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Krsek A, Baticic L, Braut T, Sotosek V. The Next Chapter in Cancer Diagnostics: Advances in HPV-Positive Head and Neck Cancer. Biomolecules 2024; 14:925. [PMID: 39199313 PMCID: PMC11352962 DOI: 10.3390/biom14080925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024] Open
Abstract
Human papillomavirus (HPV)-associated head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is an increasingly prevalent pathology worldwide, especially in developed countries. For diagnosing HPV in HNSCC, the combination of p16 immunohistochemistry (IHC) and polymerase chain reaction (PCR) offers high sensitivity and specificity, with p16 IHC being a reliable initial screen and PCR confirming HPV presence. Advanced techniques like next-generation sequencing (NGS) and RNA-based assays provide detailed insights but are primarily used in research settings. Regardless of HPV status, standard oncological treatments currently include surgery, radiation, and/or chemotherapy. This conventional approach does not account for the typically better prognosis of HPV-positive HNSCC patients, leading to increased chemo/radiation-induced secondary morbidities and reduced quality of life. Therefore, it is crucial to identify and detect HPV positivity and other molecular characteristics of HNSCC to personalize treatment strategies. This comprehensive review aims to summarize current knowledge on various HPV detection techniques and evaluate their advantages and disadvantages, with a focus on developing methodologies to identify new biomarkers in HPV-positive HNSCC. The review discusses direct and indirect HPV examination in tumor tissue, DNA- and RNA-based detection techniques, protein-based markers, liquid biopsy potentials, immune-related markers, epigenetic markers, novel biomarkers, and emerging technologies, providing an overall insight into the current state of knowledge.
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Affiliation(s)
- Antea Krsek
- Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia;
| | - Lara Baticic
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Tamara Braut
- Department of Otorhinolaryngology and Head and Neck Surgery, Clinical Hospital Centre Rijeka, 51000 Rijeka, Croatia;
| | - Vlatka Sotosek
- Department of Anesthesiology, Reanimatology, Emergency and Intensive Care Medicine, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia;
- Department of Clinical Medical Sciences I, Faculty of Health Studies, University of Rijeka, 51000 Rijeka, Croatia
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2
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Teh S, Bowland K, Halper-Stromberg E, Kotwal A, Bennett A, Skaist A, Tang J, Cai F, Macoretta A, Liang H, Kamiyama H, Wheelan S, Lin MT, Hruban R, Hung CF, Goldstein M, Scharpf R, Roberts N, Eshleman J. CRISPR-Cas9 for selective targeting of somatic mutations in pancreatic cancers. NAR Cancer 2024; 6:zcae028. [PMID: 38915758 PMCID: PMC11195629 DOI: 10.1093/narcan/zcae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Somatic mutations are desirable targets for selective elimination of cancer, yet most are found within noncoding regions. We have adapted the CRISPR-Cas9 gene editing tool as a novel, cancer-specific killing strategy by targeting the subset of somatic mutations that create protospacer adjacent motifs (PAMs), which have evolutionally allowed bacterial cells to distinguish between self and non-self DNA for Cas9-induced double strand breaks. Whole genome sequencing (WGS) of paired tumor minus normal (T-N) samples from three pancreatic cancer patients (Panc480, Panc504, and Panc1002) showed an average of 417 somatic PAMs per tumor produced from single base substitutions. Further analyses of 591 paired T-N samples from The International Cancer Genome Consortium found medians of ∼455 somatic PAMs per tumor in pancreatic, ∼2800 in lung, and ∼3200 in esophageal cancer cohorts. Finally, we demonstrated 69-99% selective cell death of three targeted pancreatic cancer cell lines using 4-9 sgRNAs designed using the somatic PAM discovery approach. We also showed no off-target activity from these tumor-specific sgRNAs in either the patient's normal cells or an irrelevant cancer using WGS. This study demonstrates the potential of CRISPR-Cas9 as a novel and selective anti-cancer strategy, and supports the genetic targeting of adult cancers.
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Affiliation(s)
- Selina Shiqing K Teh
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kirsten Bowland
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Eitan Halper-Stromberg
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akhil Kotwal
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alexis Bennett
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyza Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Tang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fidel Cai
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Antonella Macoretta
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Liang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Sarah Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Scientific Review Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chien-Fu Hung
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Goldstein
- Department of Radiation Oncology and Molecular Radiation Sciences, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J Roberts
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Bandoh N, Goto T, Kato Y, Kubota A, Sakaue S, Takeda R, Hayashi S, Hayashi M, Baba S, Yamaguchi-Isochi T, Nishihara H, Kamada H. BRAF V600E mutation co-existing with oncogenic mutations is associated with aggressive clinicopathologic features and poor prognosis in papillary thyroid carcinoma. Asian J Surg 2024; 47:413-419. [PMID: 37752023 DOI: 10.1016/j.asjsur.2023.09.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The aim of this study was to evaluate the correlation among mutations in cancer-related genes, clinicopathologic features, and clinical outcome in classical papillary thyroid carcinoma (PTC). PATIENTS AND METHODS A total of 130 patients with classical PTC who underwent curative surgery between April 2012 and June 2023 at Hokuto Hospital were included. Mutations in targeted regions of 160 cancer-related genes were detected by next-generation sequencing (NGS)-based cancer panel testing. RESULTS The BRAF V600E mutation was detected in 108 (83.1%) of 130 PTC patients. Among the 108 patients with the BRAF V600E mutation, other co-existing oncogenic mutations were found in 12 (9.2%) patients. When we divided into 3 groups of no mutations, BRAF V600E mutation alone, and BRAF V600E and other oncogenic mutations, significant differences were observed in terms of tracheal invasion (P = 0.0024), and bilateral neck lymph node metastasis (P = 0.0047). Kaplan-Meier analysis of overall survival (OS) revealed patients with BRAF V600E and other oncogenic mutations had significantly poorer survival than those with BRAF V600E mutation alone (P = 0.0026). Multivariate cox proportional hazard analysis revealed BRAF V600E and other oncogenic mutations was an independent prognostic factor for OS (HR: 10.559; 95%CI: 1.007-110.656, P = 0.0493). CONCLUSIONS The BRAF V600E mutation co-existing with other oncogenic mutations but not the BRAF V600E mutation alone was associated with aggressive clinicopathologic features, resulting in poor prognosis in patients with classical PTC. Detection of oncogenic mutations using NGS-based cancer panel testing could enhance understanding of the clinical features of classical PTC.
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Affiliation(s)
- Nobuyuki Bandoh
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan.
| | - Takashi Goto
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan
| | - Yasutaka Kato
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan
| | - Akinobu Kubota
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan; Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Shota Sakaue
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan; Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Ryuhei Takeda
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan; Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Shuto Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan; Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Misaki Hayashi
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan; Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, Hokkaido, 078-8510, Japan
| | - Shogo Baba
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan
| | - Tomomi Yamaguchi-Isochi
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan
| | - Hiroshi Nishihara
- Keio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582, Japan
| | - Hajime Kamada
- Department of Neurosurgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, Hokkaido, 080-0833, Japan
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Brás JP, Jesus TT, Prazeres H, Lima J, Soares P, Vinagre J. TERTmonitor-qPCR Detection of TERTp Mutations in Glioma. Genes (Basel) 2023; 14:1693. [PMID: 37761833 PMCID: PMC10530400 DOI: 10.3390/genes14091693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Telomerase promoter (TERTp) mutations are frequently observed in various types of tumours and commonly characterised by two specific hotspots located at positions -124 and -146 upstream of the start codon. They enhance TERTp activity, resulting in increased TERT expression. In central nervous system (CNS) tumours, they are integrated as biomarkers, aiding in the diagnosis and with a role in prognosis, where, in some settings, they are associated with aggressive behaviour. In this study, we evaluated the performance of TERTmonitor for TERTp genotyping in a series of 185 gliomas in comparison to the traditional method, Sanger sequencing. Against the gold-standard Sanger method, TERTmonitor performed with a 97.8% accuracy. Inaccuracy was mainly due to the over-detection of variants in negative cases (by Sanger) and the presence of variants that can modify the chemistry of the probe detection. The distribution of the mutations was comparable to other series, with the -124 being the most represented (38.92% for Sanger and TERTmonitor) and more prevalent in the higher-grade tumours, gliosarcoma (50.00%) and glioblastoma (52.6%). The non-matched cases are debatable, as we may be dealing with the reduced sensitivity of Sanger in detecting rare alleles, which strengthens the use of the TERTmonitor. With this study, we present a reliable and rapid potential tool for TERTp genotyping in gliomas.
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Affiliation(s)
- João Paulo Brás
- U-Monitor Lda, 4200-135 Porto, Portugal; (J.P.B.); (H.P.); (P.S.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
| | - Tito Teles Jesus
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
| | - Hugo Prazeres
- U-Monitor Lda, 4200-135 Porto, Portugal; (J.P.B.); (H.P.); (P.S.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
| | - Jorge Lima
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
- Instituto de Patologia e Imunologia Molecular, Universidade do Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Paula Soares
- U-Monitor Lda, 4200-135 Porto, Portugal; (J.P.B.); (H.P.); (P.S.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
- Instituto de Patologia e Imunologia Molecular, Universidade do Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto (FMUP), 4200-319 Porto, Portugal
| | - João Vinagre
- U-Monitor Lda, 4200-135 Porto, Portugal; (J.P.B.); (H.P.); (P.S.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal; (T.T.J.); (J.L.)
- Instituto de Patologia e Imunologia Molecular, Universidade do Porto (Ipatimup), 4200-135 Porto, Portugal
- Faculdade de Medicina, Universidade do Porto (FMUP), 4200-319 Porto, Portugal
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5
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Odgis JA, Gallagher KM, Rehman AU, Marathe P, Bonini KE, Sebastin M, Di Biase M, Brown K, Kelly NR, Ramos MA, Thomas-Wilson A, Guha S, Okur V, Ganapathi M, Elkhoury L, Edelmann L, Zinberg RE, Abul-Husn NS, Diaz GA, Greally JM, Suckiel SA, Jobanputra V, Horowitz CR, Kenny EE, Wasserstein MP, Gelb BD. Detection of mosaic variants using genome sequencing in a large pediatric cohort. Am J Med Genet A 2023; 191:699-710. [PMID: 36563179 PMCID: PMC10266700 DOI: 10.1002/ajmg.a.63062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/24/2022]
Abstract
The increased use of next-generation sequencing has expanded our understanding of the involvement and prevalence of mosaicism in genetic disorders. We describe a total of eleven cases: nine in which mosaic variants detected by genome sequencing (GS) and/or targeted gene panels (TGPs) were considered to be causative for the proband's phenotype, and two of apparent parental mosaicism. Variants were identified in the following genes: PHACTR1, SCN8A, KCNT1, CDKL5, NEXMIF, CUX1, TSC2, GABRB2, and SMARCB1. In addition, we identified one large duplication including three genes, UBE3A, GABRB3, and MAGEL2, and one large deletion including deletion of ARFGAP1, EEF1A2, CHRNA4, and KCNQ2. All patients were enrolled in the NYCKidSeq study, a research program studying the communication of genomic information in clinical care, as well as the clinical utility and diagnostic yield of GS for children with suspected genetic disorders in diverse populations in New York City. We observed variability in the correlation between reported variant allele fraction and the severity of the patient's phenotype, although we were not able to determine the mosaicism percentage in clinically relevant tissue(s). Although our study was not sufficiently powered to assess differences in mosaicism detection between the two testing modalities, we saw a trend toward better detection by GS as compared with TGP testing. This case series supports the importance of mosaicism in childhood-onset genetic conditions and informs guidelines for laboratory and clinical interpretation of mosaic variants detected by GS.
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Affiliation(s)
- Jacqueline A. Odgis
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katie M. Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Atteeq U. Rehman
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Priya Marathe
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine E. Bonini
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nicole R. Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michelle A. Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
| | | | | | | | - Randi E. Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - George A. Diaz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John M. Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Carol R. Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa P. Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce D. Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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6
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Udagawa S, Ooki A, Shinozaki E, Fukuda K, Yamaguchi K, Osumi H. Circulating Tumor DNA: The Dawn of a New Era in the Optimization of Chemotherapeutic Strategies for Metastatic Colo-Rectal Cancer Focusing on RAS Mutation. Cancers (Basel) 2023; 15:1473. [PMID: 36900264 PMCID: PMC10001242 DOI: 10.3390/cancers15051473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Genotyping of tumor tissues to assess RAS and BRAF V600E mutations enables us to select optimal molecularly targeted therapies when considering treatment strategies for patients with metastatic colorectal cancer. Tissue-based genetic testing is limited by the difficulty of performing repeated tests, due to the invasive nature of tissue biopsy, and by tumor heterogeneity, which can limit the usefulness of the information it yields. Liquid biopsy, represented by circulating tumor DNA (ctDNA), has attracted attention as a novel method for detecting genetic alterations. Liquid biopsies are more convenient and much less invasive than tissue biopsies and are useful for obtaining comprehensive genomic information on primary and metastatic tumors. Assessing ctDNA can help track genomic evolution and the status of alterations in genes such as RAS, which are sometimes altered following chemotherapy. In this review, we discuss the potential clinical applications of ctDNA, summarize clinical trials focusing on RAS, and present the future prospects of ctDNA analysis that could change daily clinical practice.
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Affiliation(s)
| | | | | | | | | | - Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
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7
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Craven KE, Fischer CG, Jiang L, Pallavajjala A, Lin MT, Eshleman JR. Optimizing Insertion and Deletion Detection Using Next-Generation Sequencing in the Clinical Laboratory. J Mol Diagn 2022; 24:1217-1231. [PMID: 36162758 PMCID: PMC9808503 DOI: 10.1016/j.jmoldx.2022.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/18/2022] [Accepted: 08/31/2022] [Indexed: 01/13/2023] Open
Abstract
Detection of insertions and deletions (InDels) by short-read next-generation sequencing (NGS) technology can be challenging because of frequent misaligned reads. A systematic analysis of short InDels (1 to 30 bases) and fms-related receptor tyrosine kinase 3 (FLT3) internal tandem duplications (ITDs; 6 to 183 bases) from 46 clinical cases of solid or hematologic malignancy processed with a clinical NGS assay identified misaligned reads in every case, ranging from 3% to 100% of reads with the InDel showing mismapped bases. Mismaps also increased with InDel size. As a consequence, the clinical NGS bioinformatics pipeline undercalled the variant allele frequency by 1% to 84%, incorrectly called simultaneous single-base substitutions along with InDels, or did not report an FLT3 ITD that had been detected by capillary electrophoresis. To improve the ability of the pipeline to better detect and quantify InDels, we utilized a software program called Assembly-Based ReAligner (ABRA2) to more accurately remap reads. ABRA2 was able to correct 41% to 100% of the reads with mismapped bases and led to absolute increases in the variant allele frequency from 1% to 61% along with correction of all of the single-base substitutions except for two cases. ABRA2 could also detect multiple FLT3 ITD clones except for one 183-base ITD. Our analysis has found that ABRA2 performs well on short InDels as well as FLT3 ITDs that are <100 bases.
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Affiliation(s)
- Kelly E Craven
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Catherine G Fischer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Division of Cancer Prevention, National Cancer Institute, Rockville, Maryland
| | - LiQun Jiang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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8
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He Q, Liu Z, Wang J. Targeting KRAS in PDAC: A New Way to Cure It? Cancers (Basel) 2022; 14:cancers14204982. [PMID: 36291766 PMCID: PMC9599866 DOI: 10.3390/cancers14204982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic cancer is one of the most intractable malignant tumors worldwide, and is known for its refractory nature and poor prognosis. The fatality rate of pancreatic cancer can reach over 90%. In pancreatic ductal carcinoma (PDAC), the most common subtype of pancreatic cancer, KRAS is the most predominant mutated gene (more than 80%). In recent decades, KRAS proteins have maintained the reputation of being “undruggable” due to their special molecular structures and biological characteristics, making therapy targeting downstream genes challenging. Fortunately, the heavy rampart formed by KRAS has been broken down in recent years by the advent of KRASG12C inhibitors; the covalent inhibitors bond to the switch-II pocket of the KRASG12C protein. The KRASG12C inhibitor sotorasib has been received by the FDA for the treatment of patients suffering from KRASG12C-driven cancers. Meanwhile, researchers have paid close attention to the development of inhibitors for other KRAS mutations. Due to the high incidence of PDAC, developing KRASG12D/V inhibitors has become the focus of attention. Here, we review the clinical status of PDAC and recent research progress in targeting KRASG12D/V and discuss the potential applications.
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Affiliation(s)
- Qianyu He
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Correspondence: (Z.L.); (J.W.)
| | - Jin Wang
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Correspondence: (Z.L.); (J.W.)
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9
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Ultrahigh sensitive and selective detection of single nucleotide polymorphism using peptide nucleic acid and ribonuclease H assembled DNA amplification (PRADA). Anal Chim Acta 2022; 1233:340423. [DOI: 10.1016/j.aca.2022.340423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/06/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
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10
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Nauheim D, Moskal D, Renslo B, Chadwick M, Jiang W, Yeo CJ, Nevler A, Bowne W, Lavu H. KRAS mutation allele frequency threshold alters prognosis in right-sided resected pancreatic cancer. J Surg Oncol 2022; 126:314-321. [PMID: 35333412 DOI: 10.1002/jso.26860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/18/2022] [Accepted: 03/05/2022] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) provides information on genetic mutations and mutant allele frequency in tumor specimens. We investigated the prognostic significance of KRAS mutant allele frequency in patients with right-sided pancreatic ductal adenocarcinoma (PDAC) treated with surgical resection. METHODS A retrospective study reviewed patients who underwent surgical resection for PDAC and analyzed tumors with an in-house mutational panel. Microdissected samples were studied using an NGS-based assay to detect over 200 hotspot mutations in 42 genes (Pan42) commonly involved in PDAC. RESULTS A total of 144 PDAC right-sided surgical patients with a Pan42 panel were evaluated between 2015 and 2020; 121 patients (84%) harbored a KRAS mutation. Detected mutant allele frequencies were categorized as less than 20% (low mKRAS, n = 92) or greater than or equal to 20% (high mKRAS, n = 29). High mKRAS (KRAS ≥ 20%) patients were noted to have shorter disease-free survival after surgery (11.5 ± 2.1 vs. 19.5 ± 3.5 months, p = 0.03), more advanced tumor stage (p = 0.02), larger tumors (3.6 vs. 2.7 cm, p = 0.001), greater tumor cellularity (26% vs. 18%, p = 0.001), and higher rate of distant recurrence (p = 0.03) than low mKRAS patients. CONCLUSION This study demonstrates the importance of KRAS mutant allele frequency on pathological characteristics and prognosis in right-sided PDAC treated with surgery.
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Affiliation(s)
- David Nauheim
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - David Moskal
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Bryan Renslo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Matthew Chadwick
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wei Jiang
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles J Yeo
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Avinoam Nevler
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Wilbur Bowne
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Harish Lavu
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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11
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Peng J, Sun J, Yang MI, Gibson RM, Arts EJ, Olabode AS, Poon AFY, Wang X, Wheeler AR, Edwards EA, Peng H. Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2022; 9:638-644. [PMID: 37552744 PMCID: PMC9236213 DOI: 10.1021/acs.estlett.2c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 05/24/2023]
Abstract
Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and liquid chromatography-mass spectrometry (nPCR-LC-MS). This method showed a greater selectivity than the current allele-specific quantitative PCR (AS-qPCR) for tracking new VOC and allowed the detection of multiple signature mutations in a single measurement. By measuring the Omicron variant in wastewaters across nine Ontario wastewater treatment plants serving over a three million population, the nPCR-LC-MS method demonstrated a better quantification accuracy than next-generation sequencing (NGS), particularly at the early stage of community spreading of Omicron. This work addresses a major challenge for current SARS-CoV-2 wastewater surveillance by rapidly and accurately measuring VOCs in wastewaters for early warning.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Jianxian Sun
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Richard M. Gibson
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Eric J. Arts
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Abayomi S. Olabode
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Art F. Y. Poon
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Xianyao Wang
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Hui Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- School of the Environment, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
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12
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Merz V, Mangiameli D, Zecchetto C, Quinzii A, Pietrobono S, Messina C, Casalino S, Gaule M, Pesoni C, Vitale P, Trentin C, Frisinghelli M, Caffo O, Melisi D. Predictive Biomarkers for a Personalized Approach in Resectable Pancreatic Cancer. Front Surg 2022; 9:866173. [PMID: 35599791 PMCID: PMC9114435 DOI: 10.3389/fsurg.2022.866173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022] Open
Abstract
The mainstay treatment for patients with immediate resectable pancreatic cancer remains upfront surgery, which represents the only potentially curative strategy. Nevertheless, the majority of patients surgically resected for pancreatic cancer experiences disease relapse, even when a combination adjuvant therapy is offered. Therefore, aiming at improving disease free survival and overall survival of these patients, there is an increasing interest in evaluating the activity and efficacy of neoadjuvant and perioperative treatments. In this view, it is of utmost importance to find biomarkers able to select patients who may benefit from a preoperative therapy rather than upfront surgical resection. Defined genomic alterations and a dynamic inflammatory microenvironment are the major culprits for disease recurrence and resistance to chemotherapeutic treatments in pancreatic cancer patients. Signal transduction pathways or tumor immune microenvironment could predict early recurrence and response to chemotherapy. In the last decade, distinct molecular subtypes of pancreatic cancer have been described, laying the bases to a tailored therapeutic approach, started firstly in the treatment of advanced disease. Patients with homologous repair deficiency, in particular with mutant germline BRCA genes, represent the first subgroup demonstrating to benefit from specific therapies. A fraction of patients with pancreatic cancer could take advantage of genome sequencing with the aim of identifying possible targetable mutations. These genomic driven strategies could be even more relevant in a potentially curative setting. In this review, we outline putative predictive markers that could help in the next future in tailoring the best therapeutic strategy for pancreatic cancer patients with a potentially curable disease.
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Affiliation(s)
- Valeria Merz
- Medical Oncology Unit, Santa Chiara Hospital, Trento, Italy
- Digestive Molecular Clinical Oncology Research Unit, Università degli Studi di Verona, Verona, Italy
| | - Domenico Mangiameli
- Digestive Molecular Clinical Oncology Research Unit, Università degli Studi di Verona, Verona, Italy
| | - Camilla Zecchetto
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Alberto Quinzii
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Silvia Pietrobono
- Digestive Molecular Clinical Oncology Research Unit, Università degli Studi di Verona, Verona, Italy
| | | | - Simona Casalino
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Marina Gaule
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Camilla Pesoni
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | | | - Chiara Trentin
- Medical Oncology Unit, Santa Chiara Hospital, Trento, Italy
| | | | - Orazio Caffo
- Medical Oncology Unit, Santa Chiara Hospital, Trento, Italy
| | - Davide Melisi
- Digestive Molecular Clinical Oncology Research Unit, Università degli Studi di Verona, Verona, Italy
- Investigational Cancer Therapeutics Clinical Unit, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
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13
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Sun KH(M, Wong YT(H, Cheung KM(C, Yuen C(M, Chan YT(T, Lai WY(J, Chao C(D, Fan WS(K, Chow YK(K, Law MF, Tam HC(T. Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12020409. [PMID: 35204500 PMCID: PMC8871212 DOI: 10.3390/diagnostics12020409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) infection has long been proposed as the major etiology of lymphomagenesis. The adoption of high-throughput sequencing has allowed us to gain more insight into the molecular mechanisms of ENKTCL, which largely involve chromosome deletion and aberrations in Janus kinase (JAK)-signal transducer and activator of transcription (STAT), programmed cell death protein-1 (PD-1)/PD-ligand 1 (PD-L1) pathways, as well as mutations in tumor suppressor genes. The molecular findings could potentially influence the traditional chemoradiotherapy approach, which is known to be associated with significant toxicity. This article will review the latest molecular findings in NKTCL and recent advances in the field of molecular diagnosis in NKTCL. Issues of quality control and technical difficulties will also be discussed, along with future prospects in the molecular diagnosis and treatment of NKTCL.
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Affiliation(s)
- Ka-Hei (Murphy) Sun
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | | | - Ka-Man (Carmen) Cheung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Carmen (Michelle) Yuen
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | - Yun-Tat (Ted) Chan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Yan (Jennifer) Lai
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Chun (David) Chao
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Sum (Katie) Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Yuen-Kiu (Karen) Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Man-Fai Law
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
- Correspondence:
| | - Ho-Chi (Tommy) Tam
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
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14
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Mishra S, Jeon J, Kang JK, Song SH, Kim TY, Ban C, Choi H, Kim Y, Kim M, Park JW. Direct Detection of Low Abundance Genes of Single Point Mutation. NANO LETTERS 2021; 21:9061-9068. [PMID: 34672610 DOI: 10.1021/acs.nanolett.1c02728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free DNA (cfDNA) analysis, specifically circulating tumor DNA (ctDNA) analysis, provides enormous opportunities for noninvasive early assessment of cancers. To date, PCR-based methods have led this field. However, the limited sensitivity/specificity of PCR-based methods necessitates the search for new methods. Here, we describe a direct approach to detect KRAS G12D mutated genes in clinical ctDNA samples with the utmost LOD and sensitivity/specificity. In this study, MutS protein was immobilized on the tip of an atomic force microscope (AFM), and the protein sensed the mismatched sites of the duplex formed between the capture probe on the surface and mutated DNA. A noteworthy LOD (3 copies, 0.006% allele frequency) was achieved, along with superb sensitivity/specificity (100%/100%). These observations demonstrate that force-based AFM, in combination with the protein found in nature and properly designed capture probes/blockers, represents an exciting new avenue for ctDNA analysis.
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Affiliation(s)
- Sourav Mishra
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jinseong Jeon
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Jun-Kyu Kang
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang-Hyun Song
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Cancer Genomics Research Laboratory, Cancer Research Institute, Seoul National University, Seoul 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 03080, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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15
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Huang J, Tseng LH, Parini V, Lokhandwala PM, Pallavajjala A, Rodriguez E, Xian R, Chen L, Gocke CD, Eshleman JR, Lin MT. IDH1 and IDH2 Mutations in Colorectal Cancers. Am J Clin Pathol 2021; 156:777-786. [PMID: 33929516 DOI: 10.1093/ajcp/aqab023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To elucidate clinicopathologic and molecular characteristics of IDH1 and IDH2 (IDH1/2) mutations in colorectal cancers (CRCs). METHODS We evaluated IDH1/2 mutations in 1,623 CRCs using a next-generation sequencing assay. RESULTS IDH1/2 mutations, predominantly IDH1 p.R132C, were detected in 15 (0.9%) CRCs and in 5 (3.0%) of 167 BRAF p.V600E-mutated CRCs. Three IDH1/2-mutated CRCs were associated with inflammatory bowel disease. They were significantly associated with old age, mucinous or signet ring cell adenocarcinoma, and high-grade histomorphology. Concordance of variant allele frequency between IDH1/2 mutants and other trunk drivers in CRCs and presence of IDH1/2 mutation in the adenoma and early adenocarcinoma indicated IDH1/2 mutations could be trunk drivers suitable for targeted therapy. CONCLUSIONS IDH1/2 mutations in CRCs were uncommon but enriched in BRAF p.V600E-mutated CRCs and perhaps colitis-associated CRCs. Further studies on IDH1/2-mutated CRCs are needed to clarify their clinicopathologic features and implications for targeted therapy.
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Affiliation(s)
- Jialing Huang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan
| | - Vamsi Parini
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aparna Pallavajjala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liam Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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16
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Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J, Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing. Nat Biotechnol 2021; 39:1141-1150. [PMID: 34504346 PMCID: PMC8506910 DOI: 10.1038/s41587-021-00994-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2021] [Indexed: 02/01/2023]
Abstract
Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.
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Affiliation(s)
- Wenming Xiao
- The Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA.
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Zhong Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Li Tai Fang
- Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., Belmont, CA, USA
| | - Yongmei Zhao
- 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
| | | | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | | | | | - Thomas M Blomquist
- Departments of Medicine and Pathology, University of Toledo Medical Center, Toledo, OH, USA
| | | | - Marc Sultan
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Kenneth Idler
- Computational Genomics, Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Charles Lu
- Computational Genomics, Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Andreas Scherer
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
| | | | - Malcolm Moos
- The Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, 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
| | - Ogan D Abaan
- Illumina Inc., Foster City, CA, USA
- Seven Bridges Genomics Inc., Cambridge, MA, USA
| | - Wanqiu Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Xin Chen
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - 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
- Centro di Riferimento Oncologico di Aviano IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Roberta Maestro
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Maurizio Polano
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Centro di Riferimento Oncologico di Aviano IRCCS, National Cancer Institute, Unit of Oncogenetics and Functional Oncogenomics, Aviano, Italy
| | - Jiri Drabek
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- IMTM, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Petr Vojta
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- IMTM, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Sulev Kõks
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Perron Institute for Neurological and Translational Science, Nedlands, Perth, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Perth, Western Australia, Australia
| | - Ene Reimann
- European Infrastructure for Translational Medicine, Amsterdam, the Netherlands
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bindu Swapna Madala
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Timothy Mercer
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia
| | - Chris Miller
- Computational Genomics, Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Howard Jacob
- Computational Genomics, Genomics Research Center, AbbVie, North Chicago, IL, USA
| | | | | | | | | | | | | | | | - Virginie Petitjean
- Biomarker Development, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ashley Walton
- 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
| | - Keyur Talsania
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Cristobal Juan Vera
- Advanced Biomedical and Computational Sciences, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | - Jennifer A Hipp
- Departments of Medicine and Pathology, University of Toledo Medical Center, Toledo, OH, USA
| | - James C Willey
- Departments of Medicine and Pathology, University of Toledo Medical Center, Toledo, OH, USA
| | - Jing Wang
- National Institute of Metrology, Beijing, China
| | - 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
| | - Arati Raziuddin
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yuanting Zheng
- 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
| | - Margaret Cam
- CCR Collaborative Bioinformatics Resource, Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA
| | - Parthav Jailwala
- CCR Collaborative Bioinformatics Resource, Office of Science and Technology Resources, Center for Cancer Research, Bethesda, MD, USA
| | - Cu Nguyen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Qingrong Chen
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Chunhua Yan
- Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | | | | | - Roderick V Jensen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Jian-Liang Li
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Brian N Papas
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Core, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fayaz Seifuddin
- 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
| | - Xuelu Liu
- Center for Information Technology, National Institutes of Health, Bethesda, MD, USA
| | - Wolfgang Resch
- Center for Information Technology, National Institutes of Health, Bethesda, MD, USA
| | | | - Leihong Wu
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Gokhan Yavas
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Corey Miles
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Baitang Ning
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Eric Donaldson
- The Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Samir Lababidi
- Office of the Chief Scientist, Office of the Commissioner, US Food and Drug Information, Silver Spring, MD, USA
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zivana Tezak
- The Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Huixiao Hong
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Charles Wang
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, USA.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
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17
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Koopman B, Cajiao Garcia BN, Kuijpers CCHJ, Damhuis RAM, van der Wekken AJ, Groen HJM, Schuuring E, Willems SM, van Kempen LC. A Nationwide Study on the Impact of Routine Testing for EGFR Mutations in Advanced NSCLC Reveals Distinct Survival Patterns Based on EGFR Mutation Subclasses. Cancers (Basel) 2021; 13:3641. [PMID: 34298851 PMCID: PMC8307492 DOI: 10.3390/cancers13143641] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 12/24/2022] Open
Abstract
EGFR mutation analysis in non-small-cell lung cancer (NSCLC) patients is currently standard-of-care. We determined the uptake of EGFR testing, test results and survival of EGFR-mutant NSCLC patients in the Netherlands, with the overall objective to characterize the landscape of clinically actionable EGFR mutations and determine the role and clinical relevance of uncommon and composite EGFR mutations. Non-squamous NSCLC patients diagnosed in 2013, 2015 and 2017 were identified in the Netherlands Cancer Registry (NCR) and matched to the Dutch Pathology Registry (PALGA). Overall, 10,254 patients were included. Between 2013-2017, the uptake of EGFR testing gradually increased from 72.7% to 80.9% (p < 0.001). Multi-gene testing via next-generation sequencing (increased from 7.8% to 78.7% (p < 0.001), but did not affect the number of detected EGFR mutations (n = 925; 11.7%; 95% confidence interval (CI), 11.0-12.4) nor the distribution of variants. For patients treated with first-line EGFR inhibitors (n = 651), exon 19 deletions were associated with longer OS than L858R (HR 1.58; 95% CI, 1.30-1.92; p < 0.001) or uncommon, actionable variants (HR 2.13; 95% CI, 1.60-2.84; p < 0.001). Interestingly, OS for patients with L858R was similar to those with uncommon, actionable variants (HR 1.31; 95% CI, 0.98-1.75; p = 0.069). Our analysis indicates that grouping exon 19 deletions and L858R into one class of 'common' EGFR mutations in a clinical trial may mask the true activity of an EGFR inhibitor towards specific mutations.
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Affiliation(s)
- Bart Koopman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Betzabel N. Cajiao Garcia
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | | | - Ronald A. M. Damhuis
- Netherlands Comprehensive Cancer Organisation (IKNL), P.O. Box 19079, 3501 DB Utrecht, The Netherlands;
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (A.J.v.d.W.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (A.J.v.d.W.); (H.J.M.G.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Stefan M. Willems
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands; (B.K.); (B.N.C.G.); (E.S.); (S.M.W.)
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18
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Adachi JI, Shirahata M, Suzuki T, Mishima K, Uchida E, Sasaki A, Nishikawa R. Droplet digital PCR assay for detecting TERT promoter mutations in patients with glioma. Brain Tumor Pathol 2021; 38:201-209. [PMID: 34128111 DOI: 10.1007/s10014-021-00403-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022]
Abstract
Two hot spot mutations (C228T, C250T) in the telomerase reverse transcriptase (TERT) gene are frequently identified in glioblastoma and oligodendroglioma. TERT mutations predicts an aggressive clinical course in isocitrate dehydrogenase (IDH) wild-type astrocytic tumors. Therefore, it is important to accurately detect TERT promoter mutations in glioma. Sanger DNA sequencing is the currently standard method for analyzing TERT mutations. However, PCR amplification in the first step of the sequencing has proven technically difficult because of the high GC content around the TERT mutation. In this report, we described a novel droplet digital PCR (ddPCR) assay to evaluate TERT hot spot mutations in fresh frozen and formalin-fixed paraffin-embedded (FFPE) specimens of glioma and verified the difference in results from the Sanger DNA sequencing results. We obtained the mutant allele fraction for TERT mutations of in a single ddPCR run in all cases, including the micro-dissected FFPE sections. On the contrary, up to twice the DNA sequences were required from fresh frozen tissue to obtain the results, consistent with ddPCR assay. When FFPE specimens were used, more time was required to evaluate TERT mutations through DNA sequencing. DdPCR is an effective and sensitive assay compared to the conventional standard Sanger DNA sequencing.
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Affiliation(s)
- Jun-Ichi Adachi
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan.
| | - Mitsuaki Shirahata
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Tomonari Suzuki
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Kazuhiko Mishima
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Eita Uchida
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan
| | - Atsushi Sasaki
- Department of Pathology, Saitama Medical University, Moroyama, Saitama, Japan
| | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, 1397-1, Yamane, Hidaka, Saitama, 350-1298, Japan
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19
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Cazacu IM, Semaan A, Stephens B, Swartzlander DB, Guerrero PA, Singh BS, Lungulescu CV, Danciulescu MM, Cherciu Harbiyeli IF, Streata I, Popescu C, Saftoiu A, Roy-Chowdhuri S, Maitra A, Bhutani MS. Diagnostic value of digital droplet polymerase chain reaction and digital multiplexed detection of single-nucleotide variants in pancreatic cytology specimens collected by EUS-guided FNA. Gastrointest Endosc 2021; 93:1142-1151.e2. [PMID: 33058885 DOI: 10.1016/j.gie.2020.09.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/29/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS EUS-guided FNA is recommended as a first-line procedure for the histopathologic diagnosis of pancreatic cancer. Molecular analysis of EUS-FNA samples might be used as an auxiliary tool to strengthen the diagnosis. The current study aimed to evaluate the diagnostic performances of K-ras testing using droplet digital polymerase chain reaction (ddPCR) and a novel single-nucleotide variant (SNV) assay performed on pancreatic EUS-FNA samples. METHODS EUS-FNA specimens from 31 patients with pancreatic masses (22 pancreatic ductal adenocarcinomas, 7 chronic pancreatitis, and 2 pancreatic neuroendocrine tumors) were included in the study. K-ras testing was initially performed by ddPCR. In addition, mutational status was evaluated using an SNV assay by NanoString technology, using digital enumeration of unique barcoded probes to detect 97 SNVs from 24 genes of clinical significance. RESULTS The overall specificity and sensitivity of cytologic examination were 100% and 63%, respectively. K-ras mutation testing was performed using ddPCR, and the sensitivity increased to 87% with specificity 90%. The SNV assay detected at least 1 variant in 90% of pancreatic ductal adenocarcinoma samples; the test was able to detect 2 K-ras codon 61 mutations in 2 cases of pancreatic ductal adenocarcinoma, which were missed by ddPCR. The overall diagnostic accuracy of the cytologic examination alone was 74%, and it increased to 91% when the results of both molecular tests were considered for the cases with negative and inconclusive results. CONCLUSIONS The current study illustrated that integration of K-ras analysis with cytologic evaluation, especially in inconclusive cases, can enhance the diagnostic accuracy of EUS-FNA for pancreatic lesions.
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Affiliation(s)
- Irina M Cazacu
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA; Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Alexander Semaan
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Bret Stephens
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Daniel B Swartzlander
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Paola A Guerrero
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Ben S Singh
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | | | | | | | - Ioana Streata
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Carmen Popescu
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Adrian Saftoiu
- Research Center of Gastroenterology and Hepatology, Craiova, Romania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Anirban Maitra
- Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Manoop S Bhutani
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
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Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A systematic review and meta-analysis. PLoS One 2021; 16:e0248775. [PMID: 33770081 PMCID: PMC7997033 DOI: 10.1371/journal.pone.0248775] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Introduction Before anti-EGFR therapy is given to patients with colorectal cancer, it is required to determine KRAS mutation status in tumor. When tumor tissue is not available, cell-free DNA (liquid biopsy) is commonly used as an alternative. Due to the low abundance of tumor-derived DNA in cell-free DNA samples, methods with high sensitivity were preferred, including digital polymerase chain reaction, amplification refractory mutation system and next-generation sequencing. The aim of this systemic review and meta-analysis was to investigate the accuracy of those methods in detecting KRAS mutation in cell-free DNA sample from patients with colorectal cancer. Methods Literature search was performed in Pubmed, Embase, and Cochrane Library. After removing duplicates from the 170 publications found by literature search, eligible studies were identified using pre-defined criteria. Quality of the publications and relevant data were assessed and extracted thereafter. Meta-DiSc and STATA softwares were used to pool the accuracy parameters from the extracted data. Results A total of 33 eligible studies were identified for this systemic review and meta-analysis. After pooling, the overall sensitivity, specificity, and diagnostic odds ratio were 0.77 (95%CI: 0.74–0.79), 0.87 (95%CI: 0.85–0.89), and 23.96 (95%CI: 13.72–41.84), respectively. The overall positive and negative likelihood ratios were 5.55 (95%CI: 3.76–8.19) and 0.29 (95%CI: 0.21–0.38), respectively. Area under curve of the summarized ROC curve was 0.8992. Conclusion Digital polymerase chain reaction, amplification refractory mutation system, and next-generation sequencing had overall high accuracy in detecting KRAS mutation in cell-free DNA sample. Large prospective randomized clinical trials are needed to further convince the accuracy and usefulness of KRAS mutation detection using cfDNA/liquid biopsy samples in clinical practice. Trial registration PROSPERO CRD42020176682; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=176682.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
| | - Peiling Cai
- Department of Anatomy and Histology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Yuanyuan Wei
- Department of Physiology, School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (PY); (YW)
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21
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Lv SD, Wang HY, Yu XP, Zhai QL, Wu YB, Wei Q, Huang WH. Integrative molecular characterization of Chinese prostate cancer specimens. Asian J Androl 2021; 22:162-168. [PMID: 31134918 PMCID: PMC7155802 DOI: 10.4103/aja.aja_36_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) exhibits epidemiological and molecular heterogeneity. Despite extensive studies of its phenotypic and genetic properties in Western populations, its molecular basis is not clear in Chinese patients. To determine critical molecular characteristics and explore correlations between genomic markers and clinical parameters in Chinese populations, we applied an integrative genetic/transcriptomic assay that combines targeted next-generation sequencing and quantitative real-time PCR (qRT-PCR) on samples from 46 Chinese patients with PCa. Lysine (K)-specific methyltransferase 2D (KMT2D), zinc finger homeobox 3 (ZFHX3), A-kinase anchoring protein 9 (AKAP9), and GLI family zinc finger 1 (GLI1) were frequently mutated in our cohort. Moreover, a clinicopathological analysis showed that RB transcriptional corepressor 1 (RB1) deletion was common in patients with a high risk of disease progression. Remarkably, four genomic events, MYC proto-oncogene (MYC) amplification, RB1 deletion, APC regulator of WNT signaling pathway (APC) mutation or deletion, and cyclin-dependent kinase 12 (CDK12) mutation, were correlated with poor disease-free survival. In addition, a close link between KMT2D expression and the androgen receptor (AR) signaling pathway was observed both in our cohort and in The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) data. In summary, our results demonstrate the feasibility and benefits of integrative molecular characterization of PCa samples in disease pathology research and personalized medicine.
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Affiliation(s)
- Shi-Dong Lv
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China.,Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Hong-Yi Wang
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Xin-Pei Yu
- Department of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou 510095, China
| | - Qi-Liang Zhai
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yao-Bin Wu
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China
| | - Qiang Wei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wen-Hua Huang
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangzhou 510515, China
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22
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Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics 2021; 14:47. [PMID: 33579278 PMCID: PMC7881461 DOI: 10.1186/s12920-021-00893-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of single allele assays (e.g., allele-specific ddPCR) commonly used for genotyping known mutations at very low alternate allelic fractions (AAFs) have limited the integration of low-level mosaic analyses into clinical and research applications. The growing importance of mosaic mutations requires a more rapid, low-cost solution for mutation detection and validation. METHODS To overcome these limitations, we developed Multiple Independent Primer PCR Sequencing (MIPP-Seq) which combines the power of ultra-deep sequencing and truly independent assays. The accuracy of MIPP-seq to quantifiable detect and measure extremely low allelic fractions was assessed using a combination of SNVs, insertions, and deletions at known allelic fractions in blood and brain derived DNA samples. RESULTS The Independent amplicon analyses of MIPP-Seq markedly reduce the impact of allelic dropout, amplification bias, PCR-induced, and sequencing artifacts. Using low DNA inputs of either 25 ng or 50 ng of DNA, MIPP-Seq provides sensitive and quantitative assessments of AAFs as low as 0.025% for SNVs, insertion, and deletions. CONCLUSIONS MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
| | - Michael B Miller
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonia N Kim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Katherine S Morillo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - August Yue Huang
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Reethika Digumarthy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Zachary Zemmel
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
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Hai X, Li Y, Zhu C, Song W, Cao J, Bi S. DNA-based label-free electrochemical biosensors: From principles to applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116098] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Allele-Specific PCR for KRAS Mutation Detection Using Phosphoryl Guanidine Modified Primers. Diagnostics (Basel) 2020; 10:diagnostics10110872. [PMID: 33114622 PMCID: PMC7692470 DOI: 10.3390/diagnostics10110872] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Establishing the Kirsten rat sarcoma (KRAS) mutational status is essential in terms of managing patients with various types of cancer. Allele-specific real-time polymerase chain reaction (AS-PCR) is a widely used method for somatic mutations detection. To improve the limited sensitivity and specificity, several blocking methods have been introduced in AS-PCR to block the amplification of wild-type templates. Herein, we used a novel modified oligonucleotide with internucleotide phosphates reshaped 1,3-dimethyl-2-imino-imidazolidine moieties (phosphoryl guanidine (PG) groups) as primers and blockers in the AS-PCR method. Four common KRAS mutations were chosen as a model to demonstrate the advantages of the PG primers and blockers utilizing a customized PCR protocol. The methods were evaluated on plasmid model systems providing a KRAS mutation detection limit of 20 copies of mutant DNA in a proportion as low as 0.1% of the total DNA, with excellent specificity. PG-modification can serve as the universal additional mismatch-like disturbance to increase the discrimination between wild-type and mutated DNA. Moreover, PG can serve to increase primer specificity by a synergetic effect with additional mismatch and would greatly facilitate medical research.
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Kim S, Lee JW, Park YS. The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers. Life (Basel) 2020; 10:E228. [PMID: 33023080 PMCID: PMC7599837 DOI: 10.3390/life10100228] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Despite the introduction of next-generation sequencing in the realm of DNA sequencing technology, it is not often used in the investigation of oral squamous cell carcinoma (OSCC). Oral cancer is one of the most frequently occurring malignancies in some parts of the world and has a high mortality rate. Patients with this malignancy are likely to have a poor prognosis and may suffer from severe facial deformity or mastication problems even after successful treatment. Therefore, a thorough understanding of this malignancy is essential to prevent and treat it. This review sought to highlight the contributions of next-generation sequencing (NGS) in unveiling the genetic alterations and differential expressions of miRNAs involved in OSCC progression. By applying an appropriate eligibility criterion, we selected relevant studies for review. Frequently identified mutations in genes such as TP53, NOTCH1, and PIK3CA are discussed. The findings of existing miRNAs (e.g., miR-21) as well as novel discoveries pertaining to OSCC are also covered. Lastly, we briefly mention the latest findings in targeted gene therapy and the potential use of miRNAs as biomarkers. Our goal is to encourage researchers to further adopt NGS in their studies and give an overview of the latest findings of OSCC treatment.
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Affiliation(s)
| | | | - Young-Seok Park
- Department of Oral Anatomy and Dental Research Institute, School of Dentistry, Seoul National University, Seoul 03968, Korea; (S.K.); (J.W.L.)
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26
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Joy RA, Thelakkattusserry SK, Vikkath N, Bhaskaran R, Krishnan S, Vasudevan D, Ariyannur PS. Somatic mutation detection efficiency in EGFR: a comparison between high resolution melting analysis and Sanger sequencing. BMC Cancer 2020; 20:902. [PMID: 32962681 PMCID: PMC7510081 DOI: 10.1186/s12885-020-07411-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Background High resolution melting curve analysis is a cost-effective rapid screening method for detection of somatic gene mutation. The performance characteristics of this technique has been explored previously, however, analytical parameters such as limit of detection of mutant allele fraction and total concentration of DNA, have not been addressed. The current study focuses on comparing the mutation detection efficiency of High-Resolution Melt Analysis (HRM) with Sanger Sequencing in somatic mutations of the EGFR gene in non-small cell lung cancer. Methods The minor allele fraction of somatic mutations was titrated against total DNA concentration using Sanger sequencing and HRM to determine the limit of detection. The mutant and wildtype allele fractions were validated by multiplex allele-specific real-time PCR. Somatic mutation detection efficiency, for exons 19 & 21 of the EGFR gene, was compared in 116 formalin fixed paraffin embedded tumor tissues, after screening 275 tumor tissues by Sanger sequencing. Results The limit of detection of minor allele fraction of exon 19 mutation was 1% with sequencing, and 0.25% with HRM, whereas for exon 21 mutation, 0.25% MAF was detected using both methods. Multiplex allele-specific real-time PCR revealed that the wildtype DNA did not impede the amplification of mutant allele in mixed DNA assays. All mutation positive samples detected by Sanger sequencing, were also detected by HRM. About 28% cases in exon 19 and 40% in exon 21, detected as mutated in HRM, were not detected by sequencing. Overall, sensitivity and specificity of HRM were found to be 100 and 67% respectively, and the negative predictive value was 100%, while positive predictive value was 80%. Conclusion The comparative series study suggests that HRM is a modest initial screening test for somatic mutation detection of EGFR, which must further be confirmed by Sanger sequencing. With the modification of annealing temperature of initial PCR, the limit of detection of Sanger sequencing can be improved.
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Affiliation(s)
- Reenu Anne Joy
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | | | - Narendranath Vikkath
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Renjitha Bhaskaran
- Department of Biostatistics, Amrita School of Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Sajitha Krishnan
- Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Damodaran Vasudevan
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India.,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Prasanth S Ariyannur
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India. .,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India.
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27
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Forman A, Sotelo J. Tumor-Based Genetic Testing and Familial Cancer Risk. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036590. [PMID: 31570381 DOI: 10.1101/cshperspect.a036590] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
As genetic testing on somatic tumor tissue becomes a more routine part of personalized cancer treatment, a growing opportunity arises to identify hereditary germline variants within those results. These germline results can affect future cancer screening for both patients and their family members. Finding this germline information can be complicated as a result of differences between somatic and germline testing processes, nomenclature, and outcome goals (e.g., treatment impact). The goal of this review is to highlight differences between somatic and germline testing and outline a potential guide to allow for appropriate clinical interpretation of somatic testing results in order to better facilitate genetic counseling referrals and confirmatory germline testing.
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Affiliation(s)
- Andrea Forman
- Department of Clinical Genetics, Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Jilliane Sotelo
- Center for Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
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28
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Yang Z, Li J, Hu Y, Chen M, Peng D, Zong D, Shang Q, Tao L, Zhao Y, Ni Y, Ye J, Xie Y, Yang L, Lin Q, Cai C, Xu N, Huang X, Dong X, Zhou Z, Yu Y, Shangguan Z, Xu Y, Ying W, Weng M, Yuan Z, Dong Z, Li J, Zheng Z, Pan J, Liu L, Ye J, Zhang Z, Li W, Zhu J, Jin S, Li Y, Ding C. Dynamics of Plasma EGFR T790M Mutation in Advanced NSCLC: A Multicenter Study. Target Oncol 2020; 14:719-728. [PMID: 31691892 DOI: 10.1007/s11523-019-00682-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Droplet digital polymerase chain reaction (ddPCR) is an emerging technology for quantitative cell-free DNA oncology applications. However, a ddPCR assay for the epidermal growth factor receptor (EGFR) p.Thr790Met (T790M) mutation suitable for clinical use remains to be established with analytical and clinical validations. OBJECTIVE We aimed to develop and validate a new ddPCR assay to quantify the T790M mutation in plasma for monitoring and predicting the progression of advanced non-small-cell lung cancer (NSCLC). METHODS Specificity of the ddPCR assay was evaluated with genomic DNA samples from healthy individuals. The inter- and intraday variations of the assay were evaluated using mixtures of plasmid DNA containing wild-type EGFR and T790M mutation sequences. We assessed the clinical utility of the T790M assay in a multicenter prospective study in patients with advanced NSCLC receiving tyrosine kinase inhibitor (TKI) treatment by analyzing longitudinal plasma DNA samples. RESULTS We set the criteria for a positive call when the following conditions were satisfied: (1) T790M mutation frequency > 0.098% (3 standard deviations above the background signal); (2) at least two positive droplets in duplicate ddPCR reactions. Among the 62 patients with advanced NSCLC exhibiting resistance to TKI treatment, 15 had one or more serial plasma samples that tested positive for T790M. T790M mutation was detected in the plasma as early as 205 days (median 95 days) before disease progression, determined by imaging analysis. Plasma T790M concentrations also correlated with intervention after disease progression. CONCLUSIONS We developed a ddPCR assay to quantify the T790M mutation in plasma. Quantification of longitudinal plasma T790M mutation may allow noninvasive assessment of drug resistance and guide follow-up treatment in TKI-treated patients with NSCLC. TRIAL REGISTRATION Clinical Trials.gov identifier: NCT02804100.
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Affiliation(s)
- Zhengquan Yang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jialu Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yujie Hu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meihua Chen
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Danli Peng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Dan Zong
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingjuan Shang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lianqin Tao
- Department of Pulmonary Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Yanling Zhao
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yiyun Ni
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jinyan Ye
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yupeng Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Li Yang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Quan Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chang Cai
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ning Xu
- Department of Respiratory Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Xiaoping Huang
- Department of Respiratory Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Xiaoting Dong
- Wenzhou Hospital of Traditional Chinese Medicine, Wenzhou, Zhejiang, China
| | - Zhonghui Zhou
- Ningbo Hospital of Traditional Chinese Medicine, Ningbo, Zhejiang, China
| | - Yali Yu
- Ningbo Hospital of Traditional Chinese Medicine, Ningbo, Zhejiang, China
| | - Zongxiao Shangguan
- The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yangyang Xu
- Zhejiang Jinhua Guangfu Hospital, Jinhua, Zhejiang, China
| | - Weiping Ying
- Zhejiang Jinhua Guangfu Hospital, Jinhua, Zhejiang, China
| | - Meiling Weng
- Department of Oncology, The People's Hospital of Quzhou, Quzhou, Zhejiang, China
| | - Zuguo Yuan
- Department of Radiotherapy and Chemotherapy, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Zhijun Dong
- ChinacoHealthcare Corporation International Hospital, Ningbo, Zhejiang, China
| | - Jifa Li
- Yue Qing General Hospital, Yue Qing, Zhejiang, China
| | - Zhe Zheng
- The Ping Yang Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiongwei Pan
- Department of Respiratory and Critical Care Medicine, Lishui People's Hospital, Lishui, Zhejiang, China
| | - Lu Liu
- Department of Interventional Radiology, Zhejiang University Lishui Hospital, Lishui, Zhejiang, China
| | - Junhui Ye
- Department of Respiratory Medicine, Sanmen People's Hospital of Zhejiang, Taizhou, Zhejiang, China
| | - Zhan Zhang
- Huangyan Hospital of Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Wenfeng Li
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junfei Zhu
- Department of Pulmonary Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China.
| | - Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yuping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang, China.
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Clonal Origin Evaluated by Trunk and Branching Drivers and Prevalence of Mutations in Multiple Lung Tumor Nodules. Mol Diagn Ther 2020; 24:461-472. [DOI: 10.1007/s40291-020-00471-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Xu CW, Lei L, Wang WX, Lin L, Zhu YC, Wang H, Miao LY, Wang LP, Zhuang W, Fang MY, Lv TF, Song Y. Molecular Characteristics and Clinical Outcomes of EGFR Exon 19 C-Helix Deletion in Non-Small Cell Lung Cancer and Response to EGFR TKIs. Transl Oncol 2020; 13:100791. [PMID: 32492620 PMCID: PMC7264750 DOI: 10.1016/j.tranon.2020.100791] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) exon 19 deletion (E19del) is the most common activating mutation in advanced non–small cell lung cancer (NSCLC) and associates with the sensitivity of EGFR tyrosine kinase inhibitors (TKIs) treatment. However, not all mutant patterns of E19del have been well studied for the limited coverage of regular EGFR mutation testing. Here, we performed a retrospective cohort study of the C-helix E19del in advanced NSCLC patients based on the screening data by the next-generation sequencing (NGS) platform. From May 2012 to December 2019, clinical information and specimen from 7544 consecutive advanced (IIIB/IV) NSCLC patients were collected and screened for EGFR gene mutations by NGS from multicenters in China. The molecular characteristics and responsiveness to first-line EGFR TKIs therapy in NSCLC patients with C-helix E19del were analyzed. The clinical characteristics were also compared between patients with classical E19del and C-helix E19del. Thirty-eight (2.6%) patients with C-helix E19del and 1400 (97.4%) patients with classical E19dels were identified from 1438 patients with E19del. No significant difference in clinical characteristics was observed between the C-helix E19del and classical E19del groups (P > .05), except for histology (P < .001). All 22 patients with C-helix E19del as p.S752_I759del, p.A750_E758del, p.A750_E758delinsP, p.T751_A755delinsNY, p.T751_I759delinsG, p.T751_I759delinsLD, p.T751_I759delinsN, p.T751_L760delinsNL, and p.T751_D761delinsLY reached the best response as partial response rate (72.7%), and the progression-free survival (PFS) was 12.0 months. The PFS after EGFR TKIs in patients with C-helix E19del tended to be longer than patients with classical E19del but has no statistical significance (12.0 months vs 8.5 months, P = .06). The C-helix E19del could be a positive biomarker for predicting response to EGFR TKIs in advanced NSCLC patients. NGS should be the appropriate platform to identify this rare population, especially when patients harbor no actionable driver mutation initially and are reluctant to accept chemotherapy as first-line therapy.
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Affiliation(s)
- Chun-Wei Xu
- Department of Respiratory Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, People's Republic of China
| | - Lei Lei
- Department of Chemotherapy, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
| | - Wen-Xian Wang
- Department of Chemotherapy, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
| | - Li Lin
- Department of Oncology, Peking University International Hospital, Beijing 102206, People's Republic of China
| | - You-Cai Zhu
- Department of Thoracic Disease Center, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang 314000, People's Republic of China
| | - Hong Wang
- Department of Lung Cancer, The Fifth Medical Center, General Hospital of PLA, Beijing 100071, People's Republic of China
| | - Li-Yun Miao
- Department of Respiratory Medicine, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, People's Republic of China.
| | - Li-Ping Wang
- Department of Thoracic Oncology, Baotou Cancer Hospital, Baotou, Inner Mongolia 014000, People's Republic of China.
| | - Wu Zhuang
- Department of Medical Oncology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, People's Republic of China
| | - Mei-Yu Fang
- Department of Chemotherapy, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, People's Republic of China
| | - Tang-Feng Lv
- Department of Respiratory Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, People's Republic of China
| | - Yong Song
- Department of Respiratory Medicine, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210002, People's Republic of China.
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Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications. J Mol Diagn 2020; 22:994-1007. [PMID: 32480002 DOI: 10.1016/j.jmoldx.2020.04.213] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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32
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Rodriguez EF, De Marchi F, Lokhandwala PM, Belchis D, Xian R, Gocke CD, Eshleman JR, Illei P, Li MT. IDH1 and IDH2 mutations in lung adenocarcinomas: Evidences of subclonal evolution. Cancer Med 2020; 9:4386-4394. [PMID: 32333643 PMCID: PMC7300411 DOI: 10.1002/cam4.3058] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Background Selective IDH1 and IDH2 inhibitors have been approved for targeted therapy of acute myeloid leukemia. Clinical trials for solid tumors with IDH1 and IDH2 (IDH1/2) mutations are ongoing. Reports of IDH1/2‐mutated non–small cell lung cancers (NSCLCs), however, are limited. Methods We evaluated IDH1/2 mutations in 1,924 NSCLC specimens (92% adenocarcinoma) using a next‐generation sequencing assay. Results Retrospective quality assessments identified false detection of IDH1 c.395G>A (p.R132H) resulting from cytosine deamination (C:G→T:A) artifact in one specimen. IDH1/2 mutations were detected in 9 (0.5%) adenocarcinomas taken by fine‐needle aspiration (n = 3), thoracentesis (n = 2) or core biopsy (n = 4). All nine adenocarcinomas showed high‐grade features. Extensive clear cell change, however, was not observed. High expression (50% or greater) of PD‐L1 was observed in two of five specimens examined. IDH1/2 mutations were associated with old age, smoking history, and coexisting KRAS mutation. Lower than expected variant allele frequency of IDH1/2 mutants and coexistence of IDH1/2 mutations with known trunk drivers in the BRAF, EGFR, and KRAS genes suggest they could be branching drivers leading to subclonal evolution in lung adenocarcinomas. Multiregional analysis of an adenocarcinoma harboring two IDH2 mutations revealed parallel evolution originating from a KRAS‐mutated lineage, further supporting subclonal evolution promoted by IDH1/2 mutations. Conclusions IDH1/2 mutations in NSCLCs are uncommon. They occur in adenocarcinomas with high‐grade features and may be branching drivers leading to subclonal evolution. Accumulation of more IDH1/2‐mutated NSCLCs is needed to clarify their clinicopathological characteristics and implications for targeted therapy.
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Affiliation(s)
- Erika F Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Federico De Marchi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deborah Belchis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Illei
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming-Tseh Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Macgregor-Das A, Yu J, Tamura K, Abe T, Suenaga M, Shindo K, Borges M, Koi C, Kohi S, Sadakari Y, Dal Molin M, Almario JA, Ford M, Chuidian M, Burkhart R, He J, Hruban RH, Eshleman JR, Klein AP, Wolfgang CL, Canto MI, Goggins M. Detection of Circulating Tumor DNA in Patients with Pancreatic Cancer Using Digital Next-Generation Sequencing. J Mol Diagn 2020; 22:748-756. [PMID: 32205290 DOI: 10.1016/j.jmoldx.2020.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/08/2020] [Accepted: 02/26/2020] [Indexed: 12/19/2022] Open
Abstract
Circulating tumor DNA (ctDNA) measurements can be used to estimate tumor burden, but avoiding false-positive results is challenging. Herein, digital next-generation sequencing (NGS) is evaluated as a ctDNA detection method. Plasma KRAS and GNAS hotspot mutation levels were measured in 140 subjects, including 67 with pancreatic ductal adenocarcinoma and 73 healthy and disease controls. To limit chemical modifications of DNA that yield false-positive mutation calls, plasma DNA was enzymatically pretreated, after which DNA was aliquoted for digital detection of mutations (up to 384 aliquots/sample) by PCR and NGS. A digital NGS score of two SDs above the mean in controls was considered positive. Thirty-seven percent of patients with pancreatic cancer, including 31% of patients with stages I/II disease, had positive KRAS codon 12 ctDNA scores; only one patient had a positive GNAS mutation score. Two disease control patients had positive ctDNA scores. Low-normal-range digital NGS scores at mutation hotspots were found at similar levels in healthy and disease controls, usually at sites of cytosine deamination, and were likely the result of chemical modification of plasma DNA and NGS error rather than true mutations. Digital NGS detects mutated ctDNA in patients with pancreatic cancer with similar yield to other methods. Detection of low-level, true-positive ctDNA is limited by frequent low-level detection of false-positive mutation calls in plasma DNA from controls.
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Affiliation(s)
- Anne Macgregor-Das
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jun Yu
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Koji Tamura
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Toshiya Abe
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Masaya Suenaga
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Koji Shindo
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael Borges
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Chiho Koi
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Shiro Kohi
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yoshihiko Sadakari
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Marco Dal Molin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jose A Almario
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Madeline Ford
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Miguel Chuidian
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Richard Burkhart
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Alison P Klein
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Christopher L Wolfgang
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Marcia I Canto
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Michael Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Medicine, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland.
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Buscail L, Bournet B, Cordelier P. Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer. Nat Rev Gastroenterol Hepatol 2020; 17:153-168. [PMID: 32005945 DOI: 10.1038/s41575-019-0245-4] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2019] [Indexed: 02/08/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to be the second most common cause of death within the next 10 years. The prognosis for this disease is poor despite diagnostic progress and new chemotherapeutic regimens. The oncogenic KRAS mutation is the major event in pancreatic cancer; it confers permanent activation of the KRAS protein, which acts as a molecular switch to activate various intracellular signalling pathways and transcription factors inducing cell proliferation, migration, transformation and survival. Several laboratory methods have been developed to detect KRAS mutations in biological samples, including digital droplet PCR (which displays high sensitivity). Clinical studies have revealed that a KRAS mutation assay in fine-needle aspiration material combined with cytopathology increases the sensitivity, accuracy and negative predictive value of cytopathology for a positive diagnosis of pancreatic cancer. In addition, the presence of KRAS mutations in serum and plasma (liquid biopsies) correlates with a worse prognosis. The presence of mutated KRAS can also have therapeutic implications, whether at the gene level per se, during its post-translational maturation, interaction with nucleotides and after activation of the various oncogenic signals. Further pharmacokinetic and toxicological studies on new molecules are required, especially small synthetic molecules, before they can be used in the therapeutic arsenal for pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Louis Buscail
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France. .,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France.
| | - Barbara Bournet
- Department of Gastroenterology, University of Toulouse III, Rangueil Hospital, Toulouse, France.,INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
| | - Pierre Cordelier
- INSERM UMR 1037, Toulouse Centre for Cancer Research, University of Toulouse III, Toulouse, France
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Brewer CJ, Gillespie M, Fierro J, Scaringe WA, Li JM, Lee CY, Yen HY, Gao H, Strom SP. The Value of Parental Testing by Next-Generation Sequencing Includes the Detection of Germline Mosaicism. J Mol Diagn 2020; 22:670-678. [PMID: 32092540 DOI: 10.1016/j.jmoldx.2020.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 10/25/2022] Open
Abstract
When a potential disease-causing variant is detected in a proband, parental testing is used to determine the mode of inheritance. This study demonstrates that next-generation sequencing (NGS) is uniquely well suited for parental testing, in particular because of its ability to detect clinically relevant germline mosaicism. Parental variant testing by NGS was performed in a clinical laboratory for 1 year. The detection of mosaicism by NGS was compared with its detection by Sanger sequencing. Eight cases of previously unrevealed mosaicism were detected by NGS across eight different genes. Mosaic variants were differentiated from sequencing noise using custom bioinformatics analyses in combination with familial inheritance data and complementary Sanger sequencing. Sanger sequencing detected mosaic variants with allele fractions ≥8% by NGS, but could not detect mosaic variants below that level. Detection of germline mosaicism by NGS is invaluable to parents, providing a more accurate recurrence risk that can alter decisions on family planning and pregnancy management. Because NGS can also confirm parentage and increase scalability, it simultaneously streamlines and strengthens the variant curation process. These features make NGS the ideal method for parental testing, superior even to Sanger sequencing for most genomic loci.
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Affiliation(s)
| | | | | | | | | | - Che-Yu Lee
- Fulgent Genetics, Temple City, California
| | | | - Hanlin Gao
- Fulgent Genetics, Temple City, California
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Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
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37
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Nong L, Zhang Z, Xiong Y, Zheng Y, Li X, Li D, He Q, Li T. Comparison of next-generation sequencing and immunohistochemistry analysis for targeted therapy-related genomic status in lung cancer patients. J Thorac Dis 2019; 11:4992-5003. [PMID: 32030215 DOI: 10.21037/jtd.2019.12.25] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Some drugs that target molecular pathways are available for the targeted treatment of lung cancer. Multiple tests are needed to detect the status of the known molecular targets to determine whether the patients can respond to the drugs. An integrated platform for various gene alteration detection including both mutations and rearrangements is necessary for patients, especially those without enough tissue. Methods In our study, detections of EGFR mutations, ALK rearrangement, ROS1 rearrangement, and alterations of other nine important lung cancer-related genes were integrated into a single next-generation sequencing (NGS) platform. The NGS analysis was performed in 107 cases of non-small cell lung cancer (NSCLC). Meanwhile, hot spots such as EGFR L858R, EGFR E746-A750Del mutations and gene rearrangement of ALK and ROS1 were detected by immunohistochemical (IHC) staining. Results NGS could explore various gene mutations and gene rearrangements with a reduced experiment time and lower amounts of tumor tissues than multiple IHC staining experiments. NGS results were more informative and reliable than IHC staining for EGFR gene alterations, especially for the exon 19 region. NGS could also increase the positive rate of ALK rearrangement and decrease the false positive results of ROS1 rearrangements detected by IHC staining. Conclusions NGS is effective for confirmation the status of various important lung cancer-related gene alterations. Furthermore, NGS is necessary for the confirmation of the IHC results of ALK and ROS1 rearrangements.
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Affiliation(s)
- Lin Nong
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | | | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Yalin Zheng
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Xin Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Dong Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Qiye He
- Singlera Genomics Inc., Shanghai 201318, China
| | - Ting Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
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38
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Fischer CG, Guthrie VB, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Molin MD, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD. Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations. Gastroenterology 2019; 157:1123-1137.e22. [PMID: 31175866 PMCID: PMC6756950 DOI: 10.1053/j.gastro.2019.06.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/20/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Intraductal papillary mucinous neoplasms (IPMNs) are lesions that can progress to invasive pancreatic cancer and constitute an important system for studies of pancreatic tumorigenesis. We performed comprehensive genomic analyses of entire IPMNs to determine the diversity of somatic mutations in genes that promote tumorigenesis. METHODS We microdissected neoplastic tissues from 6-24 regions each of 20 resected IPMNs, resulting in 227 neoplastic samples that were analyzed by capture-based targeted sequencing. Somatic mutations in genes associated with pancreatic tumorigenesis were assessed across entire IPMN lesions, and the resulting data were supported by evolutionary modeling, whole-exome sequencing, and in situ detection of mutations. RESULTS We found a high prevalence of heterogeneity among mutations in IPMNs. Heterogeneity in mutations in KRAS and GNAS was significantly more prevalent in IPMNs with low-grade dysplasia than in IPMNs with high-grade dysplasia (P < .02). Whole-exome sequencing confirmed that IPMNs contained multiple independent clones, each with distinct mutations, as originally indicated by targeted sequencing and evolutionary modeling. We also found evidence for convergent evolution of mutations in RNF43 and TP53, which are acquired during later stages of tumorigenesis. CONCLUSIONS In an analysis of the heterogeneity of mutations throughout IPMNs, we found that early-stage IPMNs contain multiple independent clones, each with distinct mutations, indicating their polyclonal origin. These findings challenge the model in which pancreatic neoplasms arise from a single clone. Increasing our understanding of the mechanisms of IPMN polyclonality could lead to strategies to identify patients at increased risk for pancreatic cancer.
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Affiliation(s)
- Catherine G. Fischer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Violeta Beleva Guthrie
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Alicia M. Braxton
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lily Zheng
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Pei Wang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Qianqian Song
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - James F. Griffin
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter E. Chianchiano
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Waki Hosoda
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Simeon Springer
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marco Dal Molin
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Masica
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B. Scharpf
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth D. Thompson
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher L. Wolfgang
- Department of Surgery, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas J. Roberts
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Marie Lennon
- Department of Medicine, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA,Correspondence: Laura D. Wood, MD, PhD, CRB2 Room 345, 1550 Orleans Street, Baltimore, MD 21231, Phone: (410) 955-3511, Fax: (410) 614-0671, , Rachel Karchin, PhD, 217A Hackerman Hall, 2400 N. Charles St. Baltimore, MD 21218, Phone: (410) 516-5578, Fax: (410) 516-5294,
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Huang JK, Fan L, Wang TY, Wu PS. A new primer construction technique that effectively increases amplification of rare mutant templates in samples. BMC Biotechnol 2019; 19:62. [PMID: 31443709 PMCID: PMC6708177 DOI: 10.1186/s12896-019-0555-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/15/2019] [Indexed: 02/07/2023] Open
Abstract
Background In personalized medicine, companion diagnostic tests provide additional information to help select a treatment option likely to be optimal for a patient. Although such tests include several techniques for detecting low levels of mutant genes in wild-type backgrounds with fairly high sensitivity, most tests are not specific, and may exhibit high false positive rates. In this study, we describe a new primer structure, named ‘stuntmer’, to selectively suppress amplification of wild-type templates, and promote amplification of mutant templates. Results A single stuntmer for a defined region of DNA can detect several kinds of mutations, including point mutations, deletions, and insertions. Stuntmer PCRs are also highly sensitive, being able to amplify mutant sequences that may make up as little as 0.1% of the DNA sample. Conclusion In conclusion, our technique, stuntmer PCR, can provide a simple, low-cost, highly sensitive, highly accurate, and highly specific platform for developing companion diagnostic tests. Electronic supplementary material The online version of this article (10.1186/s12896-019-0555-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jr-Kai Huang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Ling Fan
- Department of Nuclear Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tao-Yeuan Wang
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Pao-Shu Wu
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan. .,Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan.
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40
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Rodriguez EF, Pastorello R, Osmani L, Hopkins M, Kryatova M, Kawamoto S, Maleki Z. Ultrasound-Guided Transthoracic Fine-Needle Aspiration: A Reliable Tool in Diagnosis and Molecular Profiling of Lung Masses. Acta Cytol 2019; 64:208-215. [PMID: 31362293 DOI: 10.1159/000501421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Pulmonary adenocarcinoma is a major cause of mortality worldwide. The majority of patients present with advanced stage disease, and minimally invasive procedures are desirable for diagnosis and treatment plans. Herein, we report our experience with percutaneous/transthoracic needle aspiration (TT-NA) in the cytologic diagnosis of pulmonary adenocarcinoma. MATERIAL AND METHODS After institutional review board approval, the cytopathology electronic data system was searched for all consecutive TT-NA of the lung masses from January 2011 to November 2015. Patients' medical records were reviewed and cytologic materials were evaluated. RESULTS A total of 151 specimens were identified, with a mean age of 62.8 years; 62.9% of the patients had a prior history of malignancy. Carcinoma/adenocarcinoma was the most common (80%) diagnosis. The targeted lesions were predominantly located in the lung (56.3%, 81/151) and pleural based (27.8%, 42/151). The mean size of the lesions was 3.6 cm. Cytology specimens were adequate in 70.9% of the cases, while 72.8% (110/151) of the cases also had concurrent core biopsy. A malignant diagnosis was rendered in the majority of the cases (64.9%). In 71% of the cases, immunohistochemistry/histochemistry studies were successfully performed. Molecular/genetic studies were requested in 80% of the cases and had adequate material. Complications of the procedure were seen in 9.9% of the patients including pneumothorax (7.9%) and hemoptysis (1.9%). CONCLUSION TT-NA is a relatively safe and reliable technique in the assessment of pulmonary lesions.
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Affiliation(s)
- Erika F Rodriguez
- Department of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA,
| | - Ricardo Pastorello
- Department of Pathology, Division of Cytopathology, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Lais Osmani
- Department of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Mark Hopkins
- Department of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Maria Kryatova
- Department of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Satomi Kawamoto
- Department of Radiology, Division of Ultrasound, The Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Zahra Maleki
- Department of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, Maryland, USA
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Sarcar B, Gimbrone NT, Wright G, Remsing Rix LL, Gordian ER, Rix U, Chiappori AA, Reuther GW, Santiago-Cardona PG, Muñoz-Antonia T, Cress WD. Characterization of epidermal growth factor receptor (EGFR) P848L, an unusual EGFR variant present in lung cancer patients, in a murine Ba/F3 model. FEBS Open Bio 2019; 9:1689-1704. [PMID: 31314158 PMCID: PMC6768113 DOI: 10.1002/2211-5463.12702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/22/2019] [Accepted: 07/16/2019] [Indexed: 11/06/2022] Open
Abstract
Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) benefit from treatments targeting tyrosine kinase inhibitors (TKIs). However, both intrinsic and acquired resistance of tumors to TKIs are common, and EGFR variants have been identified that are resistant to multiple TKIs. In the present study, we characterized selected EGFR variants previously observed in lung cancer patients and expressed in a murine bone marrow pro-B Ba/F3 cell model. Among these EGFR variants, we report that an exon 20 deletion/insertion mutation S768insVGH is resistant to erlotinib (a first-generation TKI), but sensitive to osimertinib (a third-generation TKI). We also characterized a rare exon 21 germline variant, EGFR P848L, which transformed Ba/F3 cells and conferred resistance to multiple EGFR-targeting TKIs. Our analysis revealed that P848L (a) does not bind erlotinib; (b) is turned over less rapidly than L858R (a common tumor-derived EGFR mutation); (c) is not autophosphorylated at Tyr 1045 [the major docking site for Cbl proto-oncogene (c-Cbl) binding]; and (d) does not bind c-Cbl. Using viability assays including 300 clinically relevant targeted compounds, we observed that Ba/F3 cells transduced with EGFR P848L, S768insVGH, or L858R have very different drug-sensitivity profiles. In particular, EGFR P848L, but not L858R or S768insVGH, was sensitive to multiple Janus kinase 1/2 inhibitors. In contrast, cells driven by L858R, but not by P848L, were sensitive to multikinase MAPK/extracellular-signal-regulated kinase (ERK) kinase and ERK inhibitors including EGFR-specific TKIs. These observations suggest that continued investigation of rare TKI-resistant EGFR variants is warranted to identify optimal treatments for cancer.
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Affiliation(s)
- Bhaswati Sarcar
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Nicholas T Gimbrone
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gabriela Wright
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Edna R Gordian
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Alberto A Chiappori
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Gary W Reuther
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Teresita Muñoz-Antonia
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - William Douglas Cress
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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Dufraing K, van Krieken JH, De Hertogh G, Hoefler G, Oniscu A, Kuhlmann TP, Weichert W, Marchiò C, Ristimäki A, Ryška A, Scoazec JY, Dequeker E. Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study. Histopathology 2019; 75:312-319. [PMID: 31054167 PMCID: PMC6851675 DOI: 10.1111/his.13891] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
Abstract
AIMS Results from external quality assessment revealed considerable variation in neoplastic cell percentages (NCP) estimation in samples for biomarker testing. As molecular biology tests require a minimal NCP, overestimations may lead to false negative test results. We aimed to develop recommendations to improve the NCP determination in a prototypical entity - colorectal carcinoma - that can be adapted for other cancer types. METHODS AND RESULTS A modified Delphi study was conducted to reach consensus by 10 pathologists from 10 countries with experience in determining the NCP for colorectal adenocarcinoma. This study included two online surveys and a decision-making meeting. Consensus was defined a priori as an agreement of > 80%. All pathologists completed both surveys. Consensus was reached for 8 out of 19 and 2 out of 13 questions in the first and second surveys, respectively. Remaining issues were resolved during the meeting. Twenty-four recommendations were formulated. Major recommendations resulted as follows: only pathologists should conduct the morphological evaluation; nevertheless molecular biologists/technicians may estimate the NCP, if specific training has been performed and a pathologist is available for feedback. The estimation should be determined in the area with the highest density of viable neoplastic cells and lowest density of inflammatory cells. Other recommendations concerned: the determination protocol itself, needs for micro- and macro-dissection, reporting and interpreting, referral practices and applicability to other cancer types. CONCLUSION We believe these recommendations may lead to more accurate NCP estimates, ensuring the correct interpretation of test results, and might help in validating digital algorithms in the future.
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Affiliation(s)
- Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium.,Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Gert De Hertogh
- Department of Pathology, University Hospital Leuven, Leuven, Belgium
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Anca Oniscu
- Department of Molecular Pathology, Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Tine P Kuhlmann
- Department of Pathology, Herlev Hospital, Copenhagen, Denmark
| | - Wilko Weichert
- Department of Pathology, Technical University Munich, Munich, Germany
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin and Pathology Unit, Torino, Italy.,FPO-IRCCS Candiolo Cancer Institute, Candiolo, Italy
| | - Ari Ristimäki
- Department of Pathology, Research Programs Unit and HUSLAB, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Aleš Ryška
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Hradec Kralove, Czech Republic
| | | | - Elisabeth Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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43
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Rodriguez EF, Jones R, Morris CP, Ettinger D, Chowsilpa S, Maleki Z. Molecular Alterations in Pulmonary Adenocarcinoma of African Americans. Am J Clin Pathol 2019; 152:237-242. [PMID: 31114847 DOI: 10.1093/ajcp/aqz038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES Identify molecular alterations in pulmonary adenocarcinoma (ADC) in African American (AA) patients diagnosed on cytology specimens. METHODS After institutional review board approval, we searched our database from 2013 to 2017 for AA patients with a diagnosis of pulmonary ADC. Molecular and clinical data were reviewed. White patients also diagnosed with pulmonary ADC on cytology samples formed a control group. RESULTS A total of 113 patients were identified. Mean age was 63.4 years. Molecular tests were available for 91 patients. Mutations were identified in 53 (58.2%) cases. The most common mutations were EGFR (n = 19 cases, 36%) and KRAS (n = 24 cases, 45%). When compared with whites, AA patients were diagnosed at higher stages (P = .045) and demonstrated shorter overall survival (17 vs 47 months, P = .0150). No differences were noted regarding distribution of molecular alterations. CONCLUSION AA patients have similar molecular alterations in ADCs as their white counterparts. However, they have worse outcomes.
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Affiliation(s)
- Erika F Rodriguez
- Departments of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, MD
| | - Robert Jones
- Departments of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, MD
| | - C Paul Morris
- Departments of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, MD
| | - David Ettinger
- Department of Oncology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Sayanan Chowsilpa
- Departments of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, MD
- Department of Pathology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Zahra Maleki
- Departments of Pathology, Division of Cytopathology, The Johns Hopkins Hospital, Baltimore, MD
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44
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Lokhandwala PM, Tseng LH, Rodriguez E, Zheng G, Pallavajjalla A, Gocke CD, Eshleman JR, Lin MT. Clinical mutational profiling and categorization of BRAF mutations in melanomas using next generation sequencing. BMC Cancer 2019; 19:665. [PMID: 31277584 PMCID: PMC6612071 DOI: 10.1186/s12885-019-5864-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022] Open
Abstract
Background Analysis of melanomas for actionable mutations has become the standard of care. Recently, a classification scheme has been proposed that categorizes BRAF mutations based on their mechanisms for activation of the MAPK pathway. Methods In this analysis BRAF, KIT, NRAS, and PIK3CA mutations were examined by next generation sequencing (NGS) in 446 melanomas in a clinical diagnostic setting. KRAS and HRAS were also analyzed to elucidate coexisting BRAF and RAS mutations. BRAF mutations were categorized into class-1 (kinase-activated, codon 600), class-2 (kinase-activated, non-codon 600) and class-3 (kinase-impaired), based on the newly proposed classification scheme. Results NGS demonstrated high analytic sensitivity. Among 355 mutations detected, variant allele frequencies were 2–5% in 21 (5.9%) mutations and 2–10% in 47 (13%) mutations. Mutations were detected in BRAF (42%), NRAS (25%), KIT (4.9%) and PIK3CA (2.7%). The incidence of class-1, class-2 and class-3 mutations were 33% (26% p.V600E and 6.1% p.V600K), 3.1 and 4.9% respectively. With a broader reportable range of NGS, class-1, class-2 and class-3 mutations accounted for 77, 7.4 and 12% of all BRAF mutations. Class-3 mutations, commonly affecting codons 594, 466 and 467, showed a higher incidence of coexisting RAS mutations, consistent with their RAS-dependent signaling. Significant association with old age and primary tumors of head/neck/upper back suggest chronic solar damage as a contributing factor for melanomas harboring BRAF p.V600K or class-3 mutations. Conclusion This study categorizes the range, frequency, coexisting driver mutations and clinical characteristics of the three classes of BRAF mutations in a large cohort of melanomas in a clinical diagnostic setting. Further prospective studies are warranted to elucidate the clinical outcomes and benefits of newly developed targeted therapy in melanoma patients carrying each class of BRAF mutation. Electronic supplementary material The online version of this article (10.1186/s12885-019-5864-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Parvez M Lokhandwala
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.
| | - Li-Hui Tseng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Erika Rodriguez
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Gang Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Aparna Pallavajjalla
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University School of Medicine, Johns Hopkins University School of Medicine, 1812 Ashland Ave, Suite 200, Baltimore, MD, 21205, USA.
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45
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Nakajima E, Sugita M, Furukawa K, Takahashi H, Uchida O, Kawaguchi Y, Ohira T, Matsubayashi J, Ikeda N, Hirsch FR, Franklin WA. Frequency and significance of epidermal growth factor receptor mutations detected by PCR methods in patients with non-small cell lung cancer. Oncol Lett 2019; 17:5125-5131. [PMID: 31186726 DOI: 10.3892/ol.2019.10157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 02/07/2019] [Indexed: 01/16/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is the most important driver gene of non-small cell lung cancer (NSCLC) as EGFR mutations determine the efficacy of EGFR tyrosine kinase inhibitor (EGFR-TKI) therapy. In the present study, the comprehensive ability of widely used polymerase chain reaction (PCR) methods to detect EGFR mutations was determined. Among the 35 EGFR mutations detected via the direct sequencing of 73 patients with NSCLC, 11 types were identified in exons 18, 19 and 21. Among the 11 mutation types, all exon 18 and 21 mutations were identified by 2 widely used PCR methods, namely, Scorpion-Amplification Refractory Mutation System and cobas v2. However, among the 9 different exon 19 deletions, 3 types were not identified by the 2 methods. In addition, 25 samples with EGFR mutations were analyzed by the 2 methods, including a sample from a patient with an unidentified exon 19 deletion, the T751_I759 deletion and insertion S; this patient had long-term disease control as a result of EGFR-TKI therapy. The 2 methods could not detect this unidentified deletion, whereas sizing capillary electrophoresis for the comprehensive detection of exon 19 deletions detected this deletion. It is generally thought that patients with exon 19 mutations have higher response rates to EGFR-TKI therapy than patients with exon 21 mutations. The present study confirmed the EGFR mutation status by comparing the mutations with the Catalog Of Somatic Mutations In Cancer, which is the world's largest and most comprehensive resource for analyzing the effects of somatic mutations in human cancers. The predicted frequency of EGFR mutations identified by the 2 methods was 85%. The frequency of mutations detectable by the 2 methods was less for exon 19 than exon 21. Therefore, the results of the present study suggest that decreasing false-negative detection of exon 19 deletions is crucial for the clinical testing of EGFR mutations.
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Affiliation(s)
- Eiji Nakajima
- Department of Thoracic Surgery, Tokyo Medical University Ibaraki Medical Center, Ibaraki 300-0395, Japan
| | - Michio Sugita
- Department of Pathology, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
| | - Kinya Furukawa
- Department of Thoracic Surgery, Tokyo Medical University Ibaraki Medical Center, Ibaraki 300-0395, Japan
| | - Hidenobu Takahashi
- Department of Thoracic Surgery, Tokyo Medical University Hachioji Medical Center, Tokyo 193-0998, Japan
| | - Osamu Uchida
- Department of Thoracic Surgery, Tokyo Medical University Hachioji Medical Center, Tokyo 193-0998, Japan
| | - Youhei Kawaguchi
- Department of Thoracic Surgery, Tokyo Medical University Hospital, Tokyo 160-0023, Japan
| | - Tatsuo Ohira
- Department of Thoracic Surgery, Tokyo Medical University Hospital, Tokyo 160-0023, Japan
| | - Jun Matsubayashi
- Department of Pathology, Tokyo Medical University Hospital, Tokyo 160-0023, Japan
| | - Norihiko Ikeda
- Department of Thoracic Surgery, Tokyo Medical University Hospital, Tokyo 160-0023, Japan
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
| | - Wilbur A Franklin
- Department of Pathology, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
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46
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Groot VP, Mosier S, Javed AA, Teinor JA, Gemenetzis G, Ding D, Haley LM, Yu J, Burkhart RA, Hasanain A, Debeljak M, Kamiyama H, Narang A, Laheru DA, Zheng L, Lin MT, Gocke CD, Fishman EK, Hruban RH, Goggins MG, Molenaar IQ, Cameron JL, Weiss MJ, Velculescu VE, He J, Wolfgang CL, Eshleman JR. Circulating Tumor DNA as a Clinical Test in Resected Pancreatic Cancer. Clin Cancer Res 2019; 25:4973-4984. [PMID: 31142500 DOI: 10.1158/1078-0432.ccr-19-0197] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/15/2019] [Accepted: 05/23/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE In research settings, circulating tumor DNA (ctDNA) shows promise as a tumor-specific biomarker for pancreatic ductal adenocarcinoma (PDAC). This study aims to perform analytical and clinical validation of a KRAS ctDNA assay in a Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathology-certified clinical laboratory. EXPERIMENTAL DESIGN Digital-droplet PCR was used to detect the major PDAC-associated somatic KRAS mutations (G12D, G12V, G12R, and Q61H) in liquid biopsies. For clinical validation, 290 preoperative and longitudinal postoperative plasma samples were collected from 59 patients with PDAC. The utility of ctDNA status to predict PDAC recurrence during follow-up was assessed. RESULTS ctDNA was detected preoperatively in 29 (49%) patients and was an independent predictor of decreased recurrence-free survival (RFS) and overall survival (OS). Patients who had neoadjuvant chemotherapy were less likely to have preoperative ctDNA than were chemo-naïve patients (21% vs. 69%; P < 0.001). ctDNA levels dropped significantly after tumor resection. Persistence of ctDNA in the immediate postoperative period was associated with a high rate of recurrence and poor median RFS (5 months). ctDNA detected during follow-up predicted clinical recurrence [sensitivity 90% (95% confidence interval (CI), 74%-98%), specificity 88% (95% CI, 62%-98%)] with a median lead time of 84 days (interquartile range, 25-146). Detection of ctDNA during postpancreatectomy follow-up was associated with a median OS of 17 months, while median OS was not yet reached at 30 months for patients without ctDNA (P = 0.011). CONCLUSIONS Measurement of KRAS ctDNA in a CLIA laboratory setting can be used to predict recurrence and survival in patients with PDAC.
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Affiliation(s)
- Vincent P Groot
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stacy Mosier
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ammar A Javed
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan A Teinor
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Georgios Gemenetzis
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ding Ding
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Pancreatic Cancer Precision Medicine Center of Excellence Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa M Haley
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jun Yu
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Richard A Burkhart
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alina Hasanain
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marija Debeljak
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hirohiko Kamiyama
- Department of Gastroenterological Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Amol Narang
- Department of Radiation Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel A Laheru
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lei Zheng
- Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Pancreatic Cancer Precision Medicine Center of Excellence Program, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ming-Tseh Lin
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher D Gocke
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elliot K Fishman
- Department of Radiology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael G Goggins
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - I Quintus Molenaar
- Department of Surgery, UMC Utrecht Cancer Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - John L Cameron
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew J Weiss
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor E Velculescu
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jin He
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher L Wolfgang
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland. .,Molecular Pathology Laboratory, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Dhieb D, Belguith I, Capelli L, Chiadini E, Canale M, Bravaccini S, Yangui I, Boudawara O, Jlidi R, Boudawara T, Calistri D, Keskes LA, Ulivi P. Analysis of Genetic Alterations in Tunisian Patients with Lung Adenocarcinoma. Cells 2019; 8:E514. [PMID: 31141932 PMCID: PMC6627075 DOI: 10.3390/cells8060514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/23/2019] [Accepted: 05/26/2019] [Indexed: 11/16/2022] Open
Abstract
The identification of the mutations that drive lung cancer have furnished new targets for the treatment of non-small cell lung cancer (NSCLC) and led to the development of targeted therapies such as tyrosine kinase inhibitors that are used to combat the molecular changes promoting cancer progression. Furthermore, biomarkers identified from gene analysis can be used to detect early lung cancer, determine patient prognosis, and monitor response to therapy. In the present study we analyzed the molecular profile of seventy-three Tunisian patients with lung adenocarcinoma (LAD). Mutational analyses for EGFR and KRAS were performed using direct sequencing, immunohistochemistry or MassARRAY. Anaplastic lymphoma kinase (ALK) rearrangement was evaluated by immunohistochemistry using the D5F3 clone, and p53 expression was also assessed. The median age of patients at diagnosis was 61 years (range 23-82 years). Using different methodologies, EGFR mutations were found in 5.47% of patients and only exon 19 deletions "E746-A750 del" were detected. KRAS mutations were present in 9.58% of cases, while only one patient was ALK-positive. Moreover, abnormal immunostaining of p53 was detected in 56.16% of patients. In conclusion, the detected rates of EGFR and KRAS mutation and ALK rearrangement were lower than those found in European and Asian countries, whereas, abnormal p53 expression was slightly more frequent. Furthermore, given the small sample size of this study, a more comprehensive analysis of this patient set is warranted.
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Affiliation(s)
- Dhoha Dhieb
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax 3029, Tunisia.
| | - Imen Belguith
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax 3029, Tunisia.
| | - Laura Capelli
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
| | - Elisa Chiadini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
| | - Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
| | - Sara Bravaccini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
| | - Ilhem Yangui
- Department of Respiratory and Sleep Diseases, CHU Hedi Chaker, Sfax 3029, Tunisia.
| | - Ons Boudawara
- Department of Pathology, CHU Habib Bourguiba, Sfax 3029, Tunisia.
| | - Rachid Jlidi
- Laboratory of Anatomic Pathology, Sfax 3000, Tunisia.
| | - Tahya Boudawara
- Department of Pathology, CHU Habib Bourguiba, Sfax 3029, Tunisia.
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
| | - Leila Ammar Keskes
- Laboratory of Human Molecular Genetics, Faculty of Medicine of Sfax, University of Sfax, Sfax 3029, Tunisia.
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola 47014, Italy.
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Abstract
Since the discovery that DNA alterations initiate tumorigenesis, scientists and clinicians have been exploring ways to counter these changes with targeted therapeutics. The sequencing of tumor DNA was initially limited to highly actionable hot spots-areas of the genome that are frequently altered and have an approved matched therapy in a specific tumor type. Large-scale genome sequencing programs quickly developed technological improvements that enabled the deployment of whole-exome and whole-genome sequencing technologies at scale for pristine sample materials in research environments. However, the turning point for precision medicine in oncology was the innovations in clinical laboratories that improved turnaround time, depth of coverage, and the ability to reliably sequence archived, clinically available samples. Today, tumor genome sequencing no longer suffers from significant technical or financial hurdles, and the next opportunity for improvement lies in the optimal utilization of the technologies and data for many different tumor types.
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Affiliation(s)
- Kenna R Mills Shaw
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
| | - Anirban Maitra
- Khalifa Bin Zayed Institute for Personalized Cancer Therapy and Sheikh Ahmed Center for Pancreatic Cancer Research, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA;
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49
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Wang T, Liu Y, Sun HH, Yin BC, Ye BC. An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019; 58:5382-5386. [PMID: 30773764 DOI: 10.1002/anie.201901292] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 12/11/2022]
Abstract
We have developed an ingenious method, termed Cas9 nickase-based amplification reaction (Cas9nAR), to amplify a target fragment from genomic DNA at a constant temperature of 37 °C. Cas9nAR employs a sgRNA:Cas9n complex with a single-strand nicking property, a strand-displacing DNA polymerase, and two primers bearing the cleavage sequence of Cas9n, to promote cycles of DNA replication through priming, extension, nicking, and displacement reaction steps. Cas9nAR exhibits a zeptomolar limit of detection (2 copies in 20 μL of reaction system) within 60 min and a single-base discrimination capability. More importantly, the underlying principle of Cas9nAR offers simplicity in primer design and universality in application. Considering the superior sensitivity and specificity, as well as the simple-to-implement, rapid, and isothermal features, Cas9nAR holds great potential to become a routine assay for the quantitative detection of nucleic acids in basic and applied studies.
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Affiliation(s)
- Ting Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Yong Liu
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan-Huan Sun
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
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50
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Wang T, Liu Y, Sun H, Yin B, Ye B. An RNA‐Guided Cas9 Nickase‐Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ting Wang
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Yong Liu
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Huan‐Huan Sun
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bin‐Cheng Yin
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bang‐Ce Ye
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
- Institute of Engineering Biology and HealthCollaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsCollege of Pharmaceutical SciencesZhejiang University of Technology Hangzhou 310014 Zhejiang China
- School of Chemistry and Chemical EngineeringShihezi University Xinjiang 832000 China
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