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Sandhu N, Singh J, Ankush AP, Augustine G, Raigar OP, Verma VK, Pruthi G, Kumar A. Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice. RICE (NEW YORK, N.Y.) 2024; 17:33. [PMID: 38727876 PMCID: PMC11087395 DOI: 10.1186/s12284-024-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The lack of stable-high yielding and direct-seeded adapted varieties with better germination ability from deeper soil depth and availability of molecular markers are major limitation in achieving the maximum yield potential of rice under water and resource limited conditions. Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR). RESULTS Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F1s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F3:F4 and 713 BC3F2:3 progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F3:F4 and 80-100 samples from BC3F2:3 progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of LOC_Os04g34290 and LOC_Os08g32100 led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure. CONCLUSION The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs/genes providing adaptation to rice under DSR. The functional studies of the genes LOC_Os04g34290 and LOC_Os08g32100 possessing two validated SNPs may provide valuable information about these genes.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | | | | | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Arvind Kumar
- Delta Agrigenetics, Plot No. 99 & 100 Green Park Avenue, Village, Jeedimetla, Secunderabad, Telangana, 500055, India
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Trédan O, Robert C, Italiano A, Barlesi F. [Use of genome-wide testing in oncology: French expert opinion based on the Delphi methodology]. Bull Cancer 2023; 110:320-330. [PMID: 36717341 DOI: 10.1016/j.bulcan.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 01/30/2023]
Abstract
In oncology, genome-wide testing is a major element in facilitating the implementation of precision medicine. However, current recommendations do not always specify the indication and utility of these tests according to the type of cancer. A national consensus approach based on a modified Delphi methodology was set up to provide expert opinion on the use of genome-wide testing in clinical practice in France. Four groups of experts - 4 each representing the following topics of interest - were defined: non-small cell lung cancer (NSCLC), breast cancer, melanoma, and cancer of unknown primary (CUP). In each group, assertions were formulated by a lead expert (8, 5, 7 and 6, respectively) and rated by five panellists involved in the management of these cancers, on a scale from 1 (strongly disagree) to 9 (strongly agree). Consensus was reached when 75% of the scores were above 7. In case of disagreement, the panellists were asked to justify their rate. In total, 24 statements reached consensus after two to four rounds of rating, depending on the group. While the experts advocated the routine use of genome-wide testing in the diagnostic management of NSCLC and CUP, they did not recommend the systematisation of these tests for breast cancer and melanoma. Nevertheless, access to innovation in France could soon remove certain barriers and allow greater standardisation of broad molecular screening in oncology.
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Affiliation(s)
- Olivier Trédan
- Centre Léon-Bérard, CNRS UMR5286, Centre international de recherche en cancérologie, département de cancérologie médicale, Lyon, France.
| | - Caroline Robert
- Cancer Campus, Institut Gustave-Roussy, dermatologie et vénéréologie, Villejuif, France
| | - Antoine Italiano
- Institut Bergonié, Département d'oncologie médicale, Bordeaux, France; Cancer Campus, Institut Gustave-Roussy, Villejuif, France; Université de Bordeaux, Bordeaux, France
| | - Fabrice Barlesi
- Cancer Campus, Institut Gustave-Roussy, Villejuif, France; Aix-Marseille université, Marseille, France
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Alterations in Natural Killer Cells in Colorectal Cancer Patients with Stroma AReactive Invasion Front Areas (SARIFA). Cancers (Basel) 2023; 15:cancers15030994. [PMID: 36765951 PMCID: PMC9913252 DOI: 10.3390/cancers15030994] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/22/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Recently, our group introduced Stroma AReactive Invasion Front Areas (SARIFA) as an independent prognostic predictor for a poorer outcome in colon cancer patients, which is probably based on immunologic alterations combined with a direct tumor-adipocyte interaction: the two together reflecting a distinct tumor biology. Considering it is already known that peripheral immune cells are altered in colorectal cancer (CRC) patients, this study aims to investigate the changes in lymphocyte subsets in SARIFA-positive cases and correlate these changes with the local immune response. METHODS Flow cytometry was performed to analyze B, T, and natural killer (NK) cells in the peripheral blood (PB) of 45 CRC patients. Consecutively, lymphocytes in PB, tumor-infiltrating lymphocytes (TILs), and CD56+ and CD57+ lymphocytes at the invasion front and the tumor center were compared between patients with SARIFA-positive and SARIFA-negative CRCs. RESULTS Whereas no differences could be observed regarding most PB lymphocyte populations as well as TILs, NK cells were dramatically reduced in the PB of SARIFA-positive cases. Moreover, CD56 and CD57 immunohistochemistry suggested SARIFA-status-dependent changes regarding NK cells and NK-like lymphocytes in the tumor microenvironment. CONCLUSION This study proves that our newly introduced biomarker, SARIFA, comes along with distinct immunologic alterations, especially regarding NK cells.
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Durães C, Pereira Gomes C, Costa JL, Quagliata L. Demystifying the Discussion of Sequencing Panel Size in Oncology Genetic Testing. EUROPEAN MEDICAL JOURNAL 2022. [DOI: 10.33590/emj/22c9259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Clinical laboratories worldwide are implementing next-generation sequencing (NGS) to identify cancer genomic variants and ultimately improve patient outcomes. The ability to massively sequence the entire genome or exome of tumour cells has been critical to elucidating many complex biological questions. However, the depth of information obtained by these methods is strenuous to process in the clinical setting, making them currently unfeasible for broader adoption. Instead, targeted sequencing, usually on a selection of clinically relevant genes, represents the predominant approach that best balances accurate identification of genomic variants with high sensitivity and a good cost-effectiveness ratio. The information obtained from targeted sequencing can support diagnostic classification, guide therapeutic decisions, and provide prognostic insights. The use of targeted gene panels expedites sample processing, including data analysis, results interpretation, and medical reports generation, directly affecting patient management. The key decision factors for selecting sequencing methods and panel size in routine testing should include diagnostic yield and clinical utility, sample availability, and processing turnaround time.
Profiling by default all patients with late-stage cancer with large panels is not affordable for most healthcare systems and does not provide substantial clinical benefit at present. Balancing between understanding cancer biology, including patients in clinical trials, maximising testing, and ensuring a sustainable financial burden for society requires thorough consideration. This review provides an overview of the advantages and drawbacks of different sizes NGS panels for tumour molecular profiling and their clinical applicability.
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Affiliation(s)
- Cecília Durães
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | | | - Jose Luis Costa
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
| | - Luca Quagliata
- Clinical Next-Generation Sequencing Division, Genetic Sciences Group, Thermo Fisher Scientific, Carlsbad, California, USA
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Wang M, Chen X, Dai Y, Wu D, Liu F, Yang Z, Song B, Xie L, Yang L, Zhao W, Zhang C, Shen W, Fan C, Teng C, Zhao X, Gao N, Shang D, Zhao G, Xin T. Concordance Study of a 520-Gene Next-Generation Sequencing-Based Genomic Profiling Assay of Tissue and Plasma Samples. Mol Diagn Ther 2022; 26:309-322. [PMID: 35305253 DOI: 10.1007/s40291-022-00579-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Next-generation sequencing (NGS) enables simultaneous detection of actionable somatic variants and estimation of genomic signatures such as tumor mutational burden (TMB) or microsatellite instability (MSI) status, which empowers therapeutic decisions in clinical oncology. OBJECTIVE Our retrospective study investigated the clinical performance of somatic variant detection in paired tissue and blood samples using a large targeted gene panel, the OncoScreen Plus, which interrogates 520 cancer-related genes. METHODS We analyzed sequencing data derived from paired tissue and blood samples of 3005 patients spanning 20 solid tumor types, including lung (n = 1971), gastrointestinal (n = 625), breast (n = 120) and gynecological (n = 110), genitourinary (n = 38), and other cancers (n = 141). RESULTS Across tumor types, the OncoScreen Plus panel achieved a high tissue detection rate, with an average of 97.9%. The average plasma detection rate was 72.2%, with an average tissue concordance rate of 36.6%. Considering all variant types, the plasma assay yielded an average sensitivity/true positive rate of 45.7%, with a positive predictive value of 64.7% relative to tissue assay. Pearson correlation analysis revealed a strong correlation in TMB estimated from blood and tissue samples (correlation coefficient 0.845, R2 = 0.756). MSI-high status was identified in five tumor types, including endometrial cancer (28.6%), colorectal cancer (2.5%), ovarian cancer (2.0%), gastric cancer (1.5%), and lung adenocarcinoma (0.2%). CONCLUSION Paired tumor and blood samples from a large cohort of patients spanning 20 tumor types demonstrated that the OncoScreen Plus is a reliable pan-cancer panel for the accurate detection of somatic variants and genomic signatures that could guide individualized treatment strategies to improve the care of patients with advanced cancer.
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Affiliation(s)
- Minghui Wang
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510220, China
| | - Xianshan Chen
- Department of Thoracic Surgery, Hainan General Hospital, Hainan, 570311, China
| | - Yongmei Dai
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Duoguang Wu
- Department of Thoracic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510220, China
| | - Fang Liu
- Department of Pathology, The First People's Hospital of Foshan, Foshan, 528000, China
| | - Zheng Yang
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Baozhi Song
- Department of Gynecology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Li Xie
- Department of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou, 350001, China
| | - Liangwei Yang
- Department of Cardiothoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), No. 41 Xibei Road, Ningbo, 315010, Zhejiang, China
| | - Weidi Zhao
- Department of Cardiothoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), No. 41 Xibei Road, Ningbo, 315010, Zhejiang, China
| | - Chenxu Zhang
- Department of Cardiothoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), No. 41 Xibei Road, Ningbo, 315010, Zhejiang, China
| | - Weixi Shen
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Chengjuan Fan
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Chong Teng
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Xue Zhao
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Naisheng Gao
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Di Shang
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China
| | - Guofang Zhao
- Department of Cardiothoracic Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences (Ningbo No. 2 Hospital), No. 41 Xibei Road, Ningbo, 315010, Zhejiang, China.
| | - Tao Xin
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Road, Nangang, Harbin, 150081, Heilongjiang, China.
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Kalita-de Croft P, Joshi V, Saunus JM, Lakhani SR. Emerging Biomarkers for Diagnosis, Prevention and Treatment of Brain Metastases-From Biology to Clinical Utility. Diseases 2022; 10:11. [PMID: 35225863 PMCID: PMC8884016 DOI: 10.3390/diseases10010011] [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: 11/09/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022] Open
Abstract
Primary malignancies of the lung, skin (melanoma), and breast have higher propensity for metastatic spread to the brain. Advances in molecular tumour profiling have aided the development of targeted therapies, stereotactic radiotherapy, and immunotherapy, which have led to some improvement in patient outcomes; however, the overall prognosis remains poor. Continued research to identify new prognostic and predictive biomarkers is necessary to further impact patient outcomes, as this will enable better risk stratification at the point of primary cancer diagnosis, earlier detection of metastatic deposits (for example, through surveillance), and more effective systemic treatments. Brain metastases exhibit considerable inter- and intratumoural heterogeneity-apart from distinct histology, treatment history and other clinical factors, the metastatic brain tumour microenvironment is incredibly variable both in terms of subclonal diversity and cellular composition. This review discusses emerging biomarkers; specifically, the biological context and potential clinical utility of tumour tissue biomarkers, circulating tumour cells, extracellular vesicles, and circulating tumour DNA.
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Affiliation(s)
- Priyakshi Kalita-de Croft
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Vaibhavi Joshi
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Jodi M. Saunus
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, The University of Queensland Faculty of Medicine, Herston, QLD 4029, Australia; (V.J.); (J.M.S.)
- Pathology Queensland, The Royal Brisbane and Women’s Hospital Herston, Herston, QLD 4029, Australia
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da Cunha IW, de Almeida Coudry R, de Macedo MP, de Assis EACP, Stefani S, Soares FA. A call to action: molecular pathology in Brazil. SURGICAL AND EXPERIMENTAL PATHOLOGY 2021. [DOI: 10.1186/s42047-021-00096-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Adoption of molecular pathology in Brazil is currently very limited. Of note, there are no programs for training new molecular pathologists in the country; thus, documents compiling nationally applicable information on molecular pathology are few.
Methods
A selected panel of Brazilian experts in fields related to molecular pathology were provided with a series of relevant questions to address prior to the multi-day conference. Within this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion until a consensus was achieved.
Results
The panel proposes specific and realistic recommendations for implementing molecular pathology in cancer care in Brazil. In creating these recommendations, the authors strived to address all barriers to the widespread use and impediments to access mentioned previously within this manuscript.
Conclusion
This manuscript provides a review of molecular pathology principles as well as the current state of molecular pathology in Brazil. Additionally, the panel proposes practical and actionable recommendations for the implementation of molecular pathology throughout the country in order to increase awareness of the importance molecular pathology in Brazil.
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Macías M, Cañada-Higueras E, Alegre E, Bielsa A, Gracia J, Patiño-García A, Ferrer-Costa R, Sendino T, Andueza MP, Mateos B, Rodríguez J, Corral J, Gúrpide A, Lopez-Picazo JM, Perez-Gracia JL, Gil-Bazo I, Alkorta-Aranburu G, González Á. Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients. Clin Chem Lab Med 2021; 58:1341-1348. [PMID: 32623849 DOI: 10.1515/cclm-2019-1267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Background Genomic alterations studies in cell-free DNA (cfDNA) have increasing clinical use in oncology. Next-generation sequencing (NGS) technology provides the most complete mutational analysis, but nowadays limited data are available related to the comparison of results reported by different platforms. Here we compare two NGS panels for cfDNA: Oncomine™ Pan-Cancer Cell-Free Assay (Thermo Fisher Scientific), suitable for clinical laboratories, and Guardant360® (GuardantHealth), with more genes targeted but only available in an outsourcing laboratory. Methods Peripheral blood was obtained from 16 advanced cancer patients in which Guardant360® (G360) was requested as part of their clinical assistance. Blood samples were sent to be analyzed with G360 panel, and an additional blood sample was drawn to obtain and analyze cfDNA with Oncomine™ Pan-Cancer (OM) panel in an Ion GeneStudio S5™ System. Results cfDNA analysis globally rendered 101 mutations. Regarding the 55/101 mutations claimed to be included by manufacturers in both panels, 17 mutations were reported only by G360, 10 only by OM and 28 by both. In those coincident cases, there was a high correlation between the variant allele fractions (VAFs) calculated with each panel (r = 0.979, p < 0.01). Regarding the six actionable mutations with an FDA-approved therapy reported by G360, one was missed with OM. Also, 12 mutations with clinical trials available were reported by G360 but not by OM. Conclusions In summary, G360 and OM can produce different mutational profile in the same sample, even in genes included in both panels, which is especially important if these mutations are potentially druggable.
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Affiliation(s)
- Mónica Macías
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Estibaliz Alegre
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Arancha Bielsa
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Javier Gracia
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Ana Patiño-García
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Roser Ferrer-Costa
- Department of Biochemistry, Hospital Universitari Vall D'Hebron, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Teresa Sendino
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - María P Andueza
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Beatriz Mateos
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - Javier Rodríguez
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jesús Corral
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Alfonso Gúrpide
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - José M Lopez-Picazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jose L Perez-Gracia
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Gil-Bazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Program of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Álvaro González
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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Starks ER, Swanson L, Docking TR, Bosdet I, Munro S, Moore RA, Karsan A. Assessing Limit of Detection in Clinical Sequencing. J Mol Diagn 2021; 23:455-466. [PMID: 33486075 DOI: 10.1016/j.jmoldx.2020.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/05/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022] Open
Abstract
Clinical reporting of solid tumor sequencing requires reliable assessment of the accuracy and reproducibility of each assay. Somatic mutation variant allele fractions may be below 10% in many samples due to sample heterogeneity, tumor clonality, and/or sample degradation in fixatives such as formalin. The toolkits available to the clinical sequencing community for correlating assay design parameters with assay sensitivity remain limited, and large-scale empirical assessments are often relied upon due to the lack of clear theoretical grounding. To address this uncertainty, a theoretical model was developed for predicting the expected variant calling sensitivity for a given library complexity and sequencing depth. Binomial models were found to be appropriate when assay sensitivity was only limited by library complexity or sequencing depth, but functional scaling for library complexity was necessary when both library complexity and sequencing depth were co-limiting. This model was empirically validated with sequencing experiments by using a series of DNA input amounts and sequencing depths. Based on these findings, a workflow is proposed for determining the limiting factors to sensitivity in different assay designs, and the formulas for these scenarios are presented. The approach described here provides designers of clinical assays with the methods to theoretically predict assay design outcomes a priori, potentially reducing burden in clinical tumor assay design and validation efforts.
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Affiliation(s)
- Elizabeth R Starks
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
| | - Lucas Swanson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah Munro
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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11
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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12
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O'Shea A, Tam AL, Kilcoyne A, Flaherty KT, Lee SI. Image-guided biopsy in the age of personalised medicine: strategies for success and safety. Clin Radiol 2020; 76:154.e1-154.e9. [PMID: 32896425 DOI: 10.1016/j.crad.2020.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/04/2020] [Indexed: 12/28/2022]
Abstract
Oncology has progressed into an era of personalised medicine, whereby the therapeutic regimen is tailored to the molecular profile of the patient's cancer. Determining personalised therapeutic options is achieved by using tumour genomics and proteomics to identify the specific molecular targets against which candidate drugs can interact. Several dozen targeted drugs, many for multiple cancer types are already widely in clinical use. Molecular profiling of tumours is contingent on high-quality biopsy specimens and the most common method of tissue sampling is image-guided biopsy. Thus, for radiologists performing these biopsies, the paradigm has now shifted away from obtaining specimens simply for histopathological diagnosis to acquiring larger amounts of viable tumour cells for DNA, RNA, or protein analysis. These developments have highlighted the central role now played by radiologists in the delivery of personalised cancer care. This review describes the principles of molecular profiling assays and biopsy techniques for optimising yield, and describes a scoring system to assist in patient selection for percutaneous biopsy.
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Affiliation(s)
- A O'Shea
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - A L Tam
- Department of Interventional Radiology, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - A Kilcoyne
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - K T Flaherty
- Department of Medicine, Division of Oncology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - S I Lee
- Department of Radiology, Division of Abdominal Imaging, Massachusetts General Hospital, Boston, MA, 02114, USA
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13
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Dhani NC, Hirte HW, Wang L, Burnier JV, Jain A, Butler MO, Welch S, Fleming GF, Hurteau J, Matsuo K, Matei D, Jimenez W, Johnston C, Cristea M, Tonkin K, Ghatage P, Lheureux S, Mehta A, Quintos J, Tan Q, Kamel-Reid S, Ludkovski O, Tsao MS, Wright JJ, Oza AM. Phase II Trial of Cabozantinib in Recurrent/Metastatic Endometrial Cancer: A Study of the Princess Margaret, Chicago, and California Consortia (NCI9322/PHL86). Clin Cancer Res 2020; 26:2477-2486. [PMID: 31992589 DOI: 10.1158/1078-0432.ccr-19-2576] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/10/2019] [Accepted: 01/24/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE The relevance of the MET/hepatocyte growth factor pathway in endometrial cancer tumor biology supports the clinical evaluation of cabozantinib in this disease. PATIENTS AND METHODS PHL86/NCI#9322 (NCT01935934) is a single arm study that evaluated cabozantinib (60 mg once daily) in women with endometrial cancer with progression after chemotherapy. Coprimary endpoints were response rate and 12-week progression-free-survival (PFS). Patients with uncommon histology endometrial cancer (eg, carcinosarcoma and clear cell) were enrolled in a parallel exploratory cohort. RESULTS A total of 102 patients were accrued. Among 36 endometrioid histology patients, response rate was 14%, 12-week PFS rate was 67%, and median PFS was 4.8 months. In serous cohort of 34 patients, response rate was 12%, 12-week PFS was 56%, and median PFS was 4.0 months. In a separate cohort of 32 patients with uncommon histology endometrial cancer (including carcinosarcoma), response rate was 6% and 12-week PFS was 47%. Six patients were on treatment for >12 months, including two for >30 months. Common cabozantinib-related toxicities (>30% patients) included hypertension, fatigue, diarrhea, nausea, and hand-foot syndrome. Gastrointestinal fistula/perforation occurred in four of 70 (6%) patients with serous/endometrioid cancer and five of 32 (16%) patients in exploratory cohort. We observed increased frequency of responses with somatic CTNNB1 mutation [four partial responses (PRs) in 10 patients, median PFS 7.6 months] and concurrent KRAS and PTEN/PIK3CA mutations (three PRs in 12 patients, median PFS 5.9 months). CONCLUSIONS Cabozantinib has activity in serous and endometrioid histology endometrial cancer. These results support further evaluation in genomically characterized patient cohorts.
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Affiliation(s)
- Neesha C Dhani
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
| | - Hal W Hirte
- Juravinski Cancer Centre, Hamilton, Ontario, Canada
| | - Lisa Wang
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Angela Jain
- Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Stephen Welch
- London Regional Cancer Program, London, Ontario, Canada
| | | | - Jean Hurteau
- North Shore University Health System Evanston Hospital, Evanston, Illinois
| | - Koji Matsuo
- University of Southern California/Norris Comprehensive Cancer Centre, Los Angeles, California
| | | | | | | | - Mihaela Cristea
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Katia Tonkin
- The Cross Cancer Institute, Edmonton, Alberta, Canada
| | | | | | - Anjali Mehta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Judy Quintos
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Qian Tan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Olga Ludkovski
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - John J Wright
- NCI Cancer Therapy Evaluation Program (CTEP), Bethesda, Maryland
| | - Amit M Oza
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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14
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Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med 2020; 12:8. [PMID: 31937368 PMCID: PMC6961404 DOI: 10.1186/s13073-019-0703-1] [Citation(s) in RCA: 439] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The number of druggable tumor-specific molecular aberrations has grown substantially in the past decade, with a significant survival benefit obtained from biomarker matching therapies in several cancer types. Molecular pathology has therefore become fundamental not only to inform on tumor diagnosis and prognosis but also to drive therapeutic decisions in daily practice. The introduction of next-generation sequencing technologies and the rising number of large-scale tumor molecular profiling programs across institutions worldwide have revolutionized the field of precision oncology. As comprehensive genomic analyses become increasingly available in both clinical and research settings, healthcare professionals are faced with the complex tasks of result interpretation and translation. This review summarizes the current and upcoming approaches to implement precision cancer medicine, highlighting the challenges and potential solutions to facilitate the interpretation and to maximize the clinical utility of molecular profiling results. We describe novel molecular characterization strategies beyond tumor DNA sequencing, such as transcriptomics, immunophenotyping, epigenetic profiling, and single-cell analyses. We also review current and potential applications of liquid biopsies to evaluate blood-based biomarkers, such as circulating tumor cells and circulating nucleic acids. Last, lessons learned from the existing limitations of genotype-derived therapies provide insights into ways to expand precision medicine beyond genomics.
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Affiliation(s)
- Eoghan R Malone
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada
| | - Peter J B Sabatini
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Tracy L Stockley
- Department of Clinical Laboratory Genetics, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University Avenue, University of Toronto, Toronto, Ontario, M5G 1Z5, Canada.
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15
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Soverini S, Abruzzese E, Bocchia M, Bonifacio M, Galimberti S, Gozzini A, Iurlo A, Luciano L, Pregno P, Rosti G, Saglio G, Stagno F, Tiribelli M, Vigneri P, Barosi G, Breccia M. Next-generation sequencing for BCR-ABL1 kinase domain mutation testing in patients with chronic myeloid leukemia: a position paper. J Hematol Oncol 2019; 12:131. [PMID: 31801582 PMCID: PMC6894351 DOI: 10.1186/s13045-019-0815-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/27/2019] [Indexed: 12/31/2022] Open
Abstract
BCR-ABL1 kinase domain (KD) mutation status is considered to be an important element of clinical decision algorithms for chronic myeloid leukemia (CML) patients who do not achieve an optimal response to tyrosine kinase inhibitors (TKIs). Conventional Sanger sequencing is the method currently recommended to test BCR-ABL1 KD mutations. However, Sanger sequencing has limited sensitivity and cannot always discriminate between polyclonal and compound mutations. The use of next-generation sequencing (NGS) is increasingly widespread in diagnostic laboratories and represents an attractive alternative. Currently available data on the clinical impact of NGS-based mutational testing in CML patients do not allow recommendations with a high grade of evidence to be prepared. This article reports the results of a group discussion among an ad hoc expert panel with the objective of producing recommendations on the appropriateness of clinical decisions about the indication for NGS, the performance characteristics of NGS platforms, and the therapeutic changes that could be applied based on the use of NGS in CML. Overall, these recommendations might be employed to inform clinicians about the practical use of NGS in CML.
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Affiliation(s)
- Simona Soverini
- Hematology/Oncology "L. e A. Seràgnoli", Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138, Bologna, Italy.
| | | | - Monica Bocchia
- Hematology Unit, Azienda Ospedaliera Universitaria Senese, University of Siena, Siena, Italy
| | | | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Antonella Gozzini
- Department of Cellular Therapies and Transfusion Medicine, AOU Careggi, Florence, Italy
| | - Alessandra Iurlo
- Hematology Division, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | | | - Patrizia Pregno
- Hematology Unit, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Gianantonio Rosti
- Hematology/Oncology "L. e A. Seràgnoli", Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138, Bologna, Italy
| | - Giuseppe Saglio
- Department of Clinical and Biological Sciences of the University of Turin, Mauriziano Hospital, Turin, Italy
| | - Fabio Stagno
- Hematology Section and BMT Unit, Rodolico Hospital, AOU Policlinico-V. Emanuele, Catania, Italy
| | - Mario Tiribelli
- Division of Hematology and Bone Marrow Transplantation, Department of Medical Area, University of Udine, Udine, Italy
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine and Center of Experimental Oncology and Hematology, A.O.U. Policlinico-Vittorio Emanuele, Catania, Italy
| | - Giovanni Barosi
- Center for the Study of Myelofibrosis, IRCCS Policlinico S. Matteo Foundation, Pavia, Italy
| | - Massimo Breccia
- Hematology, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
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16
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Yao Y, Nishimura M, Murayama K, Kuranobu N, Tojo S, Beppu M, Ishige T, Itoga S, Tsuchida S, Mori M, Takayanagi M, Yokoyama M, Yamagata K, Kishita Y, Okazaki Y, Nomura F, Matsushita K, Tanaka T. A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing. Sci Rep 2019; 9:17411. [PMID: 31757988 PMCID: PMC6874554 DOI: 10.1038/s41598-019-53449-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing (NGS) is a revolutionary sequencing technology for analyzing genomes. However, preprocessing methods for mitochondrial DNA (mtDNA) sequencing remain complex, and it is required to develop an authenticated preprocessing method. Here, we developed a simple and easy preprocessing method based on isothermal rolling circle mtDNA amplification using commercially available reagents. Isothermal amplification of mtDNA was successfully performed using both nanoliter quantities of plasma directly and 25 ng of total DNA extracted from blood or tissue samples. Prior to mtDNA amplification, it was necessary to treat the extracted total DNA with Exonuclease V, but it was not required to treat plasma. The NGS libraries generated from the amplified mtDNA provided sequencing coverage of the entire human mitochondrial genome. Furthermore, the sequencing results successfully detected heteroplasmy in patient samples, with called mutations and variants matching those from previous, independent, Sanger sequencing analysis. Additionally, a novel single nucleotide variant was detected in a healthy volunteer. The successful analysis of mtDNA using very small samples from patients is likely to be valuable in clinical medicine, as it could reduce patient discomfort by reducing sampling-associated damage to tissues. Overall, the simple and convenient preprocessing method described herein may facilitate the future development of NGS-based clinical and forensic mtDNA tests.
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Affiliation(s)
- Yue Yao
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kei Murayama
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Naomi Kuranobu
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Satomi Tojo
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Minako Beppu
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sakae Itoga
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Masato Mori
- Department of Pediatrics, Matsudo City Hospital, Matsudo, 270-2296, Japan
| | - Masaki Takayanagi
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Yamagata
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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17
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Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA, Jones S, Sausen M, Velculescu VE, Angiuoli SV. A machine learning approach for somatic mutation discovery. Sci Transl Med 2019; 10:10/457/eaar7939. [PMID: 30185652 DOI: 10.1126/scitranslmed.aar7939] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 05/26/2018] [Accepted: 08/16/2018] [Indexed: 12/19/2022]
Abstract
Variability in the accuracy of somatic mutation detection may affect the discovery of alterations and the therapeutic management of cancer patients. To address this issue, we developed a somatic mutation discovery approach based on machine learning that outperformed existing methods in identifying experimentally validated tumor alterations (sensitivity of 97% versus 90 to 99%; positive predictive value of 98% versus 34 to 92%). Analysis of paired tumor-normal exome data from 1368 TCGA (The Cancer Genome Atlas) samples using this method revealed concordance for 74% of mutation calls but also identified likely false-positive and false-negative changes in TCGA data, including in clinically actionable genes. Determination of high-quality somatic mutation calls improved tumor mutation load-based predictions of clinical outcome for melanoma and lung cancer patients previously treated with immune checkpoint inhibitors. Integration of high-quality machine learning mutation detection in clinical next-generation sequencing (NGS) analyses increased the accuracy of test results compared to other clinical sequencing analyses. These analyses provide an approach for improved identification of tumor-specific mutations and have important implications for research and clinical management of cancer patients.
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Affiliation(s)
| | - James R White
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | | | | | | | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eniko Papp
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | | | - Peter LoVerso
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - David Riley
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Luis A Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Siân Jones
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, MD 21224, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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18
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Spaulding TP, Stockton SS, Savona MR. The evolving role of next generation sequencing in myelodysplastic syndromes. Br J Haematol 2019; 188:224-239. [PMID: 31571207 DOI: 10.1111/bjh.16212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 12/11/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal haematological disorders characterized by haematopoietic cell dysplasia, peripheral blood cytopenias, and a predisposition for developing acute myeloid leukaemia (AML). Cytogenetics have historically been important in diagnosis and prognosis in MDS, but the growing accessibility of next generation sequencing (NGS) has led to growing research in the roles of molecular genetic variation on clinical decision-making in these disorders. Multiple genes have been previously studied and found to be associated with specific outcomes or disease types within MDS and knowledge of mutations in these genes provides insight into previously defined MDS subtypes. Knowledge of these mutations also informs development of novel therapies in the treatment of MDS. The precise role of NGS in the diagnosis, prognosis and monitoring of MDS remains unclear but the improvements in NGS technology and accessibility affords clinicians an additional practice tool to provide the best care for patients.
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Affiliation(s)
- Travis P Spaulding
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shannon S Stockton
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.,Cancer Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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19
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20
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Simarro J, Murria R, Pérez-Simó G, Llop M, Mancheño N, Ramos D, Juan ID, Barragán E, Laiz B, Cases E, Ansótegui E, Gómez-Codina J, Aparicio J, Salvador C, Juan Ó, Palanca S. Development, Implementation and Assessment of Molecular Diagnostics by Next Generation Sequencing in Personalized Treatment of Cancer: Experience of a Public Reference Healthcare Hospital. Cancers (Basel) 2019; 11:E1196. [PMID: 31426418 PMCID: PMC6721584 DOI: 10.3390/cancers11081196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The establishment of precision medicine in cancer patients requires the study of several biomarkers. Single-gene testing approaches are limited by sample availability and turnaround time. Next generation sequencing (NGS) provides an alternative for detecting genetic alterations in several genes with low sample requirements. Here we show the implementation to routine diagnostics of a NGS assay under International Organization for Standardization (UNE-EN ISO 15189:2013) accreditation. For this purpose, 106 non-small cell lung cancer (NSCLC) and 102 metastatic colorectal cancer (mCRC) specimens were selected for NGS analysis with Oncomine Solid Tumor (ThermoFisher). In NSCLC the most prevalently mutated gene was TP53 (49%), followed by KRAS (31%) and EGFR (13%); in mCRC, TP53 (50%), KRAS (48%) and PIK3CA (16%) were the most frequently mutated genes. Moreover, NGS identified actionable genetic alterations in 58% of NSCLC patients, and 49% of mCRC patients did not harbor primary resistance mechanisms to anti-EGFR treatment. Validation with conventional approaches showed an overall agreement >90%. Turnaround time and cost analysis revealed that NGS implementation is feasible in the public healthcare context. Therefore, NGS is a multiplexed molecular diagnostic tool able to overcome the limitations of current molecular diagnosis in advanced cancer, allowing an improved and economically sustainable molecular profiling.
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Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Rosa Murria
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Nuria Mancheño
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - David Ramos
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Inmaculada de Juan
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Begoña Laiz
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Enrique Cases
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Emilio Ansótegui
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - José Gómez-Codina
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Jorge Aparicio
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Carmen Salvador
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Óscar Juan
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain.
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21
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Abstract
With rapid advances in genetics and genomics, the commercialization and access to new applications has become more widespread and omnipresent throughout biomedical research. Thus, increasingly, more patients will have personal genomic information they may share with primary care providers (PCPs) to better understand the clinical significance of the data. To be able to respond to patient inquiries about genomic data, variant interpretation, disease risk, and other issues, PCPs will need to be able to increase or refresh their awareness about genetics and genomics, and identify reliable resources to use or refer patients. While provider educational efforts have increased, with the rapid advances in the field, ongoing efforts will be needed to prepare PCPs to manage patient needs, integrate results into care, and refer as indicated.
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Affiliation(s)
- Susanne B Haga
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, 27708, USA.
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22
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Arbelaez JD, Dwiyanti MS, Tandayu E, Llantada K, Jarana A, Ignacio JC, Platten JD, Cobb J, Rutkoski JE, Thomson MJ, Kretzschmar T. 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. RICE (NEW YORK, N.Y.) 2019; 12:55. [PMID: 31350673 PMCID: PMC6660535 DOI: 10.1186/s12284-019-0311-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/02/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs. RESULTS Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications. CONCLUSIONS This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | | | - Erwin Tandayu
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Krizzel Llantada
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Annalhea Jarana
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Carlos Ignacio
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - John Damien Platten
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Joshua Cobb
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Jessica Elaine Rutkoski
- International Rice Research Institute, DAPO Box 7777, 1301 Los Baños, Metro Manila Philippines
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Houston, TX 77843 USA
| | - Tobias Kretzschmar
- Southern Cross Plant Sciences, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
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23
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Schumacher D, Andrieux G, Boehnke K, Keil M, Silvestri A, Silvestrov M, Keilholz U, Haybaeck J, Erdmann G, Sachse C, Templin M, Hoffmann J, Boerries M, Schäfer R, Regenbrecht CRA. Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures. PLoS Genet 2019; 15:e1008076. [PMID: 30925167 PMCID: PMC6457557 DOI: 10.1371/journal.pgen.1008076] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/10/2019] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
Organoid cultures derived from colorectal cancer (CRC) samples are increasingly used as preclinical models for studying tumor biology and the effects of targeted therapies under conditions capturing in vitro the genetic make-up of heterogeneous and even individual neoplasms. While 3D cultures are initiated from surgical specimens comprising multiple cell populations, the impact of tumor heterogeneity on drug effects in organoid cultures has not been addressed systematically. Here we have used a cohort of well-characterized CRC organoids to study the influence of tumor heterogeneity on the activity of the KRAS/MAPK-signaling pathway and the consequences of treatment by inhibitors targeting EGFR and downstream effectors. MAPK signaling, analyzed by targeted proteomics, shows unexpected heterogeneity irrespective of RAS mutations and is associated with variable responses to EGFR inhibition. In addition, we obtained evidence for intratumoral heterogeneity in drug response among parallel “sibling” 3D cultures established from a single KRAS-mutant CRC. Our results imply that separate testing of drug effects in multiple subpopulations may help to elucidate molecular correlates of tumor heterogeneity and to improve therapy response prediction in patients. Commonly occurring genetic alterations and patient-specific genetic features are increasingly used to predict the possible action of targeted cancer therapies. Although several lines of evidence have suggested that preclinical and clinical responses concur, the heterogeneity of tumors remains a severe obstacle in routinely translating preclinical data to patient treatments. Here we present a rapid work flow that integrates drug testing of three-dimensional patient tumor-derived (organoid) cultures and assessment of their genetic make-up as well as that of their donor tumors by amplicon sequencing and targeted proteomics. While the organoid cultures largely recapitulated the genomic profiles of donor tumors, the overall treatment responses and inhibitor effects on the intracellular signaling system were quite variable. Notably, organoid cultures obtained by synchronous multi-regional sampling of the same colorectal tumor showed an up to 30-fold difference in drug response. A combinatorial drug treatment improved the response. These data were confirmed in matched mouse xenograft models from the same tumor. Our findings may help to refine preclinical testing of individual tumors by modelling heterogeneity in cultures, to better understand therapeutic failure in clinical settings and to find ways to overcome treatment resistance.
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Affiliation(s)
- Dirk Schumacher
- Laboratory of Molecular Tumor Pathology, Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Geoffroy Andrieux
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Karsten Boehnke
- Eli Lilly and Company, Lilly Research Laboratories, Oncology Translational Research, New York, NY, United States of America
| | - Marlen Keil
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | | | | | | | - Johannes Haybaeck
- Department of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Department of Pathology, Neuropathology, and Molecular Pathology, Medical University of Innsbruck, Austria.,Diagnostic & Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, Austria
| | - Gerrit Erdmann
- NMI TT Pharmaservices, Berlin, Germany.,ASC Oncology GmbH, Berlin, Germany
| | - Christoph Sachse
- NMI TT Pharmaservices, Berlin, Germany.,ASC Oncology GmbH, Berlin, Germany
| | - Markus Templin
- ASC Oncology GmbH, Berlin, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jens Hoffmann
- EPO Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Reinhold Schäfer
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Charité Comprehensive Cancer Center, Berlin, Germany
| | - Christian R A Regenbrecht
- cpo-Cellular Phenomics & Oncology Berlin-Buch GmbH, Berlin, Germany.,Department of Pathology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,ASC Oncology GmbH, Berlin, Germany
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24
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Alonso CM, Llop M, Sargas C, Pedrola L, Panadero J, Hervás D, Cervera J, Such E, Ibáñez M, Ayala R, Martínez-López J, Onecha E, de Juan I, Palanca S, Martínez-Cuadrón D, Rodríguez-Veiga R, Boluda B, Montesinos P, Sanz G, Sanz MA, Barragán E. Clinical Utility of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia Diagnostics. J Mol Diagn 2019; 21:228-240. [DOI: 10.1016/j.jmoldx.2018.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 09/06/2018] [Accepted: 09/20/2018] [Indexed: 10/27/2022] Open
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25
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Haque MM, Kowtal P, Sarin R. Identification and characterization of TP53 gene Allele Dropout in Li-Fraumeni syndrome and Oral cancer cohorts. Sci Rep 2018; 8:11705. [PMID: 30076369 PMCID: PMC6076284 DOI: 10.1038/s41598-018-30238-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/21/2018] [Indexed: 12/20/2022] Open
Abstract
Allele Drop out (ADO) arising from non-amplification of one allele may produce false negative result and impact clinical management. In cancer, germline and somatic genetic analysis is being increasingly used but the prevalence, nature and implications of ADO has not been studied in any cohort. In a cohort of 290 Li Fraumeni/Li Fraumeni Like Syndrome cases undergoing TP53 genetic testing, of the 69 pathogenic mutations identified so far, 5 were initially missed and 4 were misgenotyped as homozygous mutation due to germline ADO. Of the 9 germline ADOs, 8 were sequence dependent, arising from a polymorphism (rs12951053) in the primer annealing region of exon 7. Of 35 somatic TP53 variants identified by exome sequencing in 50 oral cancer tissues registered under International Cancer Genome Consortium (ICGC), as a result of ADO, 4 were not detectable and 6 were not called as variant on Sanger Sequencing due to low peak height. High prevalence of germline and somatic ADO in the most frequently mutated cancer gene TP53, highlights the need for systematic evaluation of ADO prevalence and causes in clinically important cancer genes. False negative result for high penetrance germline mutations or actionable somatic mutations in oncogenes could have major clinical implications.
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Affiliation(s)
- Mohammed Moquitul Haque
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Pradnya Kowtal
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Rajiv Sarin
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India. .,Cancer Genetics Clinic, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, Maharashtra, India.
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26
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Alekseyev YO, Fazeli R, Yang S, Basran R, Maher T, Miller NS, Remick D. A Next-Generation Sequencing Primer-How Does It Work and What Can It Do? Acad Pathol 2018; 5:2374289518766521. [PMID: 29761157 PMCID: PMC5944141 DOI: 10.1177/2374289518766521] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/28/2022] Open
Abstract
Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.
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Affiliation(s)
- Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Roghayeh Fazeli
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Shi Yang
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Raveen Basran
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Thomas Maher
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Daniel Remick
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
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27
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Cho M, Ahn S, Hong M, Bang H, Van Vrancken M, Kim S, Lee J, Park SH, Park JO, Park YS, Lim HY, Kang WK, Sun JM, Lee SH, Ahn MJ, Park K, Kim DH, Lee S, Park W, Kim KM. Tissue recommendations for precision cancer therapy using next generation sequencing: a comprehensive single cancer center's experiences. Oncotarget 2018; 8:42478-42486. [PMID: 28477007 PMCID: PMC5522081 DOI: 10.18632/oncotarget.17199] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/05/2017] [Indexed: 02/02/2023] Open
Abstract
To generate accurate next-generation sequencing (NGS) data, the amount and quality of DNA extracted is critical. We analyzed 1564 tissue samples from patients with metastatic or recurrent solid tumor submitted for NGS according to their sample size, acquisition method, organ, and fixation to propose appropriate tissue requirements. Of the 1564 tissue samples, 481 (30.8%) consisted of fresh-frozen (FF) tissue, and 1,083 (69.2%) consisted of formalin-fixed paraffin-embedded (FFPE) tissue. We obtained successful NGS results in 95.9% of cases. Out of 481 FF biopsies, 262 tissue samples were from lung, and the mean fragment size was 2.4 mm. Compared to lung, GI tract tumor fragments showed a significantly lower DNA extraction failure rate (2.1 % versus 6.1%, p = 0.04). For FFPE biopsy samples, the size of biopsy tissue was similar regardless of tumor type with a mean of 0.8 × 0.3 cm, and the mean DNA yield per one unstained slide was 114 ng. We obtained highest amount of DNA from the colorectum (2353 ng) and the lowest amount from the hepatobiliary tract (760.3 ng) likely due to a relatively smaller biopsy size, extensive hemorrhage and necrosis, and lower tumor volume. On one unstained slide from FFPE operation specimens, the mean size of the specimen was 2.0 × 1.0 cm, and the mean DNA yield per one unstained slide was 1800 ng. In conclusions, we present our experiences on tissue requirements for appropriate NGS workflow: > 1 mm2 for FF biopsy, > 5 unstained slides for FFPE biopsy, and > 1 unstained slide for FFPE operation specimens for successful test results in 95.9% of cases.
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Affiliation(s)
- Minho Cho
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Present address: Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea
| | - Soomin Ahn
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Mineui Hong
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Heejin Bang
- Center for Cancer Companion Diagnostics, The Innovative Cancer Medicine Institute, Samsung Medical Center, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Michael Van Vrancken
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Seungtae Kim
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Joon Oh Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Suk Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ho Yeong Lim
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Won Ki Kang
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Mu Sun
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Hoon Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Myung-Ju Ahn
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keunchil Park
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk Hwan Kim
- Medical Translational Research Center, Samsung Biological Research Institute, Seoul, Korea
| | - Seunggwan Lee
- Department of Integrated Health and Environmental Science, College of Health Science, Korea University, Seoul, Korea
| | | | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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28
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High-throughput detection of clinically targetable alterations using next-generation sequencing. Oncotarget 2018; 8:40345-40358. [PMID: 28404952 PMCID: PMC5522202 DOI: 10.18632/oncotarget.15875] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 01/23/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the therapeutic care of patients by allowing high-throughput and parallel sequencing of large numbers of genes in a single run. However, most of available commercialized cancer panels target a large number of mutations that do not have direct therapeutic implications and that are not fully adapted to low quality formalin-fixed, paraffin-embedded (FFPE) samples. Here, we designed an amplicon-based NGS panel assay of 16 currently actionable genes according to the most recent recommendations of the French National Cancer Institute (NCI). We developed a panel of short amplicons (<150 bp) using dual-strand library preparation. The clinical validation of this panel was performed on well-characterized controls and 140 routine diagnostic samples, including highly degraded and cross-linked genomic DNA extracted from FFPE tumor samples. All mutations were detected with elevated inter-laboratory and inter-run reproducibility. Importantly, we could detect clinically actionable alterations in FFPE samples with variant allele frequencies as low as 1%. In addition, the overall molecular diagnosis rate was increased from 40.7% with conventional techniques to 59.2% with our NGS panel, including 41 novel actionable alterations normally not explored by conventional techniques. Taken together, we believe that this new actionable target panel represents a relevant, highly scalable and robust tool that is easy to implement and is fully adapted to daily clinical practice in hospital and academic laboratories.
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29
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Del Vecchio F, Mastroiaco V, Di Marco A, Compagnoni C, Capece D, Zazzeroni F, Capalbo C, Alesse E, Tessitore A. Next-generation sequencing: recent applications to the analysis of colorectal cancer. J Transl Med 2017; 15:246. [PMID: 29221448 PMCID: PMC5723063 DOI: 10.1186/s12967-017-1353-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics. Analysis of results is unveiling relevant perspectives aiding to evaluate the response to therapies. Novel evidences have been presented also in other directions such as gut microbiota or CRC circulating tumor cells. However, despite its unquestioned potential, NGS poses some issues calling for additional studies. This review intends to offer a view of the state of the art of NGS applications to CRC through examination of the most important technologies and discussion of recent published results.
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Affiliation(s)
- Filippo Del Vecchio
- Division of Cancer Sciences, University of Southampton, Southampton, Hampshire, SO16 6YD UK
| | - Valentina Mastroiaco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Antinisca Di Marco
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Daria Capece
- Department of Medicine, Centre for Cell Signaling and Inflammation, Imperial College London, London, W12 0NN UK
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, La Sapienza University, Rome, 00161 Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, 67100 Italy
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30
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Misyura M, Sukhai MA, Kulasignam V, Zhang T, Kamel-Reid S, Stockley TL. Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing. J Clin Pathol 2017; 71:117-124. [PMID: 28747393 PMCID: PMC5800325 DOI: 10.1136/jclinpath-2017-204520] [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: 04/19/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
Aims A standard approach in test evaluation is to compare results of the assay in validation to results from previously validated methods. For quantitative molecular diagnostic assays, comparison of test values is often performed using simple linear regression and the coefficient of determination (R2), using R2 as the primary metric of assay agreement. However, the use of R2 alone does not adequately quantify constant or proportional errors required for optimal test evaluation. More extensive statistical approaches, such as Bland-Altman and expanded interpretation of linear regression methods, can be used to more thoroughly compare data from quantitative molecular assays. Methods We present the application of Bland-Altman and linear regression statistical methods to evaluate quantitative outputs from next-generation sequencing assays (NGS). NGS-derived data sets from assay validation experiments were used to demonstrate the utility of the statistical methods. Results Both Bland-Altman and linear regression were able to detect the presence and magnitude of constant and proportional error in quantitative values of NGS data. Deming linear regression was used in the context of assay comparison studies, while simple linear regression was used to analyse serial dilution data. Bland-Altman statistical approach was also adapted to quantify assay accuracy, including constant and proportional errors, and precision where theoretical and empirical values were known. Conclusions The complementary application of the statistical methods described in this manuscript enables more extensive evaluation of performance characteristics of quantitative molecular assays, prior to implementation in the clinical molecular laboratory.
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Affiliation(s)
- Maksym Misyura
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mahadeo A Sukhai
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vathany Kulasignam
- Department of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Tong Zhang
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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31
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The AURORA pilot study for molecular screening of patients with advanced breast cancer-a study of the breast international group. NPJ Breast Cancer 2017; 3:23. [PMID: 28685159 PMCID: PMC5491498 DOI: 10.1038/s41523-017-0026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022] Open
Abstract
Several studies have demonstrated the feasibility of molecular screening of tumour samples for matching patients with cancer to targeted therapies. However, most of them have been carried out at institutional or national level. Herein, we report on the pilot phase of AURORA (NCT02102165), a European multinational collaborative molecular screening initiative for advanced breast cancer patients. Forty-one patients were prospectively enroled at four participating centres across Europe. Metastatic tumours were biopsied and profiled using an Ion Torrent sequencing platform at a central facility. Sequencing results were obtained for 63% of the patients in real-time with variable turnaround time stemming from delays between patient consent and biopsy. At least one clinically actionable mutation was identified in 73% of patients. We used the Illumina sequencing technology for orthogonal validation and achieved an average of 66% concordance of substitution calls per patient. Additionally, copy number aberrations inferred from the Ion Torrent sequencing were compared to single nucleotide polymorphism arrays and found to be 59% concordant on average. Although this study demonstrates that powerful next generation genomic techniques are logistically ready for international molecular screening programs in routine clinical settings, technical challenges remain to be addressed in order to ensure the accuracy and clinical utility of the genomic data. A pilot study demonstrated that a large-scale, international screening programme for women with metastatic breast cancer is feasible. The study, coordinated by the Institut Jules Bordet and the Breast International Group, aimed to determine whether biopsies and blood could be collected from women with metastatic breast cancer across Europe and sent to a central laboratory for targeted gene sequencing. Genetic information was successfully obtained for 26 of the 41 participants, 19 of whom had mutations that could be targeted with a known drug, potentially influencing treatment decision-making. They concluded that genomic testing is logistically ready for international molecular screening in routine clinical settings laying the groundwork for the parent European AURORA molecular screening programme which aims at recruiting 1300 metastatic breast cancer patients. However, technical challenges remain to be addressed to ensure the accuracy and robustness across different sequencing platforms.
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Preparing pathology for precision medicine: challenges and opportunities. Virchows Arch 2017; 471:141-146. [PMID: 28512674 DOI: 10.1007/s00428-017-2141-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 01/05/2023]
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Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2017; 19:341-365. [PMID: 28341590 DOI: 10.1016/j.jmoldx.2017.01.011] [Citation(s) in RCA: 433] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics. The recommendations emphasize the role of laboratory director in using an error-based approach that identifies potential sources of errors that may occur throughout the analytical process and addressing these potential errors through test design, method validation, or quality controls so that no harm comes to the patient. The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.
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Affiliation(s)
- Lawrence J Jennings
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois.
| | - Maria E Arcila
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Corless
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Suzanne Kamel-Reid
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ira M Lubin
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Pfeifer
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Washington University School of Medicine, St. Louis, Missouri
| | | | - Karl V Voelkerding
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Marina N Nikiforova
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
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Thomas M, Sukhai MA, Zhang T, Dolatshahi R, Harbi D, Garg S, Misyura M, Pugh T, Stockley TL, Kamel-Reid S. Integration of Technical, Bioinformatic, and Variant Assessment Approaches in the Validation of a Targeted Next-Generation Sequencing Panel for Myeloid Malignancies. Arch Pathol Lab Med 2017; 141:759-775. [PMID: 28557600 DOI: 10.5858/arpa.2016-0547-ra] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes. OBJECTIVE - To apply a systematic approach to evaluate and validate a commercially available next-generation sequencing panel (TruSight Myeloid Sequencing Panel, Illumina, San Diego, California) targeting 54 genes. In this manuscript, we focused on the parameters that were used to evaluate assay performance characteristics. DATA SOURCES - Analytical validation was performed using samples containing known variants that had been identified previously. Cases were selected from different disease types, with variants in a range of genes. Panel performance characteristics were assessed and genomic regions requiring additional analysis or wet-bench approaches identified. CONCLUSIONS - We validated the performance characteristics of a myeloid next-generation sequencing panel for detection of variants. The TruSight Myeloid Sequencing Panel covers more than 95% of target regions with depth greater than 500×. However, because of unique variant types such as large insertions or deletions or genomic regions of high GC content, variants in CEBPA, FLT3, and CALR required supplementation with non-next-generation sequencing assays or with informatics approaches to address deficiencies in performance. The use of multiple bioinformatics approaches (2 variant callers and informatics scripts) allows for maximizing calling of true positives, while identifying limitations in using either method alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Suzanne Kamel-Reid
- From the Laboratory Medicine Program, Advanced Molecular Diagnostics Laboratory, Departments of Pathology and Genetics (Drs Thomas, Sukhai, Garg, Misyura, Stockley, and Kamel-Reid), the Princess Margaret Cancer Centre (Drs Thomas, Sukhai, Garg, Misyura, Pugh, Stockley, and Kamel-Reid and Ms Zhang), and High Performance Computing and Bioinformatics Services, Princess Margaret Genomics Centre (Dr Harbi and Mr Dolatshahi), University Health Network, Toronto, Ontario, Canada; and the Departments of Medical Biophysics (Drs Pugh and Kamel-Reid) and Laboratory Medicine and Pathobiology (Drs Stockley and Kamel-Reid), The University of Toronto, Toronto, Ontario, Canada
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Next-Generation Sequencing in Cancer Diagnostics. J Mol Diagn 2016; 18:813-816. [PMID: 27664753 DOI: 10.1016/j.jmoldx.2016.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022] Open
Abstract
This commentary highlights the article by Misyura et al that underscores the use of next-generation sequencing platforms for detection and verification of somatic variants.
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