less sensitive molecular assays.
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Affiliation(s)
- Seung-Tae Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-Dong, Gangnam-Gu, Seoul 135-710 Korea
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[The outer quality control of identification of mutations of HIV drug resistance to anti-retrovirus preparations: the results of "HIV resistance-2009" program]. Klin Lab Diagn 2012;:35-8. [PMID: 22768716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The panel of control samples for outer quality control of laboratories functioning was developed to be implemented in the research of HIVdrug resistance to anti-retrovirus preparations. The first cycle of outer quality control was applied to identify mutations of HIV drug resistance to anti-retrovirus preparations. The results of cycle revealed certain significant issues and determined the need in regular implementation of studies of this kind in future.
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Amosenko FA, Karpov IV, Poliakov AV, Kovalenko SP, Shamanin VA, Liubchenko LN. [Comparison of different methods of molecular-genetic analysis of somatic mutations in K-ras gene in patients with colorectal cancer]. Vestn Ross Akad Med Nauk 2012:35-41. [PMID: 22642176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Two approaches to somatic point mutations in 12 and 13 codones of K-ras gene were analyzed: PCR/SSCP/ACRS/sequencing and allele-specific PCR in the real-life regimen (Russian set "KRAS-7M"). The comparison was carried out on 62 examples of genomic DNA extracted from frozen colon carcinomas, which underwent manual dissection. The results obtained in two attempts were consistent in 95,2% (N=59). Specificity and sensitivity of K-ras mutations detection using "KRAS-7M" set were 100 and 96,4% respectively, and 94,1 and 100% respectievly using PCR/SSCP/ACRS/automatic sequencing. False positive results were absent when detecting with "KRAS-7M" and accounted for 2 cases (5,9%) when using PCR/SSCP/ ACRS/automatic sequencing. The only false negative response (3,6%) was obtained analyzing mutations using "KRAS-7M".
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Affiliation(s)
- H P Kohler
- Laboratory for Hemostasis Research, Department of Hematology, University Hospital of Bern, Bern, Switzerland
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Shivarov V, Ivanova M, Hadjiev E, Naumova E. Rapid quantification of JAK2 V617F allele burden using a bead-based liquid assay with locked nucleic acid-modified oligonucleotide probes. Leuk Lymphoma 2011; 52:2023-6. [PMID: 21702645 DOI: 10.3109/10428194.2011.584995] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Bozzetti C, Negri FV, Naldi N, Nizzoli R, Bortesi B, Zobbi V, Azzoni C, Silini EM, Ardizzoni A. Reliability of K-ras mutational analysis on cytological samples from metastatic colorectal cancer. Pathologica 2011; 103:77-78. [PMID: 22007571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
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Bellon E, Ligtenberg MJL, Tejpar S, Cox K, de Hertogh G, de Stricker K, Edsjö A, Gorgoulis V, Höfler G, Jung A, Kotsinas A, Laurent-Puig P, López-Ríos F, Hansen TP, Rouleau E, Vandenberghe P, van Krieken JJM, Dequeker E. External quality assessment for KRAS testing is needed: setup of a European program and report of the first joined regional quality assessment rounds. Oncologist 2011; 16:467-78. [PMID: 21441573 DOI: 10.1634/theoncologist.2010-0429] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The use of epidermal growth factor receptor-targeting antibodies in metastatic colorectal cancer has been restricted to patients with wild-type KRAS tumors by the European Medicines Agency since 2008, based on data showing a lack of efficacy and potential harm in patients with mutant KRAS tumors. In an effort to ensure optimal, uniform, and reliable community-based KRAS testing throughout Europe, a KRAS external quality assessment (EQA) scheme was set up. The first large assessment round included 59 laboratories from eight different European countries. For each country, one regional scheme organizer prepared and distributed the samples for the participants of their own country. The samples included unstained sections of 10 invasive colorectal carcinomas with known KRAS mutation status. The samples were centrally validated by one of two reference laboratories. The laboratories were allowed to use their own preferred method for histological evaluation, DNA isolation, and mutation analysis. In this study, we analyze the setup of the KRAS scheme. We analyzed the advantages and disadvantages of the regional scheme organization by analyzing the outcome of genotyping results, analysis of tumor percentage, and written reports. We conclude that only 70% of laboratories correctly identified the KRAS mutational status in all samples. Both the false-positive and false-negative results observed negatively affect patient care. Reports of the KRAS test results often lacked essential information. We aim to further expand this program to more laboratories to provide a robust estimate of the quality of KRAS testing in Europe, and provide the basis for remedial measures and harmonization.
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Affiliation(s)
- Ellen Bellon
- University of Leuven, Centre for Human Genetics, Research Unit Biomedical Quality Assurance Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
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Psifidi A, Dovas C, Banos G. Novel quantitative real-time LCR for the sensitive detection of SNP frequencies in pooled DNA: method development, evaluation and application. PLoS One 2011; 6:e14560. [PMID: 21283808 PMCID: PMC3023722 DOI: 10.1371/journal.pone.0014560] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/20/2010] [Indexed: 11/19/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNP) have proven to be powerful genetic markers for genetic applications in medicine, life science and agriculture. A variety of methods exist for SNP detection but few can quantify SNP frequencies when the mutated DNA molecules correspond to a small fraction of the wild-type DNA. Furthermore, there is no generally accepted gold standard for SNP quantification, and, in general, currently applied methods give inconsistent results in selected cohorts. In the present study we sought to develop a novel method for accurate detection and quantification of SNP in DNA pooled samples. Methods The development and evaluation of a novel Ligase Chain Reaction (LCR) protocol that uses a DNA-specific fluorescent dye to allow quantitative real-time analysis is described. Different reaction components and thermocycling parameters affecting the efficiency and specificity of LCR were examined. Several protocols, including gap-LCR modifications, were evaluated using plasmid standard and genomic DNA pools. A protocol of choice was identified and applied for the quantification of a polymorphism at codon 136 of the ovine PRNP gene that is associated with susceptibility to a transmissible spongiform encephalopathy in sheep. Conclusions The real-time LCR protocol developed in the present study showed high sensitivity, accuracy, reproducibility and a wide dynamic range of SNP quantification in different DNA pools. The limits of detection and quantification of SNP frequencies were 0.085% and 0.35%, respectively. Significance The proposed real-time LCR protocol is applicable when sensitive detection and accurate quantification of low copy number mutations in DNA pools is needed. Examples include oncogenes and tumour suppressor genes, infectious diseases, pathogenic bacteria, fungal species, viral mutants, drug resistance resulting from point mutations, and genetically modified organisms in food.
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Affiliation(s)
- Androniki Psifidi
- Department of Animal Production, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysostomos Dovas
- Laboratory of Microbiology and Infectious Diseases, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
| | - Georgios Banos
- Department of Animal Production, Faculty of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Affiliation(s)
- E J Favaloro
- Department of Haematology, Institute of Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, Westmead, NSW, Australia.
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Abstract
Background Molecular tests for diagnosis of disease, particularly cancer, are gaining increased acceptance by physicians and their patients for disease prognosis and selection of treatment options. Gene expression profiles and genetic mutations are key parameters used for the molecular characterization of tumors. A variety of methods exist for mutation analysis but the development of assays with high selectivity tends to require a process of trial and error, and few are compatible with real-time PCR. We sought to develop a real-time PCR-based mutation assay methodology that successfully addresses these issues. Methodology/Principal Findings The method we describe is based on the widely used TaqMan® real-time PCR technology, and combines Allele-Specific PCR with a Blocking reagent (ASB-PCR) to suppress amplification of the wildype allele. ASB-PCR can be used for detection of germ line or somatic mutations in either DNA or RNA extracted from any type of tissue, including formalin-fixed paraffin-embedded tumor specimens. A set of reagent design rules was developed enabling sensitive and selective detection of single point substitutions, insertions, or deletions against a background of wild-type allele in thousand-fold or greater excess. Conclusions/Significance ASB-PCR is a simple and robust method for assaying single nucleotide mutations and polymorphisms within the widely used TaqMan® protocol for real time RT-PCR. The ASB-PCR design rules consistently produce highly selective mutation assays while obviating the need for redesign and optimization of the assay reagents. The method is compatible with formalin-fixed tissue and simultaneous analysis of gene expression by RT-PCR on the same plate. No proprietary reagents other than those for TaqMan chemistry are required, so the method can be performed in any research laboratory with real-time PCR capability.
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Affiliation(s)
- John Morlan
- Genomic Health, Inc., Redwood City, California, United States of America
| | - Joffre Baker
- Genomic Health, Inc., Redwood City, California, United States of America
| | - Dominick Sinicropi
- Genomic Health, Inc., Redwood City, California, United States of America
- * E-mail:
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Ross OA, Toft M, Haugarvoll K. Corticobasal syndrome and primary progressive aphasia as manifestations of lrrk2 gene mutations. Neurology 2008; 71:303; author reply 303-4. [PMID: 18645174 DOI: 10.1212/01.wnl.0000320511.30222.dd] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Abstract
BACKGROUND Mutations in the leucine-rich repeat kinase 2 gene (LRRK2) have become the most common known cause for developing Parkinson's disease. The frequency of mutations described in the literature varies widely depending on the population studied with most reports focusing only on screening for the most common G2019S mutation in exon 41. METHODS In this study seven exons (19, 24, 25, 31, 35, 38, and 41) in LRRK2 where mutations have been reported were screened in 230 unselected Parkinson's disease patients using denaturing high-performance liquid chromatography. RESULTS The sequencing of samples with heteroduplex profiles revealed five novel and two known intronic sequence variants. In our cohort, we were unable to detect any of the known mutations in these exons or identify novel mutations within the LRRK2 gene. CONCLUSIONS Therefore, despite the availability of diagnostic LRRK2 genetic testing it is unlikely to yield a positive result in this population.
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Affiliation(s)
- D A Grimes
- Department of Medicine, Division of Neurology, The Ottawa Hospital, Ottawa Health Research institute, University of Ottawa, ON, Canada
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Kraff J, Tang HT, Cilia R, Canesi M, Pezzoli G, Goldwurm S, Hagerman PJ, Tassone F. Screen for excess FMR1 premutation alleles among males with parkinsonism. ACTA ACUST UNITED AC 2007; 64:1002-6. [PMID: 17620491 DOI: 10.1001/archneur.64.7.1002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Individuals with fragile X-associated tremor/ataxia syndrome frequently have associated features of parkinsonism, often leading to an initial diagnosis of Parkinson disease or other parkinsonism spectrum disorders. Parkinson disease populations may thus include individuals who harbor premutation expansions (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene. OBJECTIVE To screen DNA samples (male) from an Italian Parkinson disease clinic for an excess of premutation expansions of the FMR1 gene. DESIGN DNA samples obtained from 903 unrelated males through consecutive clinic visits were analyzed by an enhanced polymerase chain reaction method for detecting expanded CGG repeats. SETTING Diagnostic assessments were performed at the Parkinson Institute, Istituti Clinici di Perfezionamento, Milan, Italy. Genotyping was conducted at the University of California Davis School of Medicine. PARTICIPANTS A cohort of unrelated males with clinical features of parkinsonism. All but 12 males were of Italian origin, and all reported Caucasian ethnicity. MAIN OUTCOME MEASURE CGG repeat number. RESULTS Three premutation carriers (61, 69, and 80 CGG repeats) were identified (0.33%), which is not significantly higher than the frequency of premutation alleles in the general population. The outcome of the current study, the largest screen of individuals with parkinsonism to date, supports previous screens of smaller parkinsonism cohorts. CONCLUSION Broad screening for premutation alleles in Parkinson disease populations is unlikely to be productive in the absence of additional clinical or family history data that suggest involvement of the FMR1 gene.
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Affiliation(s)
- Jeremy Kraff
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, One Shields Avenue, Davis, CA 95616, USA
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Abstract
Spinal muscular atrophy is a common autosomal recessive neuromuscular disorder caused by mutations in the survival motor neuron gene (SMN), which exists in 2 nearly identical copies (SMN1 and SMN2). Exon 7 of SMN1 is homozygously absent in about 95% of spinal muscular atrophy patients, whereas the loss of SMN2 does not cause spinal muscular atrophy. Small mutations are found in the other 5% of affected patients, and these mutations cluster in the 3' end of SMN1, a region important for protein oligomerization. SMN1 dosage testing can be used to determine the SMN1 copy number and to detect spinal muscular atrophy carriers and affected compound heterozygotes. Dosage testing is compromised by the presence of 2 SMN1 copies per chromosome, which occurs in about 2% of carriers. Finally, although SMN2 produces less full-length transcript than SMN1, the number of SMN2 copies modulates the phenotype.
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Affiliation(s)
- Thomas W Prior
- Department of Pathology, Ohio State University, Columbus, Ohio 43210, USA.
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Pescini F, Bianchi S, Dotti MT, Federico A, Inzitari D, Pantoni L. First report of a Romanian CADASIL patient following immigration to Italy. Eur J Neurol 2007; 14:e7-8. [PMID: 17661999 DOI: 10.1111/j.1468-1331.2007.01743.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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