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Stack JT, Rayner RE, Nouri R, Suarez CJ, Kim SH, Kanke KL, Vetter TA, Cormet-Boyaka E, Vaidyanathan S. DNA-PKcs Inhibition Improves Sequential Gene Insertion of the Full-Length CFTR cDNA in Airway Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607571. [PMID: 39185207 PMCID: PMC11343149 DOI: 10.1101/2024.08.12.607571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although many people with CF (pwCF) are treated using CFTR modulators, some are non-responsive due to their genotype or other uncharacterized reasons. Autologous airway stem cell therapies, in which the CFTR cDNA has been replaced, may enable a durable therapy for all pwCF. Previously, CRISPR-Cas9 with two AAVs was used to sequentially insert two halves of the CFTR cDNA and an enrichment cassette into the CFTR locus. However, the editing efficiency was <10% and required enrichment to restore CFTR function. Further improvement in gene insertion may enhance cell therapy production. To improve CFTR cDNA insertion in human airway basal stem cells (ABCs), we evaluated the use of the small molecules AZD7648 and ART558 which inhibit non-homologous end joining (NHEJ) and micro-homology mediated end joining (MMEJ). Adding AZD7648 alone improved gene insertion by 2-3-fold. Adding both ART558 and AZD7648 improved gene insertion but induced toxicity. ABCs edited in the presence of AZD7648 produced differentiated airway epithelial sheets with restored CFTR function after enrichment. Adding AZD7648 did not increase off-target editing. Further studies are necessary to validate if AZD7648 treatment enriches cells with oncogenic mutations.
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Affiliation(s)
- Jacob T. Stack
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Rachael E. Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Reza Nouri
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Carlos J. Suarez
- Department of Pathology, Stanford University, Palo Alto, CA 94305
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210
| | - Karen L. Kanke
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | - Tatyana A. Vetter
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
| | | | - Sriram Vaidyanathan
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210
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2
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Tsujikawa T, Ohno K, Morita KI, Saburi S, Mitsuda J, Yoshimura K, Kimura A, Morimoto H, Ogi H, Shibata S, Akashi T, Kurata M, Imoto I, Shimizu Y, Kano S, Watanabe A, Yamazaki T, Asada Y, Hayashi R, Saito Y, Ozawa H, Tsukahara K, Oridate N, Sano D, Horii A, Ueki Y, Maruo T, Mukoyama N, Hanai N, Fukusumi T, Iwai H, Fujisawa T, Fujii T, Nibu KI, Iwae S, Ueda T, Chikuie N, Yasumatsu R, Matsuo M, Umeno H, Ono T, Masuda M, Toh S, Itoh K, Hirano S, Asakage T. Clinical, genomic and immune microenvironmental determinants of nivolumab response in head and neck squamous cell carcinoma. Front Immunol 2024; 15:1390873. [PMID: 39136017 PMCID: PMC11317249 DOI: 10.3389/fimmu.2024.1390873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Background In view of improving biomarkers predicting the efficacy of immunotherapy for head and neck squamous cell carcinoma (R/M HNSCC), this multicenter retrospective study aimed to identify clinical, tumor microenvironmental, and genomic factors that are related to therapeutic response to the anti- Programmed cell death protein 1 (PD-1) antibody, nivolumab, in patients with R/M HNSCC. Methods The study compared 53 responders and 47 non-responders, analyzing formalin-fixed paraffin-embedded samples using 14-marker multiplex immunohistochemistry and targeted gene sequencing. Results Of 100 patients included, responders had significantly lower smoking and alcohol index, higher incidence of immune related adverse events, and higher PD-1 ligand (PD-L1) expression in immune cells as well as PD-L1 combined positive score (CPS) than non-responders. The frequency of natural killer cells was associated with nivolumab response in patients with prior cetuximab use, but not in cetuximab-naïve status. Age-stratified analysis showed nivolumab response was linked to high CPS and lymphoid-inflamed profiles in patients aged ≥ 65. In contrast, lower NLR in peripheral blood counts was associated with response in patients aged < 65. Notably, TP53 mutation-positive group had lower CPS and T cell densities, suggesting an immune-excluded microenvironment. Patients with altered tumor suppressor gene pathways, including TP53, CDKN2A, and SMAD4 mutations, had lower CPS, higher smoking index, and were associated with poor responses. Conclusion Nivolumab treatment efficacy in HNSCC is influenced by a combination of clinical factors, age, prior treatment, immune environmental characteristics, and gene mutation profiles.
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Affiliation(s)
- Takahiro Tsujikawa
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, United States
| | - Kazuchika Ohno
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei-ichi Morita
- Department of Maxillofacial Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sumiyo Saburi
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junichi Mitsuda
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kanako Yoshimura
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Alisa Kimura
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroki Morimoto
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Ogi
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- SCREEN Holdings, Kyoto, Japan
| | | | - Takumi Akashi
- Department of Diagnostic Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Issei Imoto
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yasushi Shimizu
- Department of Medical Oncology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Kano
- Department of Otolaryngology-Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Akihito Watanabe
- Department of Otolaryngology- Head and Neck Surgery, Keiyukai Sapporo Hospital, Sapporo, Japan
| | - Tomoko Yamazaki
- Department Head and Neck Oncology Division, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Yukinori Asada
- Department of Head and Neck Surgery, Miyagi Cancer Center, Natori, Japan
| | - Ryuichi Hayashi
- Department of Head and Neck Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yuki Saito
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kiyoaki Tsukahara
- Department of Otorhinolaryngology, Head and Neck Surgery, Tokyo Medical University, Tokyo, Japan
| | - Nobuhiko Oridate
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Daisuke Sano
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Arata Horii
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yushi Ueki
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takashi Maruo
- Department of Otorhinolaryngology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuaki Mukoyama
- Department of Otorhinolaryngology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Hanai
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Takahito Fukusumi
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Iwai
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, Osaka, Japan
| | - Takuo Fujisawa
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, Osaka, Japan
| | - Takashi Fujii
- Department of Head and Neck Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Ken-ichi Nibu
- Department of Otolaryngology–Head and Neck Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shigemichi Iwae
- Department of Head and Neck Surgery, Hyogo Cancer Center, Akashi, Japan
| | - Tsutomu Ueda
- Department of Otolaryngology and Head and Neck Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Nobuyuki Chikuie
- Department of Otolaryngology and Head and Neck Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Ryuji Yasumatsu
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Mioko Matsuo
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirohito Umeno
- Department of Otolaryngology-Head and Neck Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Takeharu Ono
- Department of Otolaryngology-Head and Neck Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Muneyuki Masuda
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Satoshi Toh
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeru Hirano
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
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Ali RH, Alateeqi M, Jama H, Alrumaidhi N, Alqallaf A, Mohammed EM, Almurshed M, Bahzad S. Evaluation of the Oncomine Comprehensive Assay v3 panel for the detection of 1p/19q codeletion in oligodendroglial tumours. J Clin Pathol 2023; 76:103-110. [PMID: 34489310 DOI: 10.1136/jclinpath-2021-207876] [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: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 01/24/2023]
Abstract
AIMS Accurate assessment of 1p/19q codeletion status in diffuse gliomas is of paramount importance for diagnostic, prognostic and predictive purposes. While targeted next generation sequencing (NGS) has been widely implemented for glioma molecular profiling, its role in detecting structural chromosomal variants is less well established, requiring supplementary informatic tools for robust detection. Herein, we evaluated a commercially available amplicon-based targeted NGS panel (Oncomine Comprehensive Assay v3) for the detection of 1p/19q losses in glioma tissues using an Ion Torrent platform and the standard built-in NGS data analysis pipeline solely. METHODS Using as little as 20 ng of DNA from formalin-fixed paraffin-embedded tissues, we analysed 25 previously characterised gliomas for multi-locus copy number losses (CNLs) on 1p and 19q, including 11 oligodendrogliomas (ODG) and 14 non-oligodendroglial (non-ODG) controls. Fluorescence in-situ hybridisation (FISH) was used as a reference standard. RESULTS The software confidently detected combined contiguous 1p/19q CNLs in 11/11 ODGs (100% sensitivity), using a copy number cut-off of ≤1.5 and a minimum of 10 amplicons covering the regions. Only partial non-specific losses were identified in non-ODGs (100% specificity). Copy number averages of ODG and non-ODG groups were significantly different (p<0.001). NGS was concordant with FISH and was superior to it in distinguishing partial from contiguous losses indicative of whole-arm chromosomal deletion. CONCLUSIONS This commercial NGS panel, along with the standard Ion Torrent algorithm, accurately detected 1p/19q losses in ODG samples, obviating the need for specialised custom-made informatic analyses. This can easily be incorporated into routine glioma workflow as an alternative to FISH.
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Affiliation(s)
- Rola H Ali
- Department of Pathology, Kuwait University, Jabriya, Kuwait .,Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Mona Alateeqi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Hiba Jama
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Noor Alrumaidhi
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | - Ali Alqallaf
- Cytogenetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
| | | | | | - Shakir Bahzad
- Molecular Genetics Laboratory, Kuwait Cancer Control Center, Shuwaikh, Kuwait
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Ben X, Tian D, Zhuang W, Chen R, Wang S, Zhou Z, Deng C, Shi R, Liu S, Zhang D, Tang J, Xie L, Zhou H, Zhang Z, Li M, Zhang X, Qiao G. Accuracy of next-generation sequencing for molecular profiling of small specimen of lung cancer: a prospective pilot study of side-by-side comparison. Diagn Pathol 2022; 17:78. [PMID: 36224661 PMCID: PMC9554964 DOI: 10.1186/s13000-022-01255-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Background Successful practice of precision medicine in advanced lung cancers relies on therapeutic regimens tailored to individual molecular characteristics. The aim of this study was to investigate the accuracy of small specimens for molecular profiling using next-generation sequencing (NGS). Methods Genetic alternations, tumor mutational burden (TMB), status of microsatellite instability (MSI), and expression of programmed death ligand 1 (PD-L1) were compared side-by-side between the concurrently obtained core needle biopsy (CNB) and resection specimens in 17 patients with resectable non-small cell lung cancers. Results DNA yield and library complexity were significantly lower in CNB specimens (both p < 0.01), whereas the insert size, sequencing depth, and Q30 ratio were similar between the matched specimens (all p > 0.05). The total numbers of genetic alternations detected in resection and CNB specimens were 186 and 211, respectively, with 156 alternations in common, yielding a specific concordance rate of 83.9%. The prevalence of mutations in 8 major driver genes was 100% identical between surgical and CNB specimens, though the allele frequency was lower in CNB specimens, with a median underestimation of 57%. Results of TMB were similar (p = 0.547) and MSI status was 100% matched in all paired specimens. Conclusions Pulmonary CNB specimens were suitable for NGS given the satisfactory accuracy when compared to corresponding surgical specimens. NGS results yielding from CNB specimens should be deemed reliable to provide instructive information for the treatment of advanced lung cancers. Supplementary Information The online version contains supplementary material available at 10.1186/s13000-022-01255-y.
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Affiliation(s)
- Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Dan Tian
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Weitao Zhuang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
| | - Rixin Chen
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China.,Research Center of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Sichao Wang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Zihao Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Cheng Deng
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Ruiqing Shi
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Songlin Liu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Dongkun Zhang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China
| | - Zhou Zhang
- Department of Data Science, Burning Rock Biotech, Guangzhou, China
| | - Min Li
- Department of Medicine, Burning Rock Biotech, Guangzhou, China
| | - Xuanye Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Second Road, Guangzhou, 510080, China.
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Winzeler B, Tufton N, S. Lim E, Challis BG, Park S, Izatt L, Carroll PV, Velusamy A, Hulse T, Whitelaw BC, Martin E, Rodger F, Maranian M, Clark GR, A. Akker S, Maher ER, Casey RT. Investigating the role of somatic sequencing platforms for phaeochromocytoma and paraganglioma in a large UK cohort. Clin Endocrinol (Oxf) 2022; 97:448-459. [PMID: 34870338 PMCID: PMC9543043 DOI: 10.1111/cen.14639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/24/2021] [Accepted: 10/21/2021] [Indexed: 12/03/2022]
Abstract
OBJECTIVES Phaeochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumours with malignant potential and a hereditary basis in almost 40% of patients. Germline genetic testing has transformed the management of PPGL enabling stratification of surveillance approaches, earlier diagnosis and predictive testing of at-risk family members. Recent studies have identified somatic mutations in a further subset of patients, indicating that molecular drivers at either a germline or tumour level can be identified in up to 80% of PPGL cases. The aim of this study was to investigate the clinical utility of somatic sequencing in a large cohort of patients with PPGL in the United Kingdom. DESIGN AND PATIENTS Prospectively collected matched germline and tumour samples (development cohort) and retrospectively collected tumour samples (validation cohort) of patients with PPGL were investigated. MEASUREMENTS Clinical characteristics of patients were assessed and tumour and germline DNA was analysed using a next-generation sequencing strategy. A screen for variants within 'mutation hotspots' in 68 human cancer genes was performed. RESULTS Of 141 included patients, 45 (32%) had a germline mutation. In 37 (26%) patients one or more driver somatic variants were identified including 26 likely pathogenic or pathogenic variants and 19 variants of uncertain significance. Pathogenic somatic variants, observed in 25 (18%) patients, were most commonly identified in the VHL, NF1, HRAS and RET genes. Pathogenic somatic variants were almost exclusively identified in patients without a germline mutation (all but one), suggesting that somatic sequencing is likely to be most informative for those patients with negative germline genetic test results. CONCLUSIONS Somatic sequencing may further stratify surveillance approaches for patients without a germline genetic driver and may also inform targeted therapeutic strategies for patients with metastatic disease.
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Affiliation(s)
- Bettina Winzeler
- Department of Endocrinology, Diabetology and MetabolismUniversity Hospital BaselBaselSwitzerland
- Department of Clinical ResearchUniversity of BaselBaselSwitzerland
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
| | - Nicola Tufton
- Department of EndocrinologySt. Bartholomew's Hospital, Barts Health NHS TrustLondonUK
- Department of Endocrinology, William Harvey Research InstituteQueen Mary University of LondonLondon
| | - Eugenie S. Lim
- Department of EndocrinologySt. Bartholomew's Hospital, Barts Health NHS TrustLondonUK
- Department of Endocrinology, William Harvey Research InstituteQueen Mary University of LondonLondon
| | - Ben G. Challis
- Department of Endocrinology, Cambridge University HospitalNHS Foundation TrustCambridgeUK
| | - Soo‐Mi Park
- Department of Clinical Genetics, Cambridge University HospitalNHS Foundation TrustCambridgeUK
| | - Louise Izatt
- Department of Clinical GeneticsGuy's and St. Thomas' NHS Foundation TrustLondonUK
| | - Paul V. Carroll
- Department of EndocrinologyGuy's and St. Thomas' NHS Foundation TrustLondonUK
| | - Anand Velusamy
- Department of EndocrinologyGuy's and St. Thomas' NHS Foundation TrustLondonUK
| | - Tony Hulse
- Department of Paediatric EndocrinologyEvelina London Children's Hospital, Guy's and St. Thomas' NHS Foundation TrustLondonUK
| | | | - Ezequiel Martin
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
- Oncology Department, Cancer Molecular Diagnostics LaboratoryUniversity of CambridgeCambridgeUK
| | - Fay Rodger
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
| | - Melanie Maranian
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
| | - Graeme R. Clark
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
| | - Scott A. Akker
- Department of EndocrinologySt. Bartholomew's Hospital, Barts Health NHS TrustLondonUK
- Department of Endocrinology, William Harvey Research InstituteQueen Mary University of LondonLondon
| | - Eamonn R. Maher
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
| | - Ruth T. Casey
- Department of Medical Genetics, and Cancer Research, UK Cambridge Centre, University of CambridgeCambridge Biomedical CampusCambridgeUK
- Department of Endocrinology, Cambridge University HospitalNHS Foundation TrustCambridgeUK
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6
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Evaluation of the TruSight Tumor 170 Assay and Its Value in Clinical Diagnostics. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Parallel sequencing technologies have become integrated into clinical practice. This study evaluated the TruSight Tumor 170 assay for the simultaneous detection of somatic gene mutations (SNPs and indels), gene fusions and CNVs, and its implementation into routine diagnostics. Methods: Forty-four formalin-fixed, paraffin-embedded tissue samples analyzed previously with validated methods were evaluated with the TruSight Tumor 170 assay (Illumina). For data analysis the TruSight Tumor 170 app, the BaseSpace Variant Interpreter (Illumina), and the Molecular Health Guide Software (Molecular Health) were used. Results: All somatic gene mutations were identified when covered by the assay. Two high-level MET amplifications were detected by CNV analysis. Focal MET amplifications with a copy number below 10 were not reliably detected at the DNA-level. Twenty-one of 31 fusions and splice variants were confirmed with the assay on the RNA-level. The remaining eight aberrations were incorrect by previous methods. In two cases, no splicing was observed. Conclusions: The TruSight Tumor 170 gives reliable results even if low DNA and RNA concentrations are applied in comparison to other methods and can be used in a routine workflow to detect somatic gene mutations, gene fusions, and splice variants. However, we were not able to detect most focal gene amplifications/deletions.
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7
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Vaidyanathan S, Baik R, Chen L, Bravo DT, Suarez CJ, Abazari SM, Salahudeen AA, Dudek AM, Teran CA, Davis TH, Lee CM, Bao G, Randell SH, Artandi SE, Wine JJ, Kuo CJ, Desai TJ, Nayak JV, Sellers ZM, Porteus MH. Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus. Mol Ther 2022; 30:223-237. [PMID: 33794364 PMCID: PMC8753290 DOI: 10.1016/j.ymthe.2021.03.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR-Cas9 and two adeno-associated viruses (AAVs) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial epithelial cells (HBECs). The modified cells were enriched to obtain 60%-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.
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Affiliation(s)
| | - Ron Baik
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lu Chen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dawn T Bravo
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Shayda M Abazari
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ameen A Salahudeen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Steven E Artandi
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey J Wine
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Calvin J Kuo
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tushar J Desai
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Zachary M Sellers
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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8
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Masago K, Fujita S, Oya Y, Takahashi Y, Matsushita H, Sasaki E, Kuroda H. Comparison between Fluorimetry (Qubit) and Spectrophotometry (NanoDrop) in the Quantification of DNA and RNA Extracted from Frozen and FFPE Tissues from Lung Cancer Patients: A Real-World Use of Genomic Tests. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:medicina57121375. [PMID: 34946321 PMCID: PMC8709233 DOI: 10.3390/medicina57121375] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 05/26/2023]
Abstract
Background and Objectives: Panel-based next-generation sequencing (NGS) has been carried out in daily clinical settings for the diagnosis and treatment guidance of patients with non-small cell lung cancer (NSCLC). The success of genomic tests including NGS depends in large part on preparing better-quality DNA or RNA; however, there are no established operating methods for preparing genomic DNA and RNA samples. Materials and Methods: We compared the following two quantitative methods, the QubitTM and NanoDropTM, using 585 surgical specimens, 278 biopsy specimens, and 82 cell block specimens of lung cancer that were used for genetic tests, including NGS. We analyzed the success rate of the genomic tests, including NGS, which were performed with DNA and RNA with concentrations that were outliers for the Qubit Fluorometer. Results: The absolute value for DNA concentrations had a tendency to be higher when measured with NanoDropTM regardless of the type of specimen; however, this was not the case for RNA. The success rate of DNA-based genomic tests using specimens with a concentration below the lower limit of QubitTM detection was as high as approximately 96%. At less than 60%, the success rate of RNA-based genomic tests, including RT-PCR, was not as satisfactory. The success rates of the AmpliSeqTM DNA panel sequencing and RNA panel sequencing were 77.8% and 91.5%, respectively. If at least one PCR amplification product could be obtained, then all RNA-based sequencing was performed successfully. Conclusions: The concentration measurements with NanoDropTM are reliable. The success rate of NGS with samples at concentrations below the limit of detection of QubitTM was relatively higher than expected, and it is worth performing PCR-based panel sequencing, especially in cases where re-biopsy cannot be performed.
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Affiliation(s)
- Katsuhiro Masago
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya 4648681, Japan;
| | - Shiro Fujita
- Department of Respiratory Medicine, Kobe Central Hospital, Kobe 651115, Japan;
| | - Yuko Oya
- Department of Thoracic Surgery, Aichi Cancer Center, Nagoya 4648681, Japan; (Y.O.); (Y.T.); (H.K.)
| | - Yusuke Takahashi
- Department of Thoracic Surgery, Aichi Cancer Center, Nagoya 4648681, Japan; (Y.O.); (Y.T.); (H.K.)
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Research Institute, Nagoya 4648681, Japan;
| | - Eiichi Sasaki
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya 4648681, Japan;
| | - Hiroaki Kuroda
- Department of Thoracic Surgery, Aichi Cancer Center, Nagoya 4648681, Japan; (Y.O.); (Y.T.); (H.K.)
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9
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Mishra SK, Kumari N, Krishnani N, Singh RK, Mohindra S. Identification and prevalence of potentially therapeutic targetable variants of major cancer driver genes in ampullary cancer patients in India through deep sequencing. Cancer Genet 2021; 258-259:41-48. [PMID: 34455261 DOI: 10.1016/j.cancergen.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/19/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
Ampulla is a complex region located at the confluence of pancreatic and common bile duct and intestinal epithelium. Tumors arising in this region are anatomically and morphologically heterogenous, however they show unique as well as overlapping molecular features. Cancers of both these anatomic sites share morphological as well as genetic profile despite having few unique differences. Targeted therapies are currently emerging as one of the demanding approaches for treatment in most cancer types especially for malignant epithelial tumors and therefore genetic profiling of cancers is the key for identification of potentially therapeutic targetable mutations to know their prevalence and prognostic impact. We studied 97 resected cases of formalin fixed paraffin-embedded AC by deep targeted sequencing using Ampliseq cancer hotspot panel comprising of 50 oncogenes and tumor suppressor genes. Potentially therapeutic targetable mutations were observed in 58/83 (70%) cases. Fourteen patients did not show any pathogenic mutation. TP53 (48.1%), KRAS (37.3%), APC (25.3%), SMAD4 (22.8%), MET (16.8%), CTNNB1 (15.6%) and PIK3CA (10.8%) were the major mutated potential therapeutic targets. KRAS mutation (43.2 Vs. 32.6%) was more prevalent in pancreatobiliary subtype, while TP53 (58.6 Vs 35.1), APC (36.9 Vs 10.8), SMAD4 (28.2 Vs 16.2), MET (21.7 Vs 10.8) and CTNNB1 (19.5 Vs 10.8) were more prevalent in intestinal subtype. WNT signaling pathway was the major altered pathway in intestinal subtype. These mutated genes and pathways may be targeted with currently available drugs and may be explored for future development of targetable agents to improve the disease course in patients of AC.
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Affiliation(s)
- Shravan Kumar Mishra
- Department of Pathology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, UP, India
| | - Niraj Kumari
- Department of Pathology and Laboratory Medicine, All India Institute of Medical Sciences, Raebareli, UP, India.
| | - Narendra Krishnani
- Department of Pathology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, UP, India
| | - Rajneesh Kumar Singh
- Department of Surgical Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, UP, India
| | - Samir Mohindra
- Department of Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, UP, India
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10
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Boyle TA, Mondal AK, Saeed-Vafa D, Ananth S, Ahluwalia P, Kothapalli R, Chaubey A, Roberts E, Qin D, Magliocco AM, Rojiani AM, Kolhe R. Guideline-Adherent Clinical Validation of a Comprehensive 170-Gene DNA/RNA Panel for Determination of Small Variants, Copy Number Variations, Splice Variants, and Fusions on a Next-Generation Sequencing Platform in the CLIA Setting. Front Genet 2021; 12:503830. [PMID: 34093633 PMCID: PMC8172991 DOI: 10.3389/fgene.2021.503830] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
We describe the clinical validation of a targeted DNA and RNA-based next-generation sequencing (NGS) assay at two clinical molecular diagnostic laboratories. This assay employs simultaneous DNA and RNA analysis of all coding exons to detect small variants (single-nucleotide variants, insertions, and deletions) in 148 genes, amplifications in 59 genes, and fusions and splice variants in 55 genes. During independent validations at two sites, 234 individual specimens were tested, including clinical formalin-fixed, paraffin-embedded (FFPE) tumor specimens, reference material, and cell lines. Samples were prepared using the Illumina TruSight Tumor 170 (TST170) kit, sequenced with Illumina sequencers, and the data were analyzed using the TST170 App. At both sites, TST170 had ≥98% success for ≥250× depth for ≥95% of covered positions. Variant calling was accurate and reproducible at allele frequencies ≥5%. Limit of detection studies determined that inputs of ≥50 ng of DNA (with ≥3.3 ng/μl) and ≥50 ng RNA (minimum of 7 copies/ng) were optimal for high analytical sensitivity. The TST170 assay results were highly concordant with prior results using different methods across all variant categories. Optimization of nucleic acid extraction and DNA shearing, and quality control following library preparation is recommended to maximize assay success rates. In summary, we describe the validation of comprehensive and simultaneous DNA and RNA-based NGS testing using TST170 at two clinical sites.
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Affiliation(s)
- Theresa A Boyle
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Daryoush Saeed-Vafa
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Ravi Kothapalli
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Evans Roberts
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Dahui Qin
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Anthony M Magliocco
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Amyn M Rojiani
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
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11
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Siemanowski J, Heydt C, Merkelbach-Bruse S. Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: Methods and quality assurance. Cancer Cytopathol 2021; 128:611-621. [PMID: 32885916 DOI: 10.1002/cncy.22293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Predictive molecular testing has become an important part of the diagnosis of any patient with lung cancer. Using reliable methods to ensure timely and accurate results is inevitable for guiding treatment decisions. In the past few years, parallel sequencing has been established for mutation testing, and its use is currently broadened for the detection of other genetic alterations, such as gene fusion and copy number variations. In addition, conventional methods such as immunohistochemistry and in situ hybridization are still being used, either for formalin-fixed, paraffin-embedded tissue or for cytological specimens. For the development and broad implementation of such complex technologies, interdisciplinary and regional networks are needed. The Network Genomic Medicine (NGM) has served as a model of centralized testing and decentralized treatment of patients and incorporates all German comprehensive cancer centers. Internal quality control, laboratory accreditation, and participation in external quality assessment is mandatory for the delivery of reliable results. Here, we provide a summary of current technologies used to identify patients who have lung cancer with gene fusions, briefly describe the structures of NGM and the national NGM (nNGM), and provide recommendations for quality assurance.
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Affiliation(s)
- Janna Siemanowski
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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12
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Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W. Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome. Arch Pathol Lab Med 2021; 144:1535-1546. [PMID: 32045275 DOI: 10.5858/arpa.2019-0162-oa] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. OBJECTIVE.— To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) trial. DESIGN.— Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. RESULTS.— High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. CONCLUSIONS.— This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.
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Affiliation(s)
- Kyung Park
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Hung Tran
- Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Kenneth W Eng
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Sinan Ramazanoglu
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Rebecca M Marrero Rolon
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Theresa Scognamiglio
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Alain Borczuk
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Qiulu Pan
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Andrea Sboner
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Mark A Rubin
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Hanna Rennert
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Helen Fernandes
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Wei Song
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
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13
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Schulte JD, Buerki RA, Lapointe S, Molinaro AM, Zhang Y, Villanueva-Meyer JE, Perry A, Phillips JJ, Tihan T, Bollen AW, Pekmezci M, Butowski N, Oberheim Bush NA, Taylor JW, Chang SM, Theodosopoulos P, Aghi MK, Hervey-Jumper SL, Berger MS, Solomon DA, Clarke JL. Clinical, radiologic, and genetic characteristics of histone H3 K27M-mutant diffuse midline gliomas in adults. Neurooncol Adv 2020; 2:vdaa142. [PMID: 33354667 PMCID: PMC7739048 DOI: 10.1093/noajnl/vdaa142] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background “Diffuse midline glioma (DMG), H3 K27M-mutant” is a new tumor entity established in the 2016 WHO classification of Tumors of the Central Nervous System that comprises a set of diffuse gliomas arising in midline structures and is molecularly defined by a K27M mutation in genes encoding the histone 3 variants H3.3 or H3.1. While this tumor entity is associated with poor prognosis in children, clinical experience in adults remains limited. Methods Patient demographics, radiologic and pathologic characteristics, treatment course, progression, and patient survival were collected for 60 adult patients with DMG, H3 K27M-mutant. A subset of tumors also underwent next-generation sequencing. Analysis of progression-free survival and overall survival was conducted using Kaplan–Meier modeling, and univariate and multivariate analysis. Results Median patient age was 32 years (range 18–71 years). Tumors were centered in the thalamus (n = 34), spinal cord (10), brainstem (5), cerebellum (4), or other midline sites (4), or were multifocal (3). Genomic profiling revealed p.K27M mutations exclusively in the H3F3A gene and an absence of mutations in HIST1H3B or HIST1H3C, which are present in approximately one-third of pediatric DMGs. Accompanying mutations in TP53, PPM1D, FGFR1, NF1, and ATRX were frequently found. The overall survival of this adult cohort was 27.6 months, longer than historical averages for both H3 K27M-mutant DMG in children and IDH-wildtype glioblastoma in adults. Conclusions Together, these findings indicate that H3 K27M-mutant DMG represents a heterogeneous disease with regard to outcomes, sites of origin, and molecular pathogenesis in adults versus children.
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Affiliation(s)
- Jessica D Schulte
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Robin A Buerki
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Sarah Lapointe
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
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14
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Comparison of Large, Medium, and Small Solid Tumor Gene Panels for Detection of Clinically Actionable Mutations in Cancer. Target Oncol 2020; 15:523-530. [PMID: 32770442 DOI: 10.1007/s11523-020-00743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Next-generation sequencing of gene panels has supplanted single-gene testing for cancer molecular diagnostics in many laboratories. Considerations for the optimal number of genes to assess in a panel depend on the purpose of the testing. OBJECTIVE To address the optimal size for the identification of clinically actionable variants in different-sized solid tumor sequencing panels. PATIENTS AND METHODS Sequencing results from 480 patients with a large, 315 gene, panel were compared against coverage of a medium, 161 gene, and small, 50 gene, panel. RESULTS The large panel detected a total of 2072 sequence variants in 480 patient specimens; 61 (12.7%) contained variants for which there is therapy approved by the US Food and Drug Administration, 89 (18.5%) had variants associated with an off-label therapy, and 312 (65.0%) contained variants eligible for a genomically matched clinical trial. The small panel covered only 737 of the 2072 variants (35.5%) and somewhat fewer therapy-related variants (on-label 88.5%, off-label 60.7%). The medium-size panel included 1354 of the 2072 (65.3%) variants reported by the large panel. All 318 patients with a clinically actionable variant would have been identified by the medium panel. CONCLUSIONS The results demonstrate that a carefully designed medium size gene panel is as effective as a large panel for the detection of clinically actionable variants and can be run by most molecular pathology laboratories.
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15
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Abstract
Genodermatoses are inherited disorders presenting with cutaneous manifestations with or without the involvement of other systems. The majority of these disorders, particularly in cases that present with a cutaneous patterning, may be explained in the context of genetic mosaicism. Despite the barriers to the genetic analysis of mosaic disorders, next-generation sequencing has led to a substantial progress in understanding their pathogenesis, which has significant implications for the clinical management and genetic counseling. Advances in paired and deep sequencing technologies in particular have made the study of mosaic disorders more feasible. In this review, we provide an overview of genetic mosaicism as well as mosaic cutaneous disorders and the techniques required to study them.
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Affiliation(s)
- Shayan Cheraghlou
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Young Lim
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Keith A Choate
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA; Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA.
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16
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Gao XH, Li J, Gong HF, Yu GY, Liu P, Hao LQ, Liu LJ, Bai CG, Zhang W. Comparison of Fresh Frozen Tissue With Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer. Front Oncol 2020; 10:310. [PMID: 32232001 PMCID: PMC7083147 DOI: 10.3389/fonc.2020.00310] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Next generation sequencing (NGS)-based multi-gene panel tests have been performed to predict the treatment response and prognosis in patients with colorectal cancer (CRC). Whether the multi-gene mutation results of formalin-fixed paraffin-embedded (FFPE) tissues are identical to those of fresh frozen tissues remains unknown. Methods: A 22-gene panel with 103 hotspots was used to detect mutations in paired fresh frozen tissue and FFPE tissue from 118 patients with CRC. Results: In our study, 117 patients (99.2%) had one or more variants, with 226 variants in FFPE tissue and 221 in fresh frozen tissue. Of the 129 variants identified in this study, 96 variants were present in both FFPE and fresh frozen tissues; 27 variants were found in FFPE tissues only; 6 variants were found only in fresh frozen tissues. The mutation results demonstrated >94.0% concordance in all variants, with Kappa coefficient >0.500 in 64.3% (83/129) of variants. At the gene level, concordance ranged from 73.8 to 100.0%, with Kappa coefficient >0.500 in 81.3% (13/16) of genes. Conclusions: The results of mutation analysis performed with a multi-gene panel and FFPE and fresh frozen tissue were highly concordant in patients with CRC, at both the variant and gene levels. There were, however, some important differences in mutation results between the two tissue types. Therefore, fresh frozen tissue should not routinely be replaced with FFPE tissue for mutation analysis with a multi-gene panel. Rather, FFPE tissue is a reasonable alternative for fresh frozen tissue when the latter is unavailable.
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Affiliation(s)
- Xian Hua Gao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Juan Li
- Department of Nephrology, Changhai Hospital, Shanghai, China
| | - Hai Feng Gong
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Guan Yu Yu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Peng Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Li Qiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Lian Jie Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Chen Guang Bai
- Department of Pathology, Changhai Hospital, Shanghai, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
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17
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Cheraghlou S, Atzmony L, Roy SF, McNiff JM, Choate KA. Mutations in KRT10 in epidermolytic acanthoma. J Cutan Pathol 2020; 47:524-529. [PMID: 32045015 DOI: 10.1111/cup.13664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/08/2020] [Accepted: 01/24/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Epidermolytic acanthoma (EA) is a rare acquired lesion demonstrating a characteristic histopathological pattern of epidermal degeneration referred to as epidermolytic hyperkeratosis (EHK). On histopathological analysis, EA appears nearly identical to inherited EHK-associated dermatoses such as epidermolytic ichthyosis and ichthyosis bullosa of Siemens. While it has been speculated that EA is caused by mutations in KRT10, KRT1, or KRT2 found in these inherited dermatoses, none have yet been identified. Herein, we aim to identify the contributions of keratin mutations to EA. METHODS Using genomic DNA extracted from paraffin-embedded samples from departmental archives, we evaluated a discovery cohort using whole-exome sequencing (WES) and assessed remaining samples using Sanger sequencing screening and restriction fragment length polymorphism (RFLP) analysis. RESULTS DNA from 16/20 cases in our sample was of sufficient quality for polymerase chain reaction amplification. WES of genomic DNA from lesional tissue revealed KRT10 c.466C > T, p.Arg156Cys mutations in 2/3 samples submitted for examination. RFLP analysis of these samples as well as eight additional samples confirmed the mutations identified via WES and identified four additional cases with Arg156 mutations. In sum, 6/11 screened cases showed hotspot mutation in KRT10. CONCLUSIONS Hotspot mutations in the Arg156 position of KRT10, known to cause epidermolytic ichthyosis, also underlie EA.
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Affiliation(s)
- Shayan Cheraghlou
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Lihi Atzmony
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Simon F Roy
- Department of Pathology, University of Montréal, Montréal, Quebec, Canada
| | - Jennifer M McNiff
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Keith A Choate
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut.,Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Department of Pathology, Yale School of Medicine, New Haven, Connecticut
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18
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Udar N, Iyer A, Porter M, Haigis R, Smith S, Dhillon S, Meier K, Ward D, Lu J, Wenz P, Buchner L, Dunn T, Wise A, Mueller A, Gutekunst K. Development and Analytical Validation of a DNA Dual-Strand Approach for the US Food and Drug Administration-Approved Next-Generation Sequencing-Based Praxis Extended RAS Panel for Metastatic Colorectal Cancer Samples. J Mol Diagn 2019; 22:159-178. [PMID: 31837434 DOI: 10.1016/j.jmoldx.2019.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 09/03/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022] Open
Abstract
A next-generation sequencing method was developed that can distinguish single-stranded modifications from low-frequency somatic mutations present on both strands of DNA in formalin-fixed paraffin-embedded colorectal cancer samples. We applied this method for analytical validation of the Praxis Extended RAS Panel, a US Food and Drug Administration-approved companion diagnostic for panitumumab, on the Illumina MiSeqDx platform. With the use of the TruSeq amplicon workflow, both strands of DNA from the starting material were interrogated independently. Mutations were reported only if found on both strands; artifacts usually present on only one strand would not be reported. A total of 56 mutations were targeted within the KRAS and NRAS genes. A minimum read depth of 1800× per amplicon is required per sample but averaged >30,000× at maximum multiplexing levels. Analytical validation studies were performed to determine the simultaneous detection of mutations on both strands, reproducibility, assay detection level, precision of the assay across various factors, and the impact of interfering substances. In conclusion, this assay can clearly distinguish single-stranded artifacts from low-frequency mutations. Furthermore, the assay is accurate, precise, and reproducible, can achieve consistent detection of a mutation at 5% mutation frequency, exhibits minimal impact from tested interfering substances, and can simultaneously detect 56 mutations in a single run using 10 samples plus controls.
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Affiliation(s)
- Nitin Udar
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Anita Iyer
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California.
| | - Margaret Porter
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Robert Haigis
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Shannon Smith
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Shivani Dhillon
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
| | - Kristen Meier
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Diane Ward
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Jing Lu
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Paul Wenz
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Leonard Buchner
- Department of Biostatistics, Illumina, Inc., San Diego, California
| | - Tamsen Dunn
- Department of Bioinformatics, Illumina, Inc., San Diego, California
| | - Aaron Wise
- Department of Bioinformatics, Illumina, Inc., San Diego, California
| | - Amy Mueller
- Department of Medical Affairs, Illumina, Inc., San Diego, California
| | - Karen Gutekunst
- Department of Clinical Genomics Assay Development and Oncology, Illumina, Inc., San Diego, California
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19
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Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma. Sci Rep 2019; 9:13995. [PMID: 31570735 PMCID: PMC6769015 DOI: 10.1038/s41598-019-50171-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
The goal of this work was to investigate the molecular profiles and metastasis markers in Chinese patients with gastric carcinoma (GC). In total, we performed whole exome sequencing (WES) on 74 GC patients with tumor and adjacent normal formalin-fixed, paraffin-embedded (FFPE) tissue samples. The mutation spectrum of these samples showed a high concordance with TCGA and other studies on GC. PTPRT is significantly associated with metastasis of GC, suggesting its predictive role in metastasis of GC. Patients carrying BRCA2 mutations tend not to metastasize, which may be related to their sensitivity to chemotherapy. Mutations in MACF1, CDC27, HMCN1, CDH1 and PDZD2 were moderately enriched in peritoneal metastasis (PM) samples. Furthermore, we found two genomic regions (1p36.21 and Xq26.3) were associated with PM of GC, and patients with amplification of 1p36.21 and Xq26.3 have a worse prognosis (P = 0.002, 0.01, respectively). Our analysis provides GC patients with potential markers for single and combination therapies.
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20
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Dehghani M, Rosenblatt KP, Li L, Rakhade M, Amato RJ. Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues. Front Mol Biosci 2019; 6:82. [PMID: 31681791 PMCID: PMC6798036 DOI: 10.3389/fmolb.2019.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/23/2019] [Indexed: 12/18/2022] Open
Abstract
Identification of somatic molecular alterations in primary and metastatic solid tumor specimens can provide critical information regarding tumor biology and its heterogeneity, and enables the detection of molecular markers for clinical personalized treatment assignment. However, the optimal methods and target genes for clinical use are still being in development. Toward this end, we validated a targeted amplification-based NGS panel (Oncomine comprehensive assay v1) on a personal genome machine sequencer for molecular profiling of solid tumors. This panel covers 143 genes, and requires low amounts of DNA (20 ng) and RNA (10 ng). We used 27 FFPE tissue specimens, 10 cell lines, and 24 commercial reference materials to evaluate the performance characteristics of this assay. We also evaluated the performance of the assay on 26 OCT-embedded fresh frozen specimens (OEFF). The assay was found to be highly specific (>99%) and sensitive (>99%), with low false-positive and false-negative rates for single-nucleotide variants, indels, copy number alterations, and gene fusions. Our results indicate that this is a reliable method to determine molecular alterations in both fixed and fresh frozen solid tumor samples, including core needle biopsies.
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Affiliation(s)
- Mehdi Dehghani
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Kevin P Rosenblatt
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States.,NX Prenatal, Inc., Bellaire, TX, United States.,Consultative Genomics, PLLC, Bellaire, TX, United States
| | - Lei Li
- Principle Health Systems, Houston, TX, United States
| | - Mrudula Rakhade
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Robert J Amato
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
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21
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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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22
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Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D. CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system. Nucleic Acids Res 2019; 47:e1. [PMID: 30215766 PMCID: PMC6326800 DOI: 10.1093/nar/gky820] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022] Open
Abstract
Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.
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Affiliation(s)
- Jeewon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Byungjin Hwang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Joon Ho Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Junhyuk Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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23
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Zar G, Smith JG, Smith ML, Andersson B, Nilsson J. Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation. PLoS One 2019; 14:e0217747. [PMID: 31166960 PMCID: PMC6550412 DOI: 10.1371/journal.pone.0217747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) of heart transplant recipient- and donor-derived cardiac biopsies may facilitate organ matching, graft failure prediction, and immunotolerance research. The objective of this study was to determine the feasibility of WGS based on formalin-fixed paraffin-embedded endomyocardial biopsies. METHODS AND RESULTS The study included serial donor- and recipient samples from patients who had undergone heart transplantation at Skane University Hospital, Lund, Sweden, between 1988 and 2009. DNA extraction and WGS were conducted. Additional WGS sequencing quality metrics and coverage were obtained with the Genome Analysis Toolkit (GATK). 455 endomyocardial samples from 37 heart transplant recipients were acquired from routine rejection monitoring and stored as formalin-fixed paraffin-embedded samples. They were analyzed after 3-26 years of storage. DNA was extracted from 114 samples and WGS was run on 85 samples. DNA extraction yielded 313 ng (IQR 96-601) for all samples. A coverage of 11.3x (IQR 9.0-15.9) was recorded for all WGS samples. Three samples stored for > 25 years yielded a coverage of > 25x. Data were generated for 1.7 billion reads per sample (IQR 1.4-2.7). A Transition/Transversion (TiTv) ratio of 2.09 ± 0.05 was calculated for all WGS samples. No associations were found among storage time, DNA yield, or sequencing quality metrics. CONCLUSIONS The present study demonstrated the feasibility of whole-genome sequencing based on endomyocardial biopsies. This process could enable large-scale retrospective genomic studies using stored histopathological samples.
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Affiliation(s)
- Gustav Zar
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - J. Gustav Smith
- Department of Clinical Sciences, Cardiology, Lund University and Skane University Hospital, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Maya Landenhed Smith
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Bodil Andersson
- Department of Clinical Sciences Lund, Surgery, Lund University and Skane University Hospital, Lund, Sweden
| | - Johan Nilsson
- Department of Clinical Sciences Lund, Cardiothoracic Surgery, Lund University and Skane University Hospital, Lund, Sweden
- * E-mail:
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24
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Haynes BC, Blidner RA, Cardwell RD, Zeigler R, Gokul S, Thibert JR, Chen L, Fujimoto J, Papadimitrakopoulou VA, Wistuba II, Latham GJ. An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer. Transl Oncol 2019; 12:836-845. [PMID: 30981944 PMCID: PMC6463765 DOI: 10.1016/j.tranon.2019.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non-small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97% agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.
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Affiliation(s)
| | | | | | | | | | | | | | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vassiliki A Papadimitrakopoulou
- Department of Thoracic/Head and Neck Medical Oncology, Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Parker JDK, Yap SQ, Starks E, Slind J, Swanson L, Docking TR, Fuller M, Zhou C, Walker B, Filipenko D, Xiong W, Karimuddin AA, Phang PT, Raval M, Brown CJ, Karsan A. Fixation Effects on Variant Calling in a Clinical Resequencing Panel. J Mol Diagn 2019; 21:705-717. [PMID: 31055024 DOI: 10.1016/j.jmoldx.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 03/15/2019] [Accepted: 03/20/2019] [Indexed: 11/16/2022] Open
Abstract
Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.
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Affiliation(s)
- Jeremy D K Parker
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Shyong Quin Yap
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Elizabeth Starks
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Jillian Slind
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Lucas Swanson
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Chen Zhou
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair Walker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Douglas Filipenko
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Wei Xiong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Ahmer A Karimuddin
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - P Terry Phang
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Manoj Raval
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Carl J Brown
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada; St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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26
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Blidner RA, Haynes BC, Hyter S, Schmitt S, Pessetto ZY, Godwin AK, Su D, Hurban P, van Kempen LC, Aguirre ML, Gokul S, Cardwell RD, Latham GJ. Design, Optimization, and Multisite Evaluation of a Targeted Next-Generation Sequencing Assay System for Chimeric RNAs from Gene Fusions and Exon-Skipping Events in Non-Small Cell Lung Cancer. J Mol Diagn 2019; 21:352-365. [PMID: 30529127 PMCID: PMC7057224 DOI: 10.1016/j.jmoldx.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/11/2018] [Accepted: 10/26/2018] [Indexed: 12/11/2022] Open
Abstract
Lung cancer accounts for approximately 14% of all newly diagnosed cancers and is the leading cause of cancer-related deaths. Chimeric RNA resulting from gene fusions (RNA fusions) and other RNA splicing errors are driver events and clinically addressable targets for non-small cell lung cancer (NSCLC). The reliable assessment of these RNA markers by next-generation sequencing requires integrated reagents, protocols, and interpretive software that can harmonize procedures and ensure consistent results across laboratories. We describe the development and verification of a system for targeted RNA sequencing for the analysis of challenging, low-input solid tumor biopsies that includes reagents for nucleic acid quantification and library preparation, run controls, and companion bioinformatics software. Assay development reconciled sequence discrepancies in public databases, created predictive formalin-fixed, paraffin-embedded RNA qualification metrics, and eliminated read misidentification attributable to index hopping events on the next-generation sequencing flow cell. The optimized and standardized system was analytically verified internally and in a multiphase study conducted at five independent laboratories. The results show accurate, reproducible, and sensitive detection of RNA fusions, alternative splicing events, and other expression markers of NSCLC. This comprehensive approach, combining sample quantification, quality control, library preparation, and interpretive bioinformatics software, may accelerate the routine implementation of targeted RNA sequencing of formalin-fixed, paraffin-embedded samples relevant to NSCLC.
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Affiliation(s)
| | | | - Stephen Hyter
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Sarah Schmitt
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Ziyan Y Pessetto
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas; University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | - Dan Su
- Q Squared Solutions Expression Analysis LLC, Morrisville, North Carolina
| | - Patrick Hurban
- Q Squared Solutions Expression Analysis LLC, Morrisville, North Carolina
| | - Léon C van Kempen
- The Molecular Pathology Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maria L Aguirre
- The Molecular Pathology Centre, Jewish General Hospital, Montreal, Quebec, Canada
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27
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Kaur P, Porras TB, Ring A, Carpten JD, Lang JE. Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer. Sci Rep 2019; 9:1482. [PMID: 30728399 PMCID: PMC6365517 DOI: 10.1038/s41598-018-37574-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
Whole exome sequencing (WES), targeted gene panel sequencing and single nucleotide polymorphism (SNP) arrays are increasingly used for the identification of actionable alterations that are critical to cancer care. Here, we compared The Cancer Genome Atlas (TCGA) and the Genomics Evidence Neoplasia Information Exchange (GENIE) breast cancer genomic datasets (array and next generation sequencing (NGS) data) in detecting genomic alterations in clinically relevant genes. We performed an in silico analysis to determine the concordance in the frequencies of actionable mutations and copy number alterations/aberrations (CNAs) in the two most common breast cancer histologies, invasive lobular and invasive ductal carcinoma. We found that targeted sequencing identified a larger number of mutational hotspots and clinically significant amplifications that would have been missed by WES and SNP arrays in many actionable genes such as PIK3CA, EGFR, AKT3, FGFR1, ERBB2, ERBB3 and ESR1. The striking differences between the number of mutational hotspots and CNAs generated from these platforms highlight a number of factors that should be considered in the interpretation of array and NGS-based genomic data for precision medicine. Targeted panel sequencing was preferable to WES to define the full spectrum of somatic mutations present in a tumor.
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Affiliation(s)
- Pushpinder Kaur
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States
- University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States
| | - Tania B Porras
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States
- University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States
| | - Alexander Ring
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States
- University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States
| | - John D Carpten
- University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States
- Department of Translational Genomics, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States
| | - Julie E Lang
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States.
- University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA, 90033, United States.
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28
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Clinical significance of multiple gene detection with a 22-gene panel in formalin-fixed paraffin-embedded specimens of 207 colorectal cancer patients. Int J Clin Oncol 2019; 24:141-152. [PMID: 30612269 DOI: 10.1007/s10147-018-1377-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 12/02/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Simultaneous detection of multiple molecular biomarkers is helpful in the prediction of treatment response and prognosis for colorectal cancer (CRC) patients. METHODS A 22-gene panel consisting of 103 hotspot regions was utilized in the formalin-fixed paraffin-embedded (FFPE) tissue samples of 207 CRC patients, using the next-generation sequencing (NGS)-based multiplex PCR technique. Those 22 genes included AKT1, ALK, BRAF, CTNNB1, DDR2, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, KRAS, MAP2K1, MET, NOTCH1, NRAS, PIK3CA, PTEN, SMAD4, STK11, and TP53. RESULTS Of the 207 patients, 193 had one or more variants, with 170, 20, and 3 having one, two, and three mutated genes, respectively. Of the total 414 variants identified in this study, 384, 25, and 5 were single-nucleotide variants, deletion, and insertion. The top four frequently mutated genes were TP53, KRAS, PIK3CA, and FBXW7. There was high consistency between the results of NGS-PCR technique and routine ARMS-PCR in KRAS and BRAF mutation detection. Univariate and multivariate analyses demonstrated that advanced TNM stage, elevated serum CEA, total variants number ≥ 2, AKT1 and PTEN mutation were independent predictors of shorter DFS; poor differentiation, advanced TNM stage, total variants number ≥ 2, BRAF, CTNNB1 and NRAS mutation were independent predictors of shorter OS. CONCLUSIONS It is feasible to detect multiple gene mutations with a 22-gene panel in FFPE CRC specimens. TNM stage and total variants number ≥ 2 were independent predictors of DFS and OS. Detection of multiple gene mutations may provide additional prognostic information to TNM stage in CRC patients.
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Martínez-Pérez C, Turnbull AK, Dixon JM. The evolving role of receptors as predictive biomarkers for metastatic breast cancer. Expert Rev Anticancer Ther 2018; 19:121-138. [PMID: 30501540 DOI: 10.1080/14737140.2019.1552138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION In breast cancer, estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2) are essential biomarkers to predict response to endocrine and anti-HER2 therapies, respectively. In metastatic breast cancer, the use of these receptors and targeted therapies present additional challenges: temporal heterogeneity, together with limited sampling methodologies, hinders receptor status assessment, and the constant evolution of the disease invariably leads to resistance to treatment. Areas covered: This review summarizes the genomic abnormalities in ER and HER2, such as mutations, amplifications, translocations, and alternative splicing, emerging as novel biomarkers that provide an insight into underlying mechanisms of resistance and hold potential predictive value to inform treatment selection. We also describe how liquid biopsies for sampling of circulating markers and ultrasensitive detection technologies have emerged which complement ongoing efforts for biomarker discovery and analysis. Expert commentary: While evidence suggests that genomic aberrations in ER and HER2 could contribute to meeting the pressing need for better predictive biomarkers, efforts need to be made to standardize assessment methods and better understand the resistance mechanisms these markers denote. Taking advantage of emerging technologies, research in upcoming years should include prospective trials incorporating these predictors into the study design to validate their potential clinical value.
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Affiliation(s)
- Carlos Martínez-Pérez
- a Breast Cancer Now Edinburgh Team, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK
| | - Arran K Turnbull
- a Breast Cancer Now Edinburgh Team, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK
| | - J Michael Dixon
- a Breast Cancer Now Edinburgh Team, Institute of Genetics and Molecular Medicine , University of Edinburgh, Western General Hospital , Edinburgh , UK.,b Edinburgh Breast Unit , Western General Hospital , Edinburgh , UK
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Dey P, Ghosh RK. Fine-needle aspiration cytology of non-small cell lung carcinoma: A paradigm shift. Diagn Cytopathol 2018; 47:351-358. [DOI: 10.1002/dc.24089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Pranab Dey
- Department of Cytology and Gynaec Pathology; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - Ratan Kumar Ghosh
- Department of Nephrology; Post Graduate Institute of Medical Education and Research; Chandigarh India
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Williams HL, Walsh K, Diamond A, Oniscu A, Deans ZC. Validation of the Oncomine ™ focus panel for next-generation sequencing of clinical tumour samples. Virchows Arch 2018; 473:489-503. [PMID: 30105577 PMCID: PMC6182325 DOI: 10.1007/s00428-018-2411-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/25/2018] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM™) and validate the Oncomine™ Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue. Using a mixture of routine FFPE and reference material across a variety of tissue and specimen types, we sequenced 86 and 31 samples on the Oncomine™ Focus DNA and RNA Fusion assays, respectively. This validation considered a number of parameters including the clinical robustness of the bioinformatics pipeline for variant detection and interpretation. The Oncomine™ Focus DNA assay had a sample and variant-based sensitivity of 99.1 and 97.1%, respectively, and an assay specificity of 100%. The Oncomine™ Focus Fusion panel had a good sensitivity and specificity based upon the samples assessed, however requires further validation to confirm findings due to limited sample numbers. We observed a good sequencing performance based upon amplicon, gene (hotspot variants within gene) and sample specific analysis with 92% of clinical samples obtaining an average amplicon coverage above 500X. Detection of some indels was challenging for the routine IonReporter™ workflow; however, the addition of NextGENe® software improved indel identification demonstrating the importance of both bench and bioinformatic validation. With an increasing number of clinically actionable targets requiring a variety of methodologies, NGS provides a cost-effective and time-saving methodology to assess multiple targets across different modalities. We suggest the use of multiple analysis software to ensure identification of clinically applicable variants.
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Affiliation(s)
- Hannah L Williams
- UKNEQAS for Molecular Genetics, Royal Infirmary of Edinburgh, Edinburgh, UK.
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK.
- University of St Andrews, School of Medicine, North Haugh, St Andrews, Fife, KY16 9TF, UK.
| | - Kathy Walsh
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Austin Diamond
- NHS Lothian, Molecular Genetics, Western General Hospital, Edinburgh, UK
| | - Anca Oniscu
- NHS Lothian, Department of Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Zandra C Deans
- UKNEQAS for Molecular Genetics, Royal Infirmary of Edinburgh, Edinburgh, UK
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Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp Mol Pathol 2018; 104:161-169. [PMID: 29608913 PMCID: PMC5993858 DOI: 10.1016/j.yexmp.2018.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Affiliation(s)
- Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
| | - Angela Santonja
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Marta Grzelak
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Harry Clifford
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Michelle Pugh
- Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mae A Goldgraben
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Helen A Bardwell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eun Yoon Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea
| | - Elena Provenzano
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Emilio Alba
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
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Abstract
BRCA1 and BRCA2 genes are implicated in 20-25% of hereditary breast and ovarian cancers. New age sequencing platforms have revolutionized massively parallel sequencing in clinical practice by providing cost effective, rapid, and sensitive sequencing. This study critically evaluates the false positives in multiplex panels and suggests the need for careful analysis. We employed multiplex PCR based BRCA1 and BRCA2 community Panel with ion torrent PGM machine for evaluation of these mutations. Out of all 41samples analyzed for BRCA1 and BRCA2 five were found with 950_951 insA(Asn319fs) at Chr13:32906565 position and one sample with 1032_1033 insA(Asn346fs) at Chr13:32906647, both being frame-shift mutations in BRCA2 gene. 950_951 insA(Asn319fs) mutation is reported as pathogenic allele in NCBI dbSNP. On examination of IGV for all these samples, it was seen that both mutations had 'A' nucleotide insertion at 950, and 1032 position in exon 10 of BRCA2 gene. Sanger Sequencing did not confirm these insertions. Next-generation sequencing shows great promise by allowing rapid mutational analysis of multiple genes in human cancer but our results indicate the need for careful sequence analysis to avoid false positive results.
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Stasik S, Schuster C, Ortlepp C, Platzbecker U, Bornhäuser M, Schetelig J, Ehninger G, Folprecht G, Thiede C. An optimized targeted Next-Generation Sequencing approach for sensitive detection of single nucleotide variants. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:6-12. [PMID: 29349042 PMCID: PMC5766748 DOI: 10.1016/j.bdq.2017.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/27/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023]
Abstract
NGS based detection of low-level SNVs is feasible with sensitivities up to 10−4. PCR-induced bias could be significantly reduced by the choice of adequate enzymes. The prevalent transition vs. transversion bias affects site-specific detection limits. Results from clinical data validated the feasibility of NGS-based MRD detection. Results help to select suitable biomarkers for MRD quantification.
Monitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torrent PGM system. As a model case we used the c.1849G > T (p.Val617Phe) mutation of the JAK2-gene. Several reaction parameters (e.g. choice of DNA-polymerase) were evaluated and a comprehensive analysis of substitution errors was performed. Using optimized conditions, we reliably detected JAK2 c.1849G > T VAFs in the range of 0.01–0.0015% which, in combination with results obtained from clinical data, validated the feasibility of NGS-based MRD detection. Particularly, PCR-induced transitions (mainly G > A and C > T) were the major source of error, which could be significantly reduced by the application of proofreading enzymes. The integration of NGS results for several common point mutations in various oncogenes (i.e. IDH1 and 2, c-KIT, DNMT3A, NRAS, KRAS, BRAF) revealed that the prevalent transition vs. transversion bias (3.57:1) has an impact on site-specific detection limits of low-level mutations. These results may help to select suitable markers for MRD detection and to identify individual cut-offs for detection and quantification.
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Affiliation(s)
- S. Stasik
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Partner Site Dresden, Germany
| | | | | | - U. Platzbecker
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - M. Bornhäuser
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Partner Site Dresden, Germany
| | - J. Schetelig
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - G. Ehninger
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - G. Folprecht
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - C. Thiede
- Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Dresden, Germany
- Corresponding author: Universitätsklinikum Carl Gustav Carus, Medizinische Klinik und Poliklinik I, Fetscherstraße 74, 01307 Dresden, Germany.
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35
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Agrawal L, Engel KB, Greytak SR, Moore HM. Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy. Semin Cancer Biol 2017; 52:26-38. [PMID: 29258857 DOI: 10.1016/j.semcancer.2017.12.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/07/2017] [Accepted: 12/13/2017] [Indexed: 12/20/2022]
Abstract
Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.
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Affiliation(s)
- Lokesh Agrawal
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch (BBRB), Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Drive, Bethesda, Maryland, USA.
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Cheng Y, Wang S, Han L, Liu P, Li H, Ren X, Yu J, Hao X. Concurrent somatic mutations in driver genes were significantly correlated with lymph node metastasis and pathological types in solid tumors. Oncotarget 2017; 8:68746-68757. [PMID: 28978153 PMCID: PMC5620293 DOI: 10.18632/oncotarget.19975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/18/2017] [Indexed: 01/10/2023] Open
Abstract
To demonstrate the mutational profiles in solid tumors, we profiled 165 solid tumor samples, including 9 cancer types and 4 sample types, by using amplicon-based next-generation sequencing panel covering 48 highly mutated tumorigenesis-related genes that were deep sequenced at an average coverage of 2000×. Both tumor and sample types had significant effect on tumor genetic mutational profiles. Concurrent driver mutations were frequently detected in solid tumor, concentrating on both modes of action driver genes (activating or loss of function). Furthermore, in non-small cell lung cancer (NSCLC), concurrent driver mutations were also significantly correlated with the lymph node metastasis status and pathological types. Higher frequency of lymph node metastasis was observed in patients with NSCLC with concurrent mutations on at least two driver genes. In addition, patients with lung adenocarcinoma were more likely to harbor concurrent driver mutations than patients with lung squamous and large cell carcinoma. Multiple mutations in the epidermal growth factor receptor gene were more frequently detected in patients with refractory NSCLC compared to untreated naive ones. Therefore, concurrent multiple driver mutations, rather than a single genetic mutation, should be investigated extensively to probe novel genetic biomarkers with clinical benefits.
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Affiliation(s)
- Yanan Cheng
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Shaojing Wang
- Tianjin Novcare Biotech., Ltd., Tianjin 300300, China
| | - Lei Han
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Hui Li
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiubao Ren
- Biotherapy Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xishan Hao
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Biotherapy Center, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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Wing MR, Reeser JW, Smith AM, Reeder M, Martin D, Jewell BM, Datta J, Miya J, Monk JP, Mortazavi A, Otterson GA, Goldberg RM, VanDeusen JB, Cole S, Dittmar K, Jaiswal S, Kinzie M, Waikhom S, Freud AG, Zhou XP, Chen W, Bhatt D, Roychowdhury S. Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer. Oncotarget 2017; 8:75822-75833. [PMID: 29100271 PMCID: PMC5652665 DOI: 10.18632/oncotarget.20616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
Multiplex somatic testing has emerged as a strategy to test patients with advanced cancer. We demonstrate our analytic validation approach for a gene hotspot panel and real-time prospective clinical application for any cancer type. The TruSight Tumor 26 assay amplifies 85 somatic hotspot regions across 26 genes. Using cell line and tumor mixes, we observed that 100% of the 14,715 targeted bases had at least 1000x raw coverage. We determined the sensitivity (100%, 95% CI: 96-100%), positive predictive value (100%, 95% CI: 96-100%), reproducibility (100% concordance), and limit of detection (3% variant allele frequency at 1000x read depth) of this assay to detect single nucleotide variants and small insertions and deletions. Next, we applied the assay prospectively in a clinical tumor sequencing study to evaluate 174 patients with metastatic or advanced cancer, including frozen tumors, formalin-fixed tumors, and enriched peripheral blood mononuclear cells in hematologic cancers. We reported one or more somatic mutations in 89 (53%) of the sequenced tumors (167 passing quality filters). Forty-three of these patients (26%) had mutations that would enable eligibility for targeted therapies. This study demonstrates the validity and feasibility of applying TruSight Tumor 26 for pan-cancer testing using multiple specimen types.
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Affiliation(s)
- Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Matthew Reeder
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Dorrelyn Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Benjamin M Jewell
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Datta
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - J Paul Monk
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Amir Mortazavi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gregory A Otterson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Richard M Goldberg
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | | | - Kristin Dittmar
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Sunny Jaiswal
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Matthew Kinzie
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Suraj Waikhom
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Aharon G Freud
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Xiao-Ping Zhou
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA.,University Pathologists, LLC, Department of Pathology, Roger Williams Medical Center, Providence, RI, USA
| | - Wei Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Darshna Bhatt
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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Pillai S, Gopalan V, Lam AKY. Review of sequencing platforms and their applications in phaeochromocytoma and paragangliomas. Crit Rev Oncol Hematol 2017; 116:58-67. [DOI: 10.1016/j.critrevonc.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 12/16/2022] Open
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39
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Sho S, Court CM, Winograd P, Lee S, Hou S, Graeber TG, Tseng HR, Tomlinson JS. Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications. BMC Cancer 2017; 17:457. [PMID: 28666423 PMCID: PMC5493892 DOI: 10.1186/s12885-017-3447-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background Sequencing analysis of circulating tumor cells (CTCs) enables “liquid biopsy” to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies. Methods Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score. Results Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA. Conclusion The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5–10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3447-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shonan Sho
- Department of Surgery, University of California Los Angeles, 10833 Le Conte Ave, California, Los Angeles, 90095, USA. .,Department of Surgery, Greater Los Angeles Veteran's Affairs Administration, 11301 Wilshire Blvd, California, Los Angeles, 90073, USA.
| | - Colin M Court
- Department of Surgery, University of California Los Angeles, 10833 Le Conte Ave, California, Los Angeles, 90095, USA.,Department of Surgery, Greater Los Angeles Veteran's Affairs Administration, 11301 Wilshire Blvd, California, Los Angeles, 90073, USA
| | - Paul Winograd
- Department of Surgery, University of California Los Angeles, 10833 Le Conte Ave, California, Los Angeles, 90095, USA.,Department of Surgery, Greater Los Angeles Veteran's Affairs Administration, 11301 Wilshire Blvd, California, Los Angeles, 90073, USA
| | - Sangjun Lee
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, 650 Charles E Young Dr S, California, Los Angeles, 90095, USA
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, 650 Charles E Young Dr S, California, Los Angeles, 90095, USA
| | - Thomas G Graeber
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, 650 Charles E Young Dr S, California, Los Angeles, 90095, USA
| | - Hsian-Rong Tseng
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, 650 Charles E Young Dr S, California, Los Angeles, 90095, USA
| | - James S Tomlinson
- Department of Surgery, University of California Los Angeles, 10833 Le Conte Ave, California, Los Angeles, 90095, USA.,Department of Surgery, Greater Los Angeles Veteran's Affairs Administration, 11301 Wilshire Blvd, California, Los Angeles, 90073, USA.,UCLA Center for Pancreatic Diseases, University of California Los Angeles, 10833 Le Conte Ave., 72-215 CHS, California, Los Angeles, 90095, USA
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40
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Mendez P, Fang LT, Jablons DM, Kim IJ. Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues. Sci Rep 2017; 7:4055. [PMID: 28642587 PMCID: PMC5481435 DOI: 10.1038/s41598-017-04419-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
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Affiliation(s)
- Pedro Mendez
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Li Tai Fang
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David M Jablons
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
| | - Il-Jin Kim
- Thoracic Oncology Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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41
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Berry AB. Analytic inquiry: Validation and practical considerations. Cancer Cytopathol 2017; 125:465-469. [DOI: 10.1002/cncy.21871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Anna B. Berry
- CellNetix Pathology and Laboratories LLC; Seattle Washington
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42
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Park J, Yoo HM, Jang W, Shin S, Kim M, Kim Y, Lee SW, Kim JG. Distribution of somatic mutations of cancer-related genes according to microsatellite instability status in Korean gastric cancer. Medicine (Baltimore) 2017; 96:e7224. [PMID: 28640116 PMCID: PMC5484224 DOI: 10.1097/md.0000000000007224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In studies of the molecular basis of gastric cancer (GC), microsatellite instability (MSI) is one of the key factors. Somatic mutations found in GC are expected to contribute to MSI-high (H) tumorigenesis. We estimated somatic mutation distribution according to MSI status in 52 matched pair GC samples using the Ion Torrent Ion S5 XL with the AmpliSeq Cancer Hotspot panel.Seventy-five (9.8%) somatic variants consisting of 34 hotspot mutations and 41 other likely pathogenic variants were identified in 34 GC samples. The TP53 mutations was most common (35%, 26/75), followed by EGFR (8%, 6/75), HNF1A (8%, 6/75), PIK3CA (8%, 6/75), and ERBB2 (5%, 4/75). To determine MSI status, 52 matched pair samples were estimated using 15 MSI markers. Thirty-nine MS stable (S), 5 MSI-low (L), and 8 MSI-H were classified. GCs with MSI-H tended to have more variants significantly compared with GCs with MS stable (MSS) and MSI-L (standardized J-T statistic = 3.161 for number of variants; P = .002). The mean number of all variants and hotspot mutations per tumor samples only in GCs with MSI-H were 3.9 (range, 1-6) and 1.1 (range, 0-3), respectively. Whereas, the mean number of all variants and hotspot mutations per tumor samples only in GCs with MSS/MSI-L were 1 (0-5)/0.8 (0-1) and 0.5 (0-3)/0.8 (0-1), respectively.In conclusion, GC with MSI-H harbored more mutations in genes that act as a tumor suppressor or oncogene compared to GC with MSS/MSI-L. This finding suggests that the accumulation of MSIs contributes to the genetic diversity and complexities of GC. In addition, targeted NGS approach allows for detection of common and also rare clinically actionable mutations and profiles of comutations in multiple patients simultaneously. Because GC shows distinctive patterns related to ethnics, further studies pertaining to different racial/ethnic groups or cancer types may reinforce our investigations.
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Affiliation(s)
| | - Han Mo Yoo
- Division of Gastrointestinal Surgery, Department of Surgery
| | | | | | | | | | - Seung-Woo Lee
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Goo Kim
- Division of Gastrointestinal Surgery, Department of Surgery
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43
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Toledo RA, Burnichon N, Cascon A, Benn DE, Bayley JP, Welander J, Tops CM, Firth H, Dwight T, Ercolino T, Mannelli M, Opocher G, Clifton-Bligh R, Gimm O, Maher ER, Robledo M, Gimenez-Roqueplo AP, Dahia PLM. Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas. Nat Rev Endocrinol 2017; 13:233-247. [PMID: 27857127 DOI: 10.1038/nrendo.2016.185] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phaeochromocytomas and paragangliomas (PPGLs) are neural-crest-derived tumours of the sympathetic or parasympathetic nervous system that are often inherited and are genetically heterogeneous. Genetic testing is recommended for patients with these tumours and for family members of patients with hereditary forms of PPGLs. Due to the large number of susceptibility genes implicated in the diagnosis of inherited PPGLs, next-generation sequencing (NGS) technology is ideally suited for carrying out genetic screening of these individuals. This Consensus Statement, formulated by a study group comprised of experts in the field, proposes specific recommendations for the use of diagnostic NGS in hereditary PPGLs. In brief, the study group recommends target gene panels for screening of germ line DNA, technical adaptations to address different modes of disease transmission, orthogonal validation of NGS findings, standardized classification of variant pathogenicity and uniform reporting of the findings. The use of supplementary assays, to aid in the interpretation of the results, and sequencing of tumour DNA, for identification of somatic mutations, is encouraged. In addition, the study group launches an initiative to develop a gene-centric curated database of PPGL variants, with annual re-evaluation of variants of unknown significance by an expert group for purposes of reclassification and clinical guidance.
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Affiliation(s)
| | - Rodrigo A Toledo
- Division of Hematology and Medical Oncology, Department of Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, MC7880, San Antonio, Texas 78229, USA
- Spanish National Cancer Research Centre, CNIO, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Nelly Burnichon
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, 20 Rue Leblanc, 75015 Paris, France
- INSERM, UMR970, Paris Cardiovascular Research Center (PARCC), 56 Rue Leblanc, 75015, Paris, France
| | - Alberto Cascon
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO) and ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Diana E Benn
- Cancer Genetics Unit, Kolling Institute, Royal North Shore Hospital, St Leonards, University of Sydney, Reserve Road, St Leonards, Sydney, New South Wales 2065, Australia
| | - Jean-Pierre Bayley
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Jenny Welander
- Department of Clinical and Experimental Medicine, Linköping University, 58183 Linköping, Sweden
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Helen Firth
- Department of Medical Genetics, University of Cambridge, Cambridge and NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge, CB2 0QQ, UK
| | - Trish Dwight
- Cancer Genetics Unit, Kolling Institute, Royal North Shore Hospital, St Leonards, University of Sydney, Reserve Road, St Leonards, Sydney, New South Wales 2065, Australia
| | - Tonino Ercolino
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale GB Morgagni 50, 50134, Florence, Italy
| | - Massimo Mannelli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Viale GB Morgagni 50, 50134, Florence, Italy
| | - Giuseppe Opocher
- Familial Cancer Clinic, Veneto Institute of Oncology, IRCCS, Via Gattamelata, 64 Padova, Veneto 35128, Padova, Italy
| | - Roderick Clifton-Bligh
- Cancer Genetics Unit, Kolling Institute, Royal North Shore Hospital, St Leonards, University of Sydney, Reserve Road, St Leonards, Sydney, New South Wales 2065, Australia
| | - Oliver Gimm
- Department of Surgery, Region Östergötland, Linköping University, 581 83 Linköping, Sweden
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge and NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge, CB2 0QQ, UK
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Centre (CNIO) and ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Anne-Paule Gimenez-Roqueplo
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Génétique; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, 20 Rue Leblanc, 75015 Paris, France
- INSERM, UMR970, Paris Cardiovascular Research Center (PARCC), 56 Rue Leblanc, 75015, Paris, France
| | - Patricia L M Dahia
- Division of Hematology and Medical Oncology, Department of Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio (UTHSCSA), 7703 Floyd Curl Drive, MC7880, San Antonio, Texas 78229, USA
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De Summa S, Malerba G, Pinto R, Mori A, Mijatovic V, Tommasi S. GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data. BMC Bioinformatics 2017; 18:119. [PMID: 28361668 PMCID: PMC5374681 DOI: 10.1186/s12859-017-1537-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on preset parameters that may not fit in a satisfactory manner for different genes. GATK, which is widely used in the academic world, is rich in parameters for variant calling. However the self-adjusting parameter calibration of GATK requires data from a large number of exomes. When these are not available, which is the standard condition of a diagnostic laboratory, the parameters must be set by the operator (hard filtering). The aim of the present paper was to set up a procedure to assess the best parameters to be used in the hard filtering of GATK. This was pursued by using classification trees on true and false variants from simulated sequences of a real dataset data. RESULTS We simulated two datasets, with different coverages, including all the sequence alterations identified in a real dataset according to their observed frequencies. Simulated sequences were aligned with standard protocols and then regression trees were built up to identify the most reliable parameters and cutoff values to discriminate true and false variant calls. Moreover, we analyzed flanking sequences of region presenting a high rate of false positive calls observing that such sequences present a low complexity make up. CONCLUSIONS Our results showed that GATK hard filtering parameter values can be tailored through a simulation study based-on the DNA region of interest to ameliorate the accuracy of the variant calling.
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Affiliation(s)
- Simona De Summa
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
| | - Giovanni Malerba
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy.
| | - Rosamaria Pinto
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
| | - Antonio Mori
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy
| | - Vladan Mijatovic
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Strada Le Grazie 8, 37135, Verona, Italy
| | - Stefania Tommasi
- IRCCS-Istituto Tumori "Giovanni Paolo II", Molecular Genetics Laboratory, viale Orazio Flacco, 65, 70124, Bari, Italy
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Merino GA, Murua YA, Fresno C, Sendoya JM, Golubicki M, Iseas S, Coraglio M, Podhajcer OL, Llera AS, Fernández EA. TarSeqQC: Quality control on targeted sequencing experiments in R. Hum Mutat 2017; 38:494-502. [DOI: 10.1002/humu.23204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/06/2017] [Accepted: 02/19/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Gabriela A. Merino
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Yanina A. Murua
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Cristóbal Fresno
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
| | - Juan M. Sendoya
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Mariano Golubicki
- Intergrupo Argentino para el Tratamiento de los Tumores Gastrointestinales; Buenos Aires Argentina
| | - Soledad Iseas
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Mariana Coraglio
- Hospital de Gastroenterología “Dr. Carlos Bonorino Udaondo”; Buenos Aires Argentina
| | - Osvaldo L. Podhajcer
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Andrea S. Llera
- Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-CONICET; Buenos Aires Argentina
| | - Elmer A. Fernández
- Ua Area Cs. Agr. Ing. Bio. Y S, Conicet; Universidad Católica de Córdoba; Córdoba Argentina
- Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
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Oikawa Y, Morita KI, Kayamori K, Tanimoto K, Sakamoto K, Katoh H, Ishikawa S, Inazawa J, Harada H. Receptor tyrosine kinase amplification is predictive of distant metastasis in patients with oral squamous cell carcinoma. Cancer Sci 2017; 108:256-266. [PMID: 27889930 PMCID: PMC5329163 DOI: 10.1111/cas.13126] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022] Open
Abstract
This study aimed to clarify the genomic factors associated with the diagnosis and prognosis of oral squamous cell carcinoma via next-generation sequencing. We evaluated data from 220 cases of oral squamous cell carcinoma. Genomic DNA was eluted using formalin-fixed, paraffin-embedded samples, and targeted resequencing of 50 cancer-related genes was performed. In total, 311 somatic mutations were detected in 220 patients, consisting of 68 synonymous mutations and 243 non-synonymous mutations. Genes carrying mutations included TP53, CDKN2A, and PIK3CA in 79 (35.9%), 35 (15.9%), and 19 patients (8.6%), respectively. Copy number analysis detected amplification of PIK3CA and AKT1 in 38 (17.3%) and 11 patients (5.0%), respectively. Amplification of receptor tyrosine kinases was found in 37 patients (16.8%). Distant metastasis was noted in nine of 37 patients (24%) with receptor tyrosine kinase amplification, accounting for 43% of the 21 cases of distant metastasis. The cumulative 5-year survival rate was 64.6% in the receptor tyrosine kinase amplification group vs 85.2% in the no receptor tyrosine kinase amplification group. Moreover, we identified significantly poorer prognosis in the TP53 mutation/receptor tyrosine kinase amplification group, for which the cumulative 5-year survival rate was 41.6%. In conclusion, the results of this study demonstrated that receptor tyrosine kinase amplification is a prognostic factor for distant metastasis of oral squamous cell carcinoma, indicating the necessity of using next-generation sequencing in clinical sequencing.
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Affiliation(s)
- Yu Oikawa
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei-Ichi Morita
- Department of Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kou Kayamori
- Department of Oral Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kousuke Tanimoto
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei Sakamoto
- Department of Oral Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroto Katoh
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shumpei Ishikawa
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan.,Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Harada
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors. J Mol Diagn 2017; 19:255-264. [DOI: 10.1016/j.jmoldx.2016.09.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/20/2016] [Accepted: 09/29/2016] [Indexed: 11/22/2022] Open
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Löser H, Heydt C, Büttner R, Markiefka B. [BRCA diagnostics of ovarian cancer : Molecular tumor testing since the introduction of PARP inhibitor therapy]. DER PATHOLOGE 2017; 38:117-126. [PMID: 28258387 DOI: 10.1007/s00292-017-0274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Approximately 9000 women are diagnosed with ovarian cancer in Germany each year. The most common subtype is high-grade serous ovarian cancer. A relevant proportion of these tumors are associated with mutations in the breast and ovarian cancer susceptibility genes (BRCA1 and BRCA2) representing highly penetrant tumor suppressor genes with autosomal inheritance and play a crucial role in DNA repair mechanisms. These patients have predominantly germline mutations and less frequently have somatic BRCA mutations. Tumors harboring BRCA mutations show a significant improvement in progression-free survival under therapy with poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors. In 2015 the first PARP inhibitor was approved for the therapy of high-grade serous ovarian cancer with BRCA mutations. Mutation analysis can be performed on formalin-fixed paraffin-embedded (FFPE) tumor tissue within a few days.
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Affiliation(s)
- H Löser
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - C Heydt
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - R Büttner
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - B Markiefka
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland.
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Abstract
CONTEXT -Molecular diagnostics play a role in the management of many cancers, including breast cancer. OBJECTIVE -To provide an update on molecular testing in current clinical practice, targeted at practicing pathologists who are not breast cancer specialists. DATA SOURCES -This study is a narrative literature review. CONCLUSIONS -In addition to routine hormone (estrogen and progesterone) receptor testing, new and recurrent tumors are tested for HER2 amplification by in situ hybridization or overexpression by immunohistochemistry. Intrinsic subtyping of tumors represents a fundamental advance in our understanding of breast cancer biology, but currently it has an indirect role in patient management. Clinical next-generation sequencing (tumor profiling) is increasingly used to identify potentially actionable mutations in tumor tissue. Multianalyte assays with algorithmic analysis, including MammaPrint, Oncotype DX, and Prosigna, play a larger role in breast cancer than in many other malignancies. Given that a proportion of breast cancers are familial, testing of nontumor tissue for cancer predisposition mutations also plays a role in breast cancer care.
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Affiliation(s)
- Ian S Hagemann
- From the Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri. Presented at the 2nd Princeton Integrated Pathology Symposium: Breast Pathology; February 8, 2015; Plainsboro, New Jersey
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50
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Single-Center Experience with a Targeted Next Generation Sequencing Assay for Assessment of Relevant Somatic Alterations in Solid Tumors. Neoplasia 2017; 19:196-206. [PMID: 28161563 PMCID: PMC5293722 DOI: 10.1016/j.neo.2017.01.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/18/2017] [Accepted: 01/18/2017] [Indexed: 02/07/2023] Open
Abstract
Companion diagnostics rely on genomic testing of molecular alterations to enable effective cancer treatment. Here we report the clinical application and validation of the Oncomine Focus Assay (OFA), an integrated, commercially available next-generation sequencing (NGS) assay for the rapid and simultaneous detection of single nucleotide variants, short insertions and deletions, copy number variations, and gene rearrangements in 52 cancer genes with therapeutic relevance. Two independent patient cohorts were investigated to define the workflow, turnaround times, feasibility, and reliability of OFA targeted sequencing in clinical application and using archival material. Cohort I consisted of 59 diagnostic clinical samples from the daily routine submitted for molecular testing over a 4-month time period. Cohort II consisted of 39 archival melanoma samples that were up to 15years old. Libraries were prepared from isolated nucleic acids and sequenced on the Ion Torrent PGM sequencer. Sequencing datasets were analyzed using the Ion Reporter software. Genomic alterations were identified and validated by orthogonal conventional assays including pyrosequencing and immunohistochemistry. Sequencing results of both cohorts, including archival formalin-fixed, paraffin-embedded material stored up to 15years, were consistent with published variant frequencies. A concordance of 100% between established assays and OFA targeted NGS was observed. The OFA workflow enabled a turnaround of 3½ days. Taken together, OFA was found to be a convenient tool for fast, reliable, broadly applicable and cost-effective targeted NGS of tumor samples in routine diagnostics. Thus, OFA has strong potential to become an important asset for precision oncology.
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