1
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Meireles SI, Cruz MV, de Godoy CD, de Testagrossa L. Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels. Diagn Cytopathol 2024; 52:171-182. [PMID: 38124281 DOI: 10.1002/dc.25267] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE. METHODS We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel. RESULTS The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples. CONCLUSIONS Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.
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Affiliation(s)
- Sibele Inácio Meireles
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Mariana Vargas Cruz
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Carla Daniele de Godoy
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
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2
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Chen H, Wang B, Zhang Y, Shu Y, Dong H, Zhao Q, Yang C, Li J, Duan X, Zhou Q. A unified DNA- and RNA-based NGS strategy for the analysis of multiple types of variants at the dual nucleic acid level in solid tumors. J Clin Lab Anal 2023; 37:e24977. [PMID: 37877443 PMCID: PMC10681543 DOI: 10.1002/jcla.24977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/27/2023] [Accepted: 10/15/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is a powerful and suitable approach to comprehensively identify multiple types of variants in tumors. RNA-based NGS is increasingly playing an important role in precision oncology. Both parallel and sequential DNA- and RNA-based approaches are expensive, burdensome, and have long turnaround times, which can be impractical in clinical practice. A streamlined, unified DNA- and RNA-based NGS approach is urgently needed in clinical practice. METHODS A DNA/RNA co-hybrid capture sequencing (DRCC-Seq) approach was designed to capture pre-capture DNA and RNA libraries in a single tube and convert them into one NGS library. The performance of the DRCC-Seq approach was evaluated by a panel of reference standards and clinical samples. RESULTS The average depth, DNA data ratio, capture ratio, and target coverage 250 (×) of the DNA panel data had a negative correlation with an increase in the proportion of RNA probes. The SNVs, indels, fusions, and MSI status were not affected by the proportion of RNA probes, but the copy numbers of the target genes were higher than expected in the standard materials, and many unexpected gene amplifications were found using D:R (1:2) and D:R (1:4) probe panels. The optimal ratio of DNA and RNA probes in the combined probe panel was 1:1 using the DRCC-Seq approach. The DRCC-Seq approach was feasible and reliable for detecting multiple types of variants in reference standards and real-world clinical samples. CONCLUSIONS The DRCC-Seq approach is more cost-effective, with a shorter turnaround time and lower labor requirements than either parallel or sequential targeted DNA NGS and RNA NGS. It is feasible to identify multiple genetic variations at the DNA and RNA levels simultaneously in clinical practice.
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Affiliation(s)
- Huijuan Chen
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- Computer Network Information Center, Chinese Academy of SciencesBeijingChina
- WillingMed Technology Beijing Co., Ltd.BeijingChina
| | - Bing Wang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yiran Zhang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yingshuang Shu
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Henan Dong
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Qian Zhao
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Chunyan Yang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Jianji Li
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Xiaohong Duan
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
- Institute of Disaster and Emergency Medicine, Medical CollegeTianjin UniversityTianJinChina
| | - Qiming Zhou
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
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3
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King AD, Deirawan H, Klein PA, Dasgeb B, Dumur CI, Mehregan DR. Next-generation sequencing in dermatology. Front Med (Lausanne) 2023; 10:1218404. [PMID: 37841001 PMCID: PMC10570430 DOI: 10.3389/fmed.2023.1218404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023] Open
Abstract
Over the past decade, Next-Generation Sequencing (NGS) has advanced our understanding, diagnosis, and management of several areas within dermatology. NGS has emerged as a powerful tool for diagnosing genetic diseases of the skin, improving upon traditional PCR-based techniques limited by significant genetic heterogeneity associated with these disorders. Epidermolysis bullosa and ichthyosis are two of the most extensively studied genetic diseases of the skin, with a well-characterized spectrum of genetic changes occurring in these conditions. NGS has also played a critical role in expanding the mutational landscape of cutaneous squamous cell carcinoma, enhancing our understanding of its molecular pathogenesis. Similarly, genetic testing has greatly benefited melanoma diagnosis and treatment, primarily due to the high prevalence of BRAF hot spot mutations and other well-characterized genetic alterations. Additionally, NGS provides a valuable tool for measuring tumor mutational burden, which can aid in management of melanoma. Lastly, NGS demonstrates promise in improving the sensitivity of diagnosing cutaneous T-cell lymphoma. This article provides a comprehensive summary of NGS applications in the diagnosis and management of genodermatoses, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma, highlighting the impact of NGS on the field of dermatology.
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Affiliation(s)
- Andrew D. King
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hany Deirawan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
| | | | - Bahar Dasgeb
- Department of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Catherine I. Dumur
- Bernhardt Laboratories, Sonic Healthcare Anatomic Pathology Division, Jacksonville, FL, United States
| | - Darius R. Mehregan
- Department of Dermatology, Wayne State University School of Medicine, Detroit, MI, United States
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4
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Finall A, Murphy K, Frazer RD. Improving care of melanoma patients through efficient, integrated cellular-molecular pathology workflows using tissue samples with low tumour nuclear content. J Clin Pathol 2023; 76:612-617. [PMID: 35428674 DOI: 10.1136/jclinpath-2022-208194] [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: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/04/2022]
Abstract
AIMS The aim of this quality improvement project was to improve the turnaround time of B-raf proto-oncogene (BRAF) mutation testing in patients with malignant melanoma to support oncologists in making timely treatment decisions. METHODS This is a prospective in-house verification of the Idylla BRAF test as compared with DNA panel next-generation sequencing (NGS) performed at an external laboratory. RESULTS The Idylla BRAF test had an overall concordance of 95% compared with NGS. This was considered sufficiently good for use in patients with a poor performance status who were at risk of rapid clinical deterioration. Reliable results can be generated using the Idylla BRAF test in tissue sections with tumour neoplastic cell content below 50%. We present a multidisciplinary clinical care algorithm to support dual testing. CONCLUSIONS The Idylla BRAF test has the potential to make a significant positive impact on progression-free survival of malignant melanoma patients due to its rapid turnaround time. The Idylla BRAF test can be used as an adjunct to NGS for timely management of patients, particularly those with a poor performance status at presentation.
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Affiliation(s)
- Alison Finall
- Cellular Pathology, Swansea Bay University Health Board, Swansea, UK
- Medical School, Swansea University, Swansea, UK
| | - Kate Murphy
- Cellular and Molecular Pathology Department, Swansea Bay University Health Board, Swansea, UK
- Institute of Life Science, Swansea University, Swansea, UK
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5
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Koga H, Takagi M, Teye K, Kuwahara-Sakurada F, Ishii N, Hamada T, Nakama T. Mosaicism for ATP2A2 Mutation and Mutant Allelic Fractions Detected by Droplet Digital PCR in Simple Segmental Darier Disease. Acta Derm Venereol 2023; 103:adv12337. [PMID: 37448212 PMCID: PMC10391532 DOI: 10.2340/actadv.v103.12337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Abstract is missing (Short communication)
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Affiliation(s)
- Hiroshi Koga
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
| | - Marie Takagi
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
| | | | - Fumi Kuwahara-Sakurada
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
| | - Norito Ishii
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
| | - Takahiro Hamada
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan.
| | - Takekuni Nakama
- Department of Dermatology, Kurume University School of Medicine, 67 Asahimachi, Kurume, Fukuoka 830-0011, Japan
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6
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Lee YJ, Woo HY, Kim YN, Park J, Nam EJ, Kim SW, Kim S, Kim YT, Park E, Joung JG, Lee JY. Dynamics of the Tumor Immune Microenvironment during Neoadjuvant Chemotherapy of High-Grade Serous Ovarian Cancer. Cancers (Basel) 2022; 14:cancers14092308. [PMID: 35565437 PMCID: PMC9104540 DOI: 10.3390/cancers14092308] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Neoadjuvant chemotherapy (NAC) induced a dynamic change in the TIME that increased the level of immune infiltration, leading to a high number of CD8 T cells with enhanced immune activity. However, increased immune infiltration and immune activity did not present any survival benefit, probably due to concomitant immunosuppression associated with an increase in the proportion of Foxp3+ regulatory T cells. Our results could provide therapeutic strategies to improve the survival benefit from immunotherapies in an NAC setting. Abstract The dynamic changes in the tumor immune microenvironment (TIME) triggered by neoadjuvant chemotherapy (NAC) have not been clearly defined in advanced-stage ovarian cancer. We analyzed the immunologic changes induced by NAC to correlate them with clinical outcomes. We compared the changes in the immune infiltration of high-grade serous carcinoma biopsies before and after NAC via immunohistochemistry (147 paired samples) and whole transcriptome sequencing (35 paired samples). Immunohistochemistry showed significantly increased PD-L1 levels and TIL levels after NAC. Whole transcriptome sequencing revealed that the stromal score, immune score, and cytolytic activity score significantly increased after NAC. An increased tumor-infiltrating lymphocyte (TIL) level in response to NAC was associated with shorter progression-free survival compared with decreased TIL level after NAC. In tumors with increased TIL levels after NAC, the relative fraction of CD8 T cells and regulatory T cells significantly increased with immunohistochemistry. Post-NAC tumors were enriched in gene sets associated with immune signaling pathways, such as regulatory T cell and JAK/STAT signaling pathways. NAC induced dynamic changes in the TIME that increased TIL levels, but their high abundance did not impart any survival benefit. Our data may provide therapeutic strategies to improve the survival benefit from immunotherapies in ovarian cancer.
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Affiliation(s)
- Yong Jae Lee
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Ha Young Woo
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul 02447, Korea;
| | - Yoo-Na Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Junsik Park
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Eun Ji Nam
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Sunghoon Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Young Tae Kim
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
| | - Eunhyang Park
- Department of Pathology, Yonsei University College of Medicine, Seoul 03722, Korea;
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea
- Correspondence: (J.-G.J.); (J.-Y.L.)
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Institute of Women’s Medical Life Science, Yonsei University College of Medicine, Seoul 03722, Korea; (Y.J.L.); (Y.-N.K.); (J.P.); (E.J.N.); (S.W.K.); (S.K.); (Y.T.K.)
- Correspondence: (J.-G.J.); (J.-Y.L.)
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7
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Safai B, Wu AG, Hamby CV. Prognostic Biomarkers in Melanoma: Tailoring Treatments to the Patient. THE JOURNAL OF CLINICAL AND AESTHETIC DERMATOLOGY 2021; 14:44-48. [PMID: 35096254 PMCID: PMC8794494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND It is often difficult to accurately predict how a melanoma will progress because melanomas can be so diverse in their genetic and histological makeup. OBJECTIVE We sought to characterize the current state and progression of biomedical markers towards their utilization as prognostic indicators for patients with melanoma. METHODS A literature search of the research repository databases PubMed and GoogleScholar was conducted using the following inclusion criteria: (1) published within the last 10 years, and (2) use of overall survival, disease progression, or clinical outcome as primary endpoints. Search terms included various permutations of "biomarkers," "prognostic," "immunologic," "serologic," "visual," and "melanoma." Results were evaluated for statistical power, results significance, and experimental design integrity. RESULTS The prognostic capabilities of clinical tests for malignant melanoma have made great strides in the last few years, with several serologic and immunohistochemical biomarkers being preliminarily linked to various measures of clinical prognosis. While clinical feasibility of a single sensitive and specific biomarker remains unfeasible, use of select combinations of tested biomarkers remain viable. CONCLUSION Diagnostic and prognostic genetic assays have begun to cross over from research to commercial application, giving physicians additional tools during the early stages of diagnosis to optimize and individualize treatments.
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Affiliation(s)
- Bijan Safai
- Dr. Safai is with the Department of Dermatology, Metropolitan Hospital in New York, New York
- Mr. Wu and Dr. Hamby are with New York Medical College School of Medicine in Valhalla, New York
| | - Albert G Wu
- Dr. Safai is with the Department of Dermatology, Metropolitan Hospital in New York, New York
- Mr. Wu and Dr. Hamby are with New York Medical College School of Medicine in Valhalla, New York
| | - Carl V Hamby
- Dr. Safai is with the Department of Dermatology, Metropolitan Hospital in New York, New York
- Mr. Wu and Dr. Hamby are with New York Medical College School of Medicine in Valhalla, New York
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8
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Masoumi-Moghaddam S, Lundy J, Gao H, Rathi V, Swan M, Desmond C, Bhutani MS, Southey MC, Vaughan R, Varma P, Tagkalidis P, Holt BA, C Pilgrim CH, Segelov E, Lee B, Harris M, Strickland A, Frentzas S, Zalcberg J, Jenkins B, Croagh D. The EUS molecular evaluation of pancreatic cancer: A prospective multicenter cohort trial. Endosc Ultrasound 2021; 10:335-343. [PMID: 34558422 PMCID: PMC8544009 DOI: 10.4103/eus-d-20-00230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background and Objectives: Patients with locally advanced or metastatic pancreatic ductal adenocarcinoma (A-PDAC) are not candidates for surgical resection and are often offered palliative chemotherapy. The ready availability of a safe and effective tumor sampling technique to provide material for both diagnosis and comprehensive genetic profiling is critical for informing precision medicine in A-PDAC, thus potentially increasing survival. The aim of this study is to examine the feasibility and benefits of routine comprehensive genomic profiling (CGP) of A-PDAC using EUS-FNA material. Methods: This is a prospective cohort study to test the clinical utility of fresh frozen or archival EUS-FNA samples in providing genetic material for CGP. The results of the CGP will be reviewed at a molecular tumor board. The proportion of participants that have a change in their treatment recommendations based on their individual genomic profiling will be assessed. Correlations between CGP and stage, prognosis, response to treatment and overall survival will also be investigated. This study will open to recruitment in 2020, with a target accrual of 150 A-PDAC patients within 36 months, with a 2-year follow-up. It is expected that the majority of participants will be those who have already consented for their tissue to be biobanked in the Victorian Pancreatic Cancer Biobank at the time of diagnostic EUS-FNA. Patients without archival or biobanked material that is suitable for CGP may be offered a EUS-FNA procedure for the purposes of obtaining fresh frozen material. Discussion: This trial is expected to provide crucial data regarding the feasibility of routine CGP of A-PDAC using EUS-FNA material. It will also provide important information about the impact of this methodology on patients’ survival.
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Affiliation(s)
- Samar Masoumi-Moghaddam
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research; Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University; Department of Surgery, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Joanne Lundy
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research; Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University; Department of Surgery, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Hugh Gao
- Department of Surgery, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Vivek Rathi
- Department of Genetics and Molecular Pathology, Monash Health, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Michael Swan
- Department of Gastroenterology, Monash Medical Centre, Monash Health, Clayton, Victoria, Australia
| | - Christopher Desmond
- Department of Gastroenterology, Monash Medical Centre, Monash Health, Clayton, Victoria, Australia
| | - Manoop S Bhutani
- Department of Gastroenterology, Hepatology and Nutrition, UT MD Anderson Cancer Centre, Houston, TX, USA
| | - Melissa C Southey
- Department of Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton; Department of Pathology, Epidemiology Laboratory, The University of Melbourne, Parkville, Victoria, Australia
| | - Rhys Vaughan
- Department of Gastroenterology, Austin Health, Heidelberg; Department of Medicine, The University of Melbourne (Austin Health), Melbourne, Victoria, Australia
| | - Poornima Varma
- Department of Gastroenterology, Austin Health, Heidelberg, Victoria, Australia
| | - Peter Tagkalidis
- Department of Gastroenterology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Bronte A Holt
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia
| | | | - Eva Segelov
- Department of Oncology, Faculty of Medicine, Nursing and Health Sciences and School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Belinda Lee
- Department of Oncology, Northern Health, Epping, Victoria; Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| | - Marion Harris
- Department of Oncology, Faculty of Medicine, Nursing and Health Sciences and School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Andrew Strickland
- Department of Oncology, Faculty of Medicine, Nursing and Health Sciences and School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Sophia Frentzas
- Department of Oncology, Faculty of Medicine, Nursing and Health Sciences and School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - John Zalcberg
- Department of Gastroenterology, Royal Melbourne Hospital; School of Public Health and Preventative Medicine, Monash University, Melbourne, Victoria, Australia
| | - Brendan Jenkins
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research; Department of Molecular Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Daniel Croagh
- Department of Surgery, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
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9
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Serna-Blasco R, Sánchez-Herrero E, Berrocal Renedo M, Calabuig-Fariñas S, Molina-Vila MÁ, Provencio M, Romero A. R-Score: A New Parameter to Assess the Quality of Variants' Calls Assessed by NGS Using Liquid Biopsies. BIOLOGY 2021; 10:954. [PMID: 34681053 PMCID: PMC8533561 DOI: 10.3390/biology10100954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 11/17/2022]
Abstract
Next-generation sequencing (NGS) has enabled a deeper knowledge of the molecular landscape in non-small cell lung cancer (NSCLC), identifying a growing number of targetable molecular alterations in key genes. However, NGS profiling of liquid biopsies risk for false positive and false negative calls and parameters assessing the quality of NGS calls remains lacking. In this study, we have evaluated the positive percent agreement (PPA) between NGS and digital PCR calls when assessing EGFR mutation status using 85 plasma samples from 82 EGFR-positive NSCLC patients. According to our data, variant allele fraction (VAF) was significantly lower in discordant calls and the median of the absolute values of all pairwise differences (MAPD) was significantly higher in discordant calls (p < 0.001 in both cases). Based on these results, we propose a new parameter that integrates both variables, named R-score. Next, we sought to evaluate the PPA for EGFR mutation calls between two independent NGS platforms using a subset of 40 samples from the same cohort. Remarkably, there was a significant linear correlation between the PPA and the R-score (r = 0.97; p < 0.001). Specifically, the PPA of samples with an R-score ≤ -1.25 was 95.83%, whereas PPA falls to 81.63% in samples with R-score ≤ 0.25. In conclusion, R-score significantly correlates with PPA and can assist laboratory medicine specialists and data scientists to select reliable variants detected by NGS.
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Affiliation(s)
- Roberto Serna-Blasco
- Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain; (R.S.-B.); (E.S.-H.); (M.B.R.)
| | - Estela Sánchez-Herrero
- Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain; (R.S.-B.); (E.S.-H.); (M.B.R.)
- Atrys Health, I+D Department, 08025 Barcelona, Spain
| | - María Berrocal Renedo
- Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain; (R.S.-B.); (E.S.-H.); (M.B.R.)
| | - Silvia Calabuig-Fariñas
- CIBERONC, Liquid Biopsy WM, 28029 Madrid, Spain;
- Mixed Unit TRIAL, Príncipe Felipe Research Center & General University Hospital of Valencia Research Foundation, 46012 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Miguel Ángel Molina-Vila
- Laboratory of Oncology/Pangaea Oncology, Quirón-Dexeus University Hospital, 08028 Barcelona, Spain;
| | - Mariano Provencio
- Medical Oncology, University Hospital Puerta de Hierro, 28222 Madrid, Spain;
| | - Atocha Romero
- Liquid Biopsy Laboratory, University Hospital Puerta de Hierro, 28222 Madrid, Spain; (R.S.-B.); (E.S.-H.); (M.B.R.)
- Medical Oncology, University Hospital Puerta de Hierro, 28222 Madrid, Spain;
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10
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Bidshahri R, Fakhfakh K, McNeil K, Won JR, Wolber R, Hughesman C, Haynes C. Analysis of
KRAS
G12
/
G13
in colorectal cancer using an economical digital
PCR
assay that unequivocally differentiates missense and synonymous alleles. CAN J CHEM ENG 2021. [DOI: 10.1002/cjce.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Roza Bidshahri
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
| | - Kareem Fakhfakh
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
| | - Kelly McNeil
- Department of Genetics and Molecular Diagnostics British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Jennifer R. Won
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
| | - Robert Wolber
- Canadian Immunohistochemistry Quality Control, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver British Columbia Canada
- Department of Pathology Lion's Gate Hospital North Vancouver British Columbia Canada
| | - Curtis Hughesman
- Cancer Genetics and Genomics Lab British Columbia Cancer Agency Vancouver British Columbia Canada
| | - Charles Haynes
- Michael Smith Laboratories University of British Columbia Vancouver British Columbia Canada
- Biomedical Engineering Program University of British Columbia Vancouver British Columbia Canada
- Department of Chemical and Biological Engineering University of British Columbia Vancouver British Columbia Canada
- Genome Sciences and Technology Program Vancouver British Columbia Canada
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11
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Boyle TA, Mondal AK, Saeed-Vafa D, Ananth S, Ahluwalia P, Kothapalli R, Chaubey A, Roberts E, Qin D, Magliocco AM, Rojiani AM, Kolhe R. Guideline-Adherent Clinical Validation of a Comprehensive 170-Gene DNA/RNA Panel for Determination of Small Variants, Copy Number Variations, Splice Variants, and Fusions on a Next-Generation Sequencing Platform in the CLIA Setting. Front Genet 2021; 12:503830. [PMID: 34093633 PMCID: PMC8172991 DOI: 10.3389/fgene.2021.503830] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
We describe the clinical validation of a targeted DNA and RNA-based next-generation sequencing (NGS) assay at two clinical molecular diagnostic laboratories. This assay employs simultaneous DNA and RNA analysis of all coding exons to detect small variants (single-nucleotide variants, insertions, and deletions) in 148 genes, amplifications in 59 genes, and fusions and splice variants in 55 genes. During independent validations at two sites, 234 individual specimens were tested, including clinical formalin-fixed, paraffin-embedded (FFPE) tumor specimens, reference material, and cell lines. Samples were prepared using the Illumina TruSight Tumor 170 (TST170) kit, sequenced with Illumina sequencers, and the data were analyzed using the TST170 App. At both sites, TST170 had ≥98% success for ≥250× depth for ≥95% of covered positions. Variant calling was accurate and reproducible at allele frequencies ≥5%. Limit of detection studies determined that inputs of ≥50 ng of DNA (with ≥3.3 ng/μl) and ≥50 ng RNA (minimum of 7 copies/ng) were optimal for high analytical sensitivity. The TST170 assay results were highly concordant with prior results using different methods across all variant categories. Optimization of nucleic acid extraction and DNA shearing, and quality control following library preparation is recommended to maximize assay success rates. In summary, we describe the validation of comprehensive and simultaneous DNA and RNA-based NGS testing using TST170 at two clinical sites.
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Affiliation(s)
- Theresa A Boyle
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Daryoush Saeed-Vafa
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Ravi Kothapalli
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Evans Roberts
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Dahui Qin
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Anthony M Magliocco
- Department of Pathology and Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Amyn M Rojiani
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA, United States
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12
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Hu T, Chitnis N, Monos D, Dinh A. Next-generation sequencing technologies: An overview. Hum Immunol 2021; 82:801-811. [PMID: 33745759 DOI: 10.1016/j.humimm.2021.02.012] [Citation(s) in RCA: 248] [Impact Index Per Article: 82.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
Since the days of Sanger sequencing, next-generation sequencing technologies have significantly evolved to provide increased data output, efficiencies, and applications. These next generations of technologies can be categorized based on read length. This review provides an overview of these technologies as two paradigms: short-read, or "second-generation," technologies, and long-read, or "third-generation," technologies. Herein, short-read sequencing approaches are represented by the most prevalent technologies, Illumina and Ion Torrent, and long-read sequencing approaches are represented by Pacific Biosciences and Oxford Nanopore technologies. All technologies are reviewed along with reported advantages and disadvantages. Until recently, short-read sequencing was thought to provide high accuracy limited by read-length, while long-read technologies afforded much longer read-lengths at the expense of accuracy. Emerging developments for third-generation technologies hold promise for the next wave of sequencing evolution, with the co-existence of longer read lengths and high accuracy.
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Affiliation(s)
- Taishan Hu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Nilesh Chitnis
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Surgery, Baylor College of Medicine, Houston, TX, United States
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Anh Dinh
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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13
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Doan RN, Miller MB, Kim SN, Rodin RE, Ganz J, Bizzotto S, Morillo KS, Huang AY, Digumarthy R, Zemmel Z, Walsh CA. MIPP-Seq: ultra-sensitive rapid detection and validation of low-frequency mosaic mutations. BMC Med Genomics 2021; 14:47. [PMID: 33579278 PMCID: PMC7881461 DOI: 10.1186/s12920-021-00893-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mosaic mutations contribute to numerous human disorders. As such, the identification and precise quantification of mosaic mutations is essential for a wide range of research applications, clinical diagnoses, and early detection of cancers. Currently, the low-throughput nature of single allele assays (e.g., allele-specific ddPCR) commonly used for genotyping known mutations at very low alternate allelic fractions (AAFs) have limited the integration of low-level mosaic analyses into clinical and research applications. The growing importance of mosaic mutations requires a more rapid, low-cost solution for mutation detection and validation. METHODS To overcome these limitations, we developed Multiple Independent Primer PCR Sequencing (MIPP-Seq) which combines the power of ultra-deep sequencing and truly independent assays. The accuracy of MIPP-seq to quantifiable detect and measure extremely low allelic fractions was assessed using a combination of SNVs, insertions, and deletions at known allelic fractions in blood and brain derived DNA samples. RESULTS The Independent amplicon analyses of MIPP-Seq markedly reduce the impact of allelic dropout, amplification bias, PCR-induced, and sequencing artifacts. Using low DNA inputs of either 25 ng or 50 ng of DNA, MIPP-Seq provides sensitive and quantitative assessments of AAFs as low as 0.025% for SNVs, insertion, and deletions. CONCLUSIONS MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
| | - Michael B Miller
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sonia N Kim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Katherine S Morillo
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - August Yue Huang
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Reethika Digumarthy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Zachary Zemmel
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Center for Life Sciences 15062, 300 Longwood Avenue, BCH3150, Boston, MA, 02115, USA.
- Allen Discovery Center for Human Brain Evolution, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA.
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14
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Quindipan C, Cotter JA, Ji J, Mitchell WG, Moke DJ, Navid F, Thomas SM, VanHirtum-Das M, Wang L, Saitta SC, Biegel JA, Hiemenz MC. Custom Pediatric Oncology Next-Generation Sequencing Panel Identifies Somatic Mosaicism in Archival Tissue and Enhances Targeted Clinical Care. Pediatr Neurol 2021; 114:55-59. [PMID: 33221597 DOI: 10.1016/j.pediatrneurol.2020.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/06/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Disorders in the PIK3CA-related overgrowth spectrum because of somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore archival tissue may be the only relevant available specimen for testing. Although this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders. METHODS PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing panel (OncoKids) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We used OncoKids on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by next-generation sequencing ranged from two to 13 years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention. RESULTS PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8% to 11%) than in brain (20% to 32%) and lipomatous (16% to 23%) tissues. CONCLUSIONS Our study highlights the clinical utility of using a robust, oncology-focused next-generation sequencing assay to identify PIK3CA mosaicism in noncancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis, which can then be used to improve health care management.
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Affiliation(s)
- Catherine Quindipan
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Wendy G Mitchell
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Diana J Moke
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Fariba Navid
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Stefanie M Thomas
- Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California; Division of Hematology and Oncology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California
| | - Michele VanHirtum-Das
- Division of Pediatric Neurology, Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, California; Department of Pediatrics, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Larry Wang
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
| | - Sulagna C Saitta
- Division of Medical Genets, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, California
| | - Jaclyn A Biegel
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine at the University of Southern California, Los Angeles, California
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15
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Louveau B, Jouenne F, Têtu P, Sadoux A, Gruber A, Lopes E, Delyon J, Serror K, Marco O, Da Meda L, Ndiaye A, Lermine A, Dumaz N, Battistella M, Baroudjian B, Lebbe C, Mourah S. A Melanoma-Tailored Next-Generation Sequencing Panel Coupled with a Comprehensive Analysis to Improve Routine Melanoma Genotyping. Target Oncol 2020; 15:759-771. [PMID: 33151472 DOI: 10.1007/s11523-020-00764-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Tumor molecular deciphering is crucial in clinical management. Pan-cancer next-generation sequencing panels have moved towards exhaustive molecular characterization. However, because of treatment resistance and the growing emergence of pharmacological targets, tumor-specific customized panels are needed to guide therapeutic strategies. OBJECTIVE The objective of this study was to present such a customized next-generation sequencing panel in melanoma. METHODS Melanoma patients with somatic molecular profiling performed as part of routine care were included. High-throughput sequencing was performed with a melanoma tailored next-generation sequencing panel of 64 genes involved in molecular classification, prognosis, theranostic, and therapeutic resistance. Single nucleotide variants and copy number variations were screened, and a comprehensive molecular analysis identified clinically relevant alterations. RESULTS Four hundred and twenty-one melanoma cases were analyzed (before any treatment initiation for 94.8% of patients). After bioinformatic prioritization, we uncovered 561 single nucleotide variants, 164 copy number variations, and four splice-site mutations. At least one alteration was detected in 368 (87.4%) lesions, with BRAF, NRAS, CDKN2A, CCND1, and MET as the most frequently altered genes. Among patients with BRAFV600 mutated melanoma, 44.5% (77 of 173) harbored at least one concurrent alteration driving potential resistance to mitogen-activated protein kinase inhibitors. In patients with RAS hotspot mutated lesions and in patients with neither BRAFV600 nor RAS hotspot mutations, alterations constituting potential pharmacological targets were found in 56.9% (66 of 116) and 47.7% (63 of 132) of cases, respectively. CONCLUSIONS Our tailored next-generation sequencing assay coupled with a comprehensive analysis may improve therapeutic management in a significant number of patients with melanoma. Updating such a panel and implementing multi-omic approaches will further enhance patients' clinical management.
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Affiliation(s)
- Baptiste Louveau
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Fanélie Jouenne
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France.,Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Pauline Têtu
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aurélie Sadoux
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Aurélia Gruber
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Eddie Lopes
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France
| | - Julie Delyon
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Kevin Serror
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Oren Marco
- Department of Plastic, Reconstructive and Esthetic Surgery, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Da Meda
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Aminata Ndiaye
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alban Lermine
- MOABI-APHP Bioinformatics Platform-WIND-DSI, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicolas Dumaz
- INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France
| | - Maxime Battistella
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Pathology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Barouyr Baroudjian
- Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céleste Lebbe
- Université de Paris, Paris, France.,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.,Department of Dermatology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Samia Mourah
- Department of Pharmacology and Solid Tumor Genomics, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, 1 Avenue Claude Vellefaux, 75475, Paris Cedex 10, France. .,Université de Paris, Paris, France. .,INSERM UMR-S 976, Team 1, Human Immunology Pathophysiology and Immunotherapy (HIPI), Paris, France.
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16
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Prieto-Potin I, Carvajal N, Plaza-Sánchez J, Manso R, Aúz-Alexandre CL, Chamizo C, Zazo S, López-Sánchez A, Rodríguez-Pinilla SM, Camacho L, Longarón R, Bellosillo B, Somoza R, Hernández-Losa J, Fernández-Soria VM, Ramos-Ruiz R, Cristóbal I, García-Foncillas J, Rojo F. Validation and clinical application of a targeted next-generation sequencing gene panel for solid and hematologic malignancies. PeerJ 2020; 8:e10069. [PMID: 33083132 PMCID: PMC7546223 DOI: 10.7717/peerj.10069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/09/2020] [Indexed: 01/29/2023] Open
Abstract
Background Next-generation sequencing (NGS) is a high-throughput technology that has become widely integrated in molecular diagnostics laboratories. Among the large diversity of NGS-based panels, the Trusight Tumor 26 (TsT26) enables the detection of low-frequency variants across 26 genes using the MiSeq platform. Methods We describe the inter-laboratory validation and subsequent clinical application of the panel in 399 patients presenting a range of tumor types, including gastrointestinal (GI, 29%), hematologic (18%), lung (13%), gynecological and breast (8% each), among others. Results The panel is highly accurate with a test sensitivity of 92%, and demonstrated high specificity and positive predictive values (95% and 96%, respectively). Sequencing testing was successful in two-thirds of patients, while the remaining third failed due to unsuccessful quality-control filtering. Most detected variants were observed in the TP53 (28%), KRAS (16%), APC (10%) and PIK3CA (8%) genes. Overall, 372 variants were identified, primarily distributed as missense (81%), stop gain (9%) and frameshift (7%) altered sequences and mostly reported as pathogenic (78%) and variants of uncertain significance (19%). Only 14% of patients received targeted treatment based on the variant determined by the panel. The variants most frequently observed in GI and lung tumors were: KRAS c.35G > A (p.G12D), c.35G > T (p.G12V) and c.34G > T (p.G12C). Conclusions Prior panel validation allowed its use in the laboratory daily practice by providing several relevant and potentially targetable variants across multiple tumors. However, this study is limited by high sample inadequacy rate, raising doubts as to continuity in the clinical setting.
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Affiliation(s)
- Iván Prieto-Potin
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Nerea Carvajal
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jenifer Plaza-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Rebeca Manso
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Carmen Laura Aúz-Alexandre
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Cristina Chamizo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Sandra Zazo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Almudena López-Sánchez
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | | | - Laura Camacho
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Raquel Longarón
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Del Mar Medical Research Institute, Barcelona, Spain
| | - Rosa Somoza
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | | | - Ion Cristóbal
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Jesús García-Foncillas
- Translational Oncology Division, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Federico Rojo
- Department of Pathology, CIBERONC, UAM, Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
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17
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Woo HY, Na K, Yoo J, Chang JH, Park YN, Shim HS, Kim SH. Glioblastomas harboring gene fusions detected by next-generation sequencing. Brain Tumor Pathol 2020; 37:136-144. [PMID: 32761533 DOI: 10.1007/s10014-020-00377-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022]
Abstract
Oncogenic gene fusions have been reported in diffuse gliomas and may serve as potential therapeutic targets. Here, using next-generation sequencing analysis (Illumina TruSight Tumor 170 panel), we analyzed a total of 356 diffuse gliomas collected from 2017 to 2019 to evaluate clinical, pathological, and genetic features of gene fusion. We found 53 cases of glioblastomas harboring the following oncogenic gene fusions: MET (n = 18), EGFR (n = 14), FGFR (n = 12), NTRK (n = 5), RET (n = 2), AKT3 (n = 1), and PDGFRA fusions (n = 1). Gene fusions were consistently observed in both IDH-wildtype and IDH-mutant glioblastomas (8.8% and 9.4%, p = 1.000). PTPRZ1-MET fusion was the only fusion that genetically resembled secondary glioblastomas (i.e., high frequency of IDH mutation, ATRX loss, TP53 mutation, and absence of EGFR amplification), whereas other gene fusion types were similar to primary glioblastomas (i.e., high frequency of IDH-wildtype, TERT mutation, EGFR amplification, and PTEN mutation). In IDH-wildtype glioblastoma patients, multivariable analysis revealed that the PTPRZ1-MET fusion was associated with poor progression-free survival (HR [95% CI]: 5.42 (1.72-17.05), p = 0.004). Additionally, we described two novel cases of CCDC6-RET fusion in glioma. Collectively, our findings indicate that targetable gene fusions are associated with aggressive biological behavior and can aid the clinical treatment strategy for glioma patients.
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Affiliation(s)
- Ha Young Woo
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, 26 Kyungheedae-Ro, Dongdaemun-gu, Seoul, 02447, South Korea
| | - Jihwan Yoo
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Young Nyun Park
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, 50-1, Yonsei-Ro, Seodaemun-gu, Seoul, 03722, South Korea.
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Obeng RC, Arnold RS, Ogan K, Master VA, Pattaras JG, Petros JA, Osunkoya AO. Molecular characteristics and markers of advanced clear cell renal cell carcinoma: Pitfalls due to intratumoral heterogeneity and identification of genetic alterations associated with metastasis. Int J Urol 2020; 27:790-797. [PMID: 32638444 DOI: 10.1111/iju.14302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES To identify clear cell renal cell carcinoma-related gene mutations potentially associated with aggressive disease, sarcomatoid differentiation or poor prognosis. METHODS We carried out genomic analysis of 217 tumor foci from 25 patients with conventional clear cell renal cell carcinoma (14 patients), clear cell renal cell carcinoma with sarcomatoid differentiation (six patients) and non-clear cell renal cell carcinoma (five patients). Each tumor nodule on the tissue block that corresponded to the same focus on the slide was separated from the normal parenchyma and other histologically distinct areas of tumor. The isolated tumor foci were used for subsequent analyses and sequencing. Deoxyribonucleic acid from the formalin-fixed paraffin-embedded tissues was extracted. Multiplex bar-coded polymerase chain reaction amplification was carried out using next-generation sequencing libraries. RESULTS Overall, 67 protein alterations, including amino acid alterations, frame shifts and splice site mutations in seven genes were identified in the cohort of renal cell carcinoma tumors included in this study. Fewer patients with clear cell renal cell carcinoma with sarcomatoid differentiation had clear cell renal cell carcinoma-related mutations in comparison with patients with conventional clear cell renal cell carcinoma. Additionally, the average number of unique clear cell renal cell carcinoma-related protein alterations per patient was significantly lower in clear cell renal cell carcinoma with sarcomatoid differentiation than in conventional clear cell renal cell carcinoma. Mutations in PBRM1 were identified in a higher proportion of patients with high-grade tumors (World Health Organization/International Society of Urological Pathology grade 4) and in the primary tumors of six of 10 (60%) patients with metastatic disease. CONCLUSIONS Although there are pitfalls due to intratumoral heterogeneity and sampling bias, mutations in PBRM1 may be associated with metastasis and aggressive disease in clear cell renal cell carcinoma.
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Affiliation(s)
- Rebecca C Obeng
- Departments of, Department of, Pathology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rebecca S Arnold
- Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Kenneth Ogan
- Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Viraj A Master
- Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - John G Pattaras
- Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - John A Petros
- Departments of, Department of, Pathology, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA.,Departments of, Department of, Urology, Veterans Affairs Medical Center, Decatur, Georgia, USA
| | - Adeboye O Osunkoya
- Departments of, Department of, Pathology, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of, Urology, Emory University School of Medicine, Atlanta, Georgia, USA.,Winship Cancer Institute of Emory University, Atlanta, Georgia, USA.,Department of, Pathology, Veterans Affairs Medical Center, Decatur, Georgia, USA
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19
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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20
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Chen L, Chen M, Lin J, Chen X, Yu X, Chen Z, Jin L. Identifying a wide range of actionable variants using capture-based ultra-deep targeted sequencing in treatment-naive patients with primary lung adenocarcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:525-535. [PMID: 32269691 PMCID: PMC7137022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/07/2020] [Indexed: 06/11/2023]
Abstract
Precision medicine requires accurate multi-gene clinical diagnostics. In current clinical practice, the minimum confidence threshold for variant calling of targeted next-generation sequencing (NGS) on surgical specimens is set to 2%-5%. However, few studies have been conducted to identify a wide range of actionable variants using capture-based ultra-deep targeted sequencing, which has limit of detection (LOD) of 1%. The AmoyDx® Essential NGS panel for capture-based ultra-deep targeted sequencing (dual-indexed sequencing adapters with UMIs) was performed on 372 surgical specimens obtained from treatment-naive patients with primary lung adenocarcinoma, to detect actionable somatic driver mutations associated with each patient. Single-nucleotide variants, insertion/deletion events, and rearrangements were reported. Amplification-refractory mutation system (ARMS) assay and fluorescence in situ hybridization (FISH) were performed for the validation of hotspot mutations in EGFR and ALK, ROS1, and RET fusions. Potentially actionable variants were identified in 80.5% (352/437) of the nonsynonymous variants that were able to be sequenced, and were most commonly found in EGFR mutations (59.7%, 261/437), followed by KRAS mutations (5.5%, 24/437), PIK3CA mutations (3.7%, 16/437), ALK rearrangements (3.4%, 15/437), BRAF mutations (2.7%, 12/437), ERBB2 mutations (2.5%, 11/437), and RET rearrangements (2.3%, 10/437). A total of 7.2% (28/372) of the samples had multiple actionable mutations. Among the 93 triple-negative cases, which did not harbor mutations in EGFR, KRAS, or BRAF, gene fusions were detected in 26 cases (28%). Of the 328 samples, concordance of EGFR between the ARMS assay and NGS was observed in 318 samples (97.0%), and among 32 samples, concordance between ARMS/FISH test and NGS for ALK/ROS1/RET fusion genes was observed in 30 samples (93.8%). Here, we demonstrated that the capture-based ultra-deep targeted sequencing method, which has a LOD of 1% to profile a wide range of actionable variants in surgical specimens of treatment-naive lung adenocarcinoma patients, highlights the need for treatment-naive patients to undergo genomic profiling.
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Affiliation(s)
- Lingfeng Chen
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
| | - Minyan Chen
- Department of Breast Surgery, Fujian Medical University Union HospitalFuzhou, Fujian Province, China
- Department of General Surgery, Fujian Medical University Union HospitalFuzhou, Fujian Province, China
| | - Jie Lin
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
| | - Xiaoyan Chen
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
| | - Xunbin Yu
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
| | - Zhizhong Chen
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
| | - Long Jin
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou, Fujian Province, China
- Department of Pathology, Fujian Provincial HospitalFuzhou, Fujian Province, China
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21
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Suzuki T, Tsukumo Y, Furihata C, Naito M, Kohara A. Preparation of the standard cell lines for reference mutations in cancer gene-panels by genome editing in HEK 293 T/17 cells. Genes Environ 2020; 42:8. [PMID: 32071619 PMCID: PMC7014756 DOI: 10.1186/s41021-020-0147-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Next Generation Sequencer (NGS) is a powerful tool for a high-throughput sequencing of human genome. It is important to ensure reliability and sensitivity of the sequence data for a clinical use of the NGS. Various cancer-related gene panels such as Oncomine™ or NCC OncoPanel have been developed and used for clinical studies. Because these panels contain multiple genes, it is difficult to ensure the performance of mutation detection for every gene. In addition, various platforms of NGS are developed and their cross-platform validation has become necessity. In order to create mutant standards in a defined background, we have used CRISPR/Cas9 genome-editing system in HEK 293 T/17 cells. RESULTS Cancer-related genes that are frequently used in NGS-based cancer panels were selected as the target genes. Target mutations were selected based on their frequency reported in database, and clinical significance and on the applicability of CRISPR/Cas9 by considering distance from PAM site, and off-targets. We have successfully generated 88 hetero- and homozygous mutant cell lines at the targeted sites of 36 genes representing a total of 125 mutations. CONCLUSIONS These knock-in HEK293T/17 cells can be used as the reference mutant standards with a steady and continuous supply for NGS-based cancer panel tests from the JCRB cell bank. In addition, these cell lines can provide a tool for the functional analysis of targeted mutations in cancer-related genes in the isogenic background.
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Affiliation(s)
- Takayoshi Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Yoshinori Tsukumo
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Chie Furihata
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Mikihiko Naito
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, 3-25-26, Tonomachi-ku, Kawasaki, 210-9501 Japan
| | - Arihiro Kohara
- JCRB Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki City, Osaka, 567-0085 Japan
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22
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Cai H, Hou X, Ding Y, Fu Z, Wang L, Du Y. Prediction of gastric cancer prognosis in the next-generation sequencing era. TRADITIONAL MEDICINE AND MODERN MEDICINE 2019. [DOI: 10.1142/s2575900019300029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gastric cancer (GC) is one of the most commonly diagnosed malignancies worldwide, and is caused by complex interactions of multiple risk factors such as environmental (Helicobacter pylori and Epstein–Barr Virus), hereditary (genetic alterations and epigenetic modifications), as well as dietary and lifestyle factors. GC is usually detected at an advanced stage, with a dismal prognosis. Even for patients with similar clinical or pathologic stage receiving similar treatment, the outcomes are still uneven and unpredictable. To better incorporate genetic and epigenetic profiles into GC prognostic predication, gene expression signatures have been developed to predict GC outcomes. More recently, the advancement of high-throughput sequencing technology, also known as next-generation sequencing (NGS) technology, and analysis has provided the basis for accurate molecular classification of GC tumors. Here, we summarized and updated the literature related to NGS studies of GC, including whole-genome sequencing, whole-exome sequencing, RNA sequencing, and targeted sequencing, and discussed current progresses. NGS has facilitated the identification of genetic/epigenetic targets for screening as well as development of targeted agent therapy, thus enabling individualized patient management and treatment.
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Affiliation(s)
- Hui Cai
- Department of General Surgery, Changhai Hospital, Second Military Medical University Shanghai, 200433, P. R. China
| | - Xiaomei Hou
- PLA Marine Corps Hospital, Chaozhou, Guangdong 521000, P. R. China
| | - Yibo Ding
- Department of Epidemiology, Second Military Medical University, Shanghai 200433, P. R. China
| | - Zhongxing Fu
- Ningguo Bio-Leader Biotechnology Co., Ltd., Anhui, Hefei, P. R. China
| | - Ling Wang
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Road, Shanghai 200090, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
- Shanghai Key Laboratory of Female Reproductive, Endocrine-related Diseases, Shanghai, P. R. China
| | - Yan Du
- Obstetrics and Gynecology Hospital of Fudan University, 419 Fangxie Road, Shanghai 200090, P. R. China
- Institutes of Integrative Medicine, Fudan University, Shanghai, P. R. China
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23
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Park J, Yoo HM, Sul HJ, Shin S, Lee SW, Kim JG. Genetic Characterization of Molecular Targets in Korean Patients with Gastrointestinal Stromal Tumors. J Gastric Cancer 2019; 20:29-40. [PMID: 32269842 PMCID: PMC7105413 DOI: 10.5230/jgc.2020.20.e2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose Gastrointestinal stromal tumors (GISTs) frequently harbor activating gene mutations in either KIT or platelet-derived growth factor receptor A (PDGFRA) and are highly responsive to several selective tyrosine kinase inhibitors. In this study, a targeted next-generation sequencing (NGS) assay with an Oncomine Focus Assay (OFA) panel was used for the genetic characterization of molecular targets in 30 Korean patients with GIST. Materials and Methods Using the OFA that enables rapid and simultaneous detection of hotspots, single nucleotide variants (SNVs), insertion and deletions (Indels), copy number variants (CNVs), and gene fusions across 52 genes relevant to solid tumors, targeted NGS was performed using genomic DNA extracted from formalin-fixed and paraffin-embedded samples of 30 GISTs. Results Forty-three hotspot/other likely pathogenic variants (33 SNVs, 8 Indels, and 2 amplifications) in 16 genes were identified in 26 of the 30 GISTs. KIT variants were most frequent (44%, 19/43), followed by 6 variants in PIK3CA, 3 in PDGFRA, 2 each in JAK1 and EGFR, and 1 each in AKT1, ALK, CCND1, CTNNB1, FGFR3, FGFR4, GNA11, GNAQ, JAK3, MET, and SMO. Based on the mutation types, majority of the variants carried missense mutations (60%, 26/43), followed by 8 frameshifts, 6 nonsense, 1 stop-loss, and 2 amplifications. Conclusions Our study confirmed the advantage of using targeted NGS with a cancer gene panel to efficiently identify mutations associated with GISTs. These findings may provide a molecular genetic basis for developing new drugs targeting these gene mutations for GIST therapy.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Han Mo Yoo
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hae Jung Sul
- Department of Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Soyoung Shin
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung Woo Lee
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jeong Goo Kim
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Pinsolle J, McLeer-Florin A, Giaj Levra M, de Fraipont F, Emprou C, Gobbini E, Toffart AC. Translating Systems Medicine Into Clinical Practice: Examples From Pulmonary Medicine With Genetic Disorders, Infections, Inflammations, Cancer Genesis, and Treatment Implication of Molecular Alterations in Non-small-cell Lung Cancers and Personalized Medicine. Front Med (Lausanne) 2019; 6:233. [PMID: 31737634 PMCID: PMC6828737 DOI: 10.3389/fmed.2019.00233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/03/2019] [Indexed: 12/30/2022] Open
Abstract
Non-small-cell lung cancers (NSCLC) represent 85% of all lung cancers, with adenocarcinoma as the most common subtype. Since the 2000's, the discovery of molecular alterations including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements together with the development of specific tyrosine kinase inhibitors (TKIs) has facilitated the development of personalized medicine in the management of this disease. This review focuses on the biology of molecular alterations in NSCLC as well as the diagnostic tools and therapeutic alternatives available for each targetable alteration. Rapid and sensitive methods are essential to detect gene alterations, using tumor tissue biopsies or liquid biopsies. Massive parallel sequencing or Next Generation Sequencing (NGS) allows to simultaneously analyze numerous genes from relatively low amounts of DNA. The detection of oncogenic fusions can be conducted using fluorescence in situ hybridization, reverse-transcription polymerase chain reaction, immunohistochemistry, or NGS. EGFR mutations, ALK and ROS1 rearrangements, MET (MET proto-oncogenereceptor tyrosine kinase), BRAF (B-Raf proto-oncogen serine/threonine kinase), NTRK (neurotrophic tropomyosin receptor kinase), and RET (ret proto-oncogene) alterations are described with their respective TKIs, either already authorized or still in development. We have herein paid particular attention to the mechanisms of resistance to EGFR and ALK-TKI. As a wealth of diagnostic tools and personalized treatments are currently under development, a close collaboration between molecular biologists, pathologists, and oncologists is crucial.
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Affiliation(s)
- Julian Pinsolle
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
| | - Anne McLeer-Florin
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
| | - Matteo Giaj Levra
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Florence de Fraipont
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Camille Emprou
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Elisa Gobbini
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Cancer Research Center Lyon, Centre Léon Bérard, Lyon, France
| | - Anne-Claire Toffart
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
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Lee YJ, Kim D, Kim HS, Na K, Lee JY, Nam EJ, Kim SW, Kim S, Kim YT. Integrating a Next Generation Sequencing Panel into Clinical Practice in Ovarian Cancer. Yonsei Med J 2019; 60:914-923. [PMID: 31538426 PMCID: PMC6753345 DOI: 10.3349/ymj.2019.60.10.914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Few efforts have been made to integrate a next generation sequencing (NGS) panel into standard clinical treatment of ovarian cancer. The aim of this study was to investigate the clinical utility of NGS and to identify clinically impactful information beyond targetable alterations. MATERIALS AND METHODS We conducted a retrospective review of 84 patients with ovarian cancer who underwent NGS between March 1, 2017, and July 31, 2018, at the Yonsei Cancer Hospital. We extracted DNA from formalin-fixed, paraffin-embedded tissue samples of ovarian cancer. The TruSight Tumor 170 gene panel was used to prepare libraries, and the MiSeq instrument was used for NGS. RESULTS Of the 84 patients, 55 (65.1%) had high-grade serous carcinomas. Seventy-three (86.7%) patients underwent NGS at the time of diagnosis, and 11 (13.3%) underwent NGS upon relapse. The most common genetic alterations were in TP53 (64%), PIK3CA (15%), and BRCA1/2 (13%), arising as single nucleotide variants and indels. MYC amplification (27%) was the most common copy number variation and fusion. Fifty-seven (67.9%) patients had more than one actionable alteration other than TP53. Seven (8.3%) cases received matched-target therapy based on the following sequencing results: BRCA1 or 2 mutation, poly ADP ribose polymerase inhibitor (n=5); PIK3CA mutation, AKT inhibitor (n=1); and MLH1 mutation, PD-1 inhibitor (n=1). Fifty-three (63.0%) patients had a possibility of treatment change, and 8 (9.5%) patients received genetic counseling. CONCLUSION Implementation of NGS may help in identifying patients who might benefit from targeted treatment therapies and genetic counseling.
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Affiliation(s)
- Yong Jae Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Dachan Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Soo Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kiyong Na
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jung Yun Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Eun Ji Nam
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sunghoon Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Young Tae Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
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Shi X, Duose DY, Mehrotra M, Harmon MA, Hu P, Wistuba II, Kopetz S, Luthra R. Non-invasive genotyping of metastatic colorectal cancer using circulating cell free DNA. Cancer Genet 2019; 237:82-89. [PMID: 31447070 DOI: 10.1016/j.cancergen.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/03/2019] [Accepted: 06/09/2019] [Indexed: 02/07/2023]
Abstract
Circulating cell-free DNA (ccfDNA) in plasma provides an easily accessible source of circulating tumor DNA (ctDNA) for detecting actionable genomic alterations that can be used to guide colorectal cancer (CRC) treatment and surveillance. The goal of this study was to test the feasibility of using a traditional amplicon-based next-generation sequencing (NGS) on Ion Torrent platform to detect low-frequency alleles in ctDNA and compare it with a digital NGS assay specifically designed to detect low-frequency variants (as low as 0.1%) to provide evidence for the standard care of CRC. The study cohort consisted of 48 CRC patients for whom matched samples of formalin-fixed, paraffin-embedded tumor tissue, plasma, and peripheral blood mononuclear cells were available. DNA samples from different sources were sequenced on different platforms using commercial protocols. Our results demonstrate that the ccfDNA sequencing with the traditional NGS can be reliably used in an integrated workflow to detect low-frequency somatic variants in CRC. We found a high degree of concordance between traditional NGS and digital NGS in profiling mutant alleles in ccfDNA. These findings suggest that the traditional NGS is a viable alternative to digital sequencing of ccfDNA at allele frequency above 1%. ccfDNA sequencing can not only provide real-time monitoring of CRC, but also lay the basis for its application as a clinical diagnostic test to guide personalized therapy.
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Affiliation(s)
- Xuemei Shi
- Diagnostic Genetics, School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Michael A Harmon
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Peter Hu
- Diagnostic Genetics, School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, 6565 MD Anderson Blvd., Houston, TX 77030, United States; Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.
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Mallampati S, Duose DY, Harmon MA, Mehrotra M, Kanagal-Shamanna R, Zalles S, Wistuba II, Sun X, Luthra R. Rational "Error Elimination" Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies. J Mol Diagn 2019; 21:471-482. [PMID: 30794984 PMCID: PMC6521894 DOI: 10.1016/j.jmoldx.2019.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 12/18/2022] Open
Abstract
The emergence of highly sensitive molecular diagnostic approaches, such as droplet digital PCR, has allowed the accurate identification of low-frequency variant alleles in clinical specimens; however, the multiplex capabilities of droplet digital PCR for variant detection are inadequate. The incorporation of molecular barcodes or unique IDs into next-generation sequencing libraries through PCR has enabled the detection of low-frequency variant alleles across multiple genomic regions. However, rational library preparation and sequencing data analytic strategies that integrate molecular barcodes have rarely been applied to clinical settings. In this study, we evaluated the parameters that are crucial in the use of molecular barcodes in next-generation sequencing for genotyping clinical specimens from patients with hematologic malignancies. The uniform incorporation of molecular barcodes into DNA templates through PCR was found to be crucial, and the extent of uniformity was governed by multiple interdependent variables. An error elimination strategy was developed for removing sequencing background errors by using molecular barcode sequence information as an alternative to the conventional error correction approach. This approach was successfully used to identify mutations with frequencies as low as 0.15%, and the clonal heterogeneity of hematologic malignancies was revealed. These findings have implications for elucidating heterogeneity and temporal and spatial clonal evolution, evaluating response to therapy, and monitoring relapse in patients with hematologic malignancies.
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Affiliation(s)
- Saradhi Mallampati
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Zalles
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoping Sun
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Na K, Kim HS, Shim HS, Chang JH, Kang SG, Kim SH. Targeted next-generation sequencing panel (TruSight Tumor 170) in diffuse glioma: a single institutional experience of 135 cases. J Neurooncol 2019; 142:445-454. [PMID: 30710203 DOI: 10.1007/s11060-019-03114-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE The TruSight Tumor 170 (TST-170) panel consists of a DNA workflow for the identification of single-nucleotide variants, small insertions and deletions, and copy number variation, as well as a panel of 55 genes for a RNA workflow for the identification of splice variants and gene fusions. To date, the application of TST-170 in diffuse gliomas (DGs) has not been described. METHODS We analyzed 135 samples of DG, which were diagnosed by WHO criteria based on histological features and conventional molecular tests including immunostaining, 1p/19q FISH, and analysis of MGMT methylation and TERT promoter mutation. RESULTS A total of 135 cases consisted of 38 IDH-mutant [17 astrocytoma (AC), 13 oligodendroglioma (OD) and eight glioblastoma (GBM)], 87 IDH-wildtype (six AC, three OD and 78 GBM), and 10 diffuse midline glioma, H3K27M-mutant. DNA analysis enabled the detection of all mutations identified in these samples by conventional techniques, and the results were highly comparable to the known mutations in each subtype. RNA analysis detected four fusion genes including PTPRZ1-MET, FGFR3-TACC3, FAM131B-BRAF, and RET-CCDC6 and one splicing variant (EGFR vIII mutant). Clustered copy number loss in 1p and 19q loci genes were detected in 1p/19q-codeleted OD. CONCLUSIONS The application of TST-170 panel based NGS in clinical and laboratory setting is expected to improve diagnostic accuracy and prognostication. Most benefits are expected in IDH-wildtype DG, a group of genetically heterogenous tumors harboring DNA sequence changes, copy number alterations, and fusions in a large number of oncogenes and tumor suppressor genes.
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Affiliation(s)
- Kiyong Na
- Department of Pathology, Kyung Hee University School of Medicine, Seoul, Republic of Korea.,Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Jong Hee Chang
- Department of Neurosurgery, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Seok-Gu Kang
- Department of Neurosurgery, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea.
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Huang SW, Hung SJ, Wang JR. Application of deep sequencing methods for inferring viral population diversity. J Virol Methods 2019; 266:95-102. [PMID: 30690049 DOI: 10.1016/j.jviromet.2019.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/11/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022]
Abstract
The first deep sequencing method was announced in 2005. Due to an increasing number of sequencing data and a reduction in the costs of each sequencing dataset, this innovative technique was soon applied to genetic investigations of viral genome diversity in various viruses, particularly RNA viruses. These deep sequencing findings documented viral epidemiology and evolution and provided high-resolution data on the genetic changes in viral populations. Here, we review deep sequencing platforms that have been applied in viral quasispecies studies. Further, we discuss recent deep sequencing studies on viral inter- and intrahost evolution, drug resistance, and humoral immune selection, especially in emerging and re-emerging viruses. Deep sequencing methods are becoming the standard for providing comprehensive results of viral population diversity, and their applications are discussed.
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Affiliation(s)
- Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Su-Jhen Hung
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
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Barcelos D, Neto RA, Cardili L, Fernandes M, Carapeto FCL, Comodo AN, Funabashi K, Iwamura ESM. KIT exon 11 and PDGFRA exon 18 gene mutations in gastric GIST: proposal of a short panel for predicting therapeutic response. SURGICAL AND EXPERIMENTAL PATHOLOGY 2018. [DOI: 10.1186/s42047-018-0021-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
GIST is the most common mesenchymal tumor of gastrointestinal tract and is more frequent in stomach. Its main mutations affect KIT and PDGFRA genes. Full genetic analysis panels are currently used to study mutations in GIST and other tumors. Considering that in gastric GIST KIT gene mutations in exon 11 are sensitive to IM whereas PDGFRΑ gene mutations in exon 18 (D842V) are resistant to the same drug, the aim of this study is to focus on these two molecular targets as a short alternative panel for predicting therapeutic response in gastric GIST which might optimize resources.
Methods
The genotypes of 38 cases of primary GIST were determined by performing bidirectional DNA sequencing.
Results
Exon 11 of KIT gene showed mutations in 65.3% and the exon 18 of PDGFRA gene showed 9% of cases. So it was possible to determine a subgroup of tumors which presented mutations in KIT exon 11 and PDGFRA exon 18.
Conclusion
Considering all of the foregoing analyzed globally, the application of short panel has impact on the cost and time of release of results to the physician, allowing a rapid approach to patients eligible for treatment with the target therapy.
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Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. Nat Commun 2018; 9:3962. [PMID: 30262806 PMCID: PMC6160438 DOI: 10.1038/s41467-018-06485-7] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
To evaluate the potential of an integrated clinical test to detect diverse classes of somatic and germline mutations relevant to pediatric oncology, we performed three-platform whole-genome (WGS), whole exome (WES) and transcriptome (RNA-Seq) sequencing of tumors and normal tissue from 78 pediatric cancer patients in a CLIA-certified, CAP-accredited laboratory. Our analysis pipeline achieves high accuracy by cross-validating variants between sequencing types, thereby removing the need for confirmatory testing, and facilitates comprehensive reporting in a clinically-relevant timeframe. Three-platform sequencing has a positive predictive value of 97–99, 99, and 91% for somatic SNVs, indels and structural variations, respectively, based on independent experimental verification of 15,225 variants. We report 240 pathogenic variants across all cases, including 84 of 86 known from previous diagnostic testing (98% sensitivity). Combined WES and RNA-Seq, the current standard for precision oncology, achieved only 78% sensitivity. These results emphasize the critical need for incorporating WGS in pediatric oncology testing. Clinical oncology is rapidly adopting next-generation sequencing technology for nucleotide variant and indel detection. Here the authors present a three-platform approach (whole-genome, whole-exome, and whole-transcriptome) in pediatric patients for the detection of diverse types of germline and somatic variants.
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32
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Tessema M, Rossi MR, Picchi MA, Yingling CM, Lin Y, Ramalingam SS, Belinsky SA. Common cancer-driver mutations and their association with abnormally methylated genes in lung adenocarcinoma from never-smokers. Lung Cancer 2018; 123:99-106. [PMID: 30089603 PMCID: PMC6331003 DOI: 10.1016/j.lungcan.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/28/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Lung adenocarcinoma in never-smokers accounts for 15-20% of all lung cancer. Although targetable mutations are more prevalent in these tumors, the biological and clinical importance of coexisting and/or mutually exclusive abnormalities is just emerging. This study evaluates the relationships between common genetic and epigenetic aberrations in these tumors. MATERIALS AND METHODS Next-generation sequencing was employed to screen 20 commonly mutated cancer-driver genes in 112 lung adenocarcinomas from never-smokers. The relationship of these mutations with cancer-related methylation of 59 genes, and geographical/ethnic differences in the prevalence for mutations compared to multiple East Asian never-smoker lung adenocarcinoma cohorts was studied. RESULTS The most common driver mutation detected in 40% (45/112) of the tumors was EGFR, followed by TP53 (18%), SETD2 (11%), and SMARCA4 (11%). Over 72% (81/112) of the cases have mutation of at least one driver gene. While 30% (34/112) of the tumors have co-mutations of two or more genes, 42% (47/112) have only one driver gene mutation. Differences in the prevalence for some of these mutations were seen between adenocarcinomas in East Asian versus US (mainly Caucasian) never-smokers including a significantly lower rate of EGFR mutation among the US patients. Interestingly, aberrant methylation of multiple cancer-related genes was significantly associated with EGFR wildtype tumors. Among 15 differentially methylated genes by EGFR mutation, 14 were more commonly methylated in EGFR wildtype compared to mutant tumors. These findings were independently validated using publicly available data. CONCLUSION Most lung adenocarcinomas from never-smokers harbor targetable mutation/co-mutations. In the absence of EGFR mutation that drives 40% of these tumors, EGFR wildtype tumors appear to develop by acquiring aberrant promoter methylation that silences tumor-suppressor genes.
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
| | - Michael R Rossi
- Departments of Pathology and Laboratory Medicine, Radiation Oncology, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Suresh S Ramalingam
- Hematology and Oncology, Emory University School of Medicine, Winship Cancer Institute, Atlanta, GA, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
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Press RH, Zhang C, Cassidy RJ, Ferris MJ, Zhong J, Steuer CE, Pillai RN, Owonikoko TK, Kahn S, Ramalingam SS, Patel PR, Curran WJ, Shu HKG, Sica GL, Higgins KA. Targeted sequencing and intracranial outcomes of patients with lung adenocarcinoma brain metastases treated with radiotherapy. Cancer 2018; 124:3586-3595. [DOI: 10.1002/cncr.31589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Robert H. Press
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Chao Zhang
- Bioinformatics and Biostatistics; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Richard J. Cassidy
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Matthew J. Ferris
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Jim Zhong
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Conor E. Steuer
- Department of Hematology and Medical Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Rathi N. Pillai
- Department of Hematology and Medical Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Taofeek K. Owonikoko
- Department of Hematology and Medical Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Shannon Kahn
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Suresh S. Ramalingam
- Department of Hematology and Medical Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Pretesh R. Patel
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Walter J. Curran
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Hui-Kuo G. Shu
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Gabriel L. Sica
- Department of Pathology; Winship Cancer Institute, Emory University; Atlanta Georgia
| | - Kristin A. Higgins
- Department of Radiation Oncology; Winship Cancer Institute, Emory University; Atlanta Georgia
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Giardina T, Robinson C, Grieu-Iacopetta F, Millward M, Iacopetta B, Spagnolo D, Amanuel B. Implementation of next generation sequencing technology for somatic mutation detection in routine laboratory practice. Pathology 2018; 50:389-401. [DOI: 10.1016/j.pathol.2018.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/21/2017] [Accepted: 01/09/2018] [Indexed: 02/08/2023]
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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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36
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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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Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients. Cancers (Basel) 2018; 10:cancers10040088. [PMID: 29561830 PMCID: PMC5923343 DOI: 10.3390/cancers10040088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023] Open
Abstract
Background: With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS) has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods: Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively) with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR, KRAS, BRAF, NRAS, ALK, PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results: Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r2 = 0.93 for the retrospective patients and r2 = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion: We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.
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Validation of a Customized Bioinformatics Pipeline for a Clinical Next-Generation Sequencing Test Targeting Solid Tumor-Associated Variants. J Mol Diagn 2018; 20:355-365. [PMID: 29471113 DOI: 10.1016/j.jmoldx.2018.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 01/01/2023] Open
Abstract
Bioinformatic analysis is an integral and critical part of clinical next-generation sequencing. It is especially challenging for some pipelines to consistently identify insertions and deletions. We present the validation of an open source tumor amplicon pipeline (OTA-pipeline) for clinical next-generation sequencing targeting solid tumor-associated variants. Raw data generated from 557 TruSight Tumor 26 samples and in silico data were analyzed by the OTA-pipeline and legacy pipeline and compared. Discrepant results were confirmed by orthogonal methods. The OTA-pipeline reported 22 variants that were not detected by the previously validated pipeline, including seven synonymous or intronic single-nucleotide variants, five single-nucleotide variants at frequency <5%, one insertion, and nine deletions. Variant allele frequencies reported by the two pipelines were highly concordant, although a few significant discrepancies were present. Analysis of in silico FASTQ files demonstrated a higher sensitivity of detecting complex insertions and deletions with the OTA-pipeline. The higher sensitivity came at a cost, because false-positive calls were increased in difficult-to-sequence regions. However, these calls were all flagged by our strand bias filter, distinguishing them from true variants. Our validation process provides a model for laboratories that want to establish an in-house bioinformatics pipeline for clinical next-generation sequencing.
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39
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Verma R, Sharma PC. Next generation sequencing-based emerging trends in molecular biology of gastric cancer. Am J Cancer Res 2018; 8:207-225. [PMID: 29511593 PMCID: PMC5835690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer related mortality in the world. Being asymptomatic in nature till advanced stage, diagnosis of gastric cancer becomes difficult in early stages of the disease. The onset and progression of gastric cancer has been attributed to multiple factors including genetic alterations, epigenetic modifications, Helicobacter pylori and Epstein-Barr Virus (EBV) infection, and dietary habits. Next Generation Sequencing (NGS) based approaches viz. Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-Seq, and targeted sequencing have expanded the knowledge base of molecular pathogenesis of gastric cancer. In this review, we highlight recent NGS-based advances covering various genetic alterations (Microsatellite Instability, Single Nucleotide Variations, and Copy Number Variations), epigenetic changes (DNA methylation, histone modification, microRNAs) and differential gene expression during gastric tumorigenesis. We also briefly discuss the current and future potential biomarkers, drugs and therapeutic approaches available for the management of gastric cancer.
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Affiliation(s)
- Renu Verma
- University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew Delhi 110078, India
| | - Prakash C Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew Delhi 110078, India
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40
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Wing MR, Reeser JW, Smith AM, Reeder M, Martin D, Jewell BM, Datta J, Miya J, Monk JP, Mortazavi A, Otterson GA, Goldberg RM, VanDeusen JB, Cole S, Dittmar K, Jaiswal S, Kinzie M, Waikhom S, Freud AG, Zhou XP, Chen W, Bhatt D, Roychowdhury S. Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer. Oncotarget 2017; 8:75822-75833. [PMID: 29100271 PMCID: PMC5652665 DOI: 10.18632/oncotarget.20616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
Multiplex somatic testing has emerged as a strategy to test patients with advanced cancer. We demonstrate our analytic validation approach for a gene hotspot panel and real-time prospective clinical application for any cancer type. The TruSight Tumor 26 assay amplifies 85 somatic hotspot regions across 26 genes. Using cell line and tumor mixes, we observed that 100% of the 14,715 targeted bases had at least 1000x raw coverage. We determined the sensitivity (100%, 95% CI: 96-100%), positive predictive value (100%, 95% CI: 96-100%), reproducibility (100% concordance), and limit of detection (3% variant allele frequency at 1000x read depth) of this assay to detect single nucleotide variants and small insertions and deletions. Next, we applied the assay prospectively in a clinical tumor sequencing study to evaluate 174 patients with metastatic or advanced cancer, including frozen tumors, formalin-fixed tumors, and enriched peripheral blood mononuclear cells in hematologic cancers. We reported one or more somatic mutations in 89 (53%) of the sequenced tumors (167 passing quality filters). Forty-three of these patients (26%) had mutations that would enable eligibility for targeted therapies. This study demonstrates the validity and feasibility of applying TruSight Tumor 26 for pan-cancer testing using multiple specimen types.
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Affiliation(s)
- Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Matthew Reeder
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Dorrelyn Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Benjamin M Jewell
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Datta
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - J Paul Monk
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Amir Mortazavi
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Gregory A Otterson
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Richard M Goldberg
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | | | | | - Kristin Dittmar
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Sunny Jaiswal
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Matthew Kinzie
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Suraj Waikhom
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Radiology, The Ohio State University, Columbus, OH, USA
| | - Aharon G Freud
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Xiao-Ping Zhou
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA.,University Pathologists, LLC, Department of Pathology, Roger Williams Medical Center, Providence, RI, USA
| | - Wei Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Darshna Bhatt
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
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41
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Cassidy RJ, Zhang X, Patel PR, Shelton JW, Escott CE, Sica GL, Rossi MR, Hill CE, Steuer CE, Pillai RN, Ramalingam SS, Owonikoko TK, Behera M, Force SD, Fernandez FG, Curran WJ, Higgins KA. Next-generation sequencing and clinical outcomes of patients with lung adenocarcinoma treated with stereotactic body radiotherapy. Cancer 2017; 123:3681-3690. [PMID: 28608966 DOI: 10.1002/cncr.30794] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/04/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic aberrations are well characterized in lung adenocarcinomas (LACs) and clinical outcomes have been influenced by targeted therapies in the advanced setting. Stereotactic body radiotherapy (SBRT) is the standard-of-care therapy for patients with nonoperable, early-stage LAC, but to the authors' knowledge, no information is available regarding the impact of genomic changes in these patients. The current study sought to determine the frequency and clinical impact of genetic aberrations in this population. METHODS Under an Institutional Review Board-approved protocol, the records of 242 consecutive patients with early-stage lung cancers were reviewed; inclusion criteria included LAC histology with an adequate tumor sample for the successful use of next-generation sequencing and fluorescence in situ hybridization testing. Univariate analysis was performed to identify factors associated with clinical outcomes. RESULTS LAC samples from 98 of the 242 patients were reviewed (40.5%), of whom 45 patients (46.0%) had genetic testing. The following mutations were noted: KRAS in 20.0% of samples, BRAF in 2.2% of samples, SMAD family member 4 (SMAD4) in 4.4% of samples, epidermal growth factor receptor (EGFR) in 15.6% of samples, STK1 in 2.2% of samples, tumor protein 53 (TP53) in 15.6% of samples, and phosphatase and tensin homolog (PTEN) in 2.2% of samples. The following gene rearrangements were observed: anaplastic lymphoma kinase (ALK) in 8.9% of samples, RET in 2.2% of samples, and MET amplification in 17.8% of samples. The median total delivered SBRT dose was 50 grays (range, 48-60 grays) over a median of 5 fractions (range, 3-8 fractions). The KRAS mutation was associated with worse local control (odds ratio [OR], 3.64; P<.05). MET amplification was associated with worse regional (OR, 4.64; P<.05) and distant (OR, 3.73; P<.05) disease control. CONCLUSIONS To the authors' knowledge, the current series is the first to quantify genetic mutations and their association with clinical outcomes in patients with early-stage LAC treated with SBRT. KRAS mutations were associated with worse local control and MET amplification was associated with worse regional and distant disease control, findings that need to be validated in a prospective setting. Cancer 2017;123:3681-3690. © 2017 American Cancer Society.
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Affiliation(s)
- Richard J Cassidy
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Xinyan Zhang
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Pretesh R Patel
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Joseph W Shelton
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Chase E Escott
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Gabriel L Sica
- Department of Pathology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Michael R Rossi
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Charles E Hill
- Department of Pathology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Conor E Steuer
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Rathi N Pillai
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Suresh S Ramalingam
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Taofeek K Owonikoko
- Department of Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Madhusmita Behera
- Department of Biostatistics and Bioinformatics, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Seth D Force
- Department of Thoracic Surgery, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Felix G Fernandez
- Department of Thoracic Surgery, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Walter J Curran
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Kristin A Higgins
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
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42
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Lindquist KE, Karlsson A, Levéen P, Brunnström H, Reuterswärd C, Holm K, Jönsson M, Annersten K, Rosengren F, Jirström K, Kosieradzki J, Ek L, Borg Å, Planck M, Jönsson G, Staaf J. Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer. Oncotarget 2017; 8:34796-34810. [PMID: 28415793 PMCID: PMC5471012 DOI: 10.18632/oncotarget.16276] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.
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Affiliation(s)
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Per Levéen
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
| | - Hans Brunnström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karolina Holm
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Annersten
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Frida Rosengren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Jirström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Jaroslaw Kosieradzki
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Lars Ek
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- Department of Oncology, Skåne University Hospital, Lund SE 22381, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
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43
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Hosny Mohammed K, Ewaz A, Cohen C, Siddiqui MT. Double staining: diagnostic utility in non-small cell lung carcinoma in the era of tissue conservation. J Am Soc Cytopathol 2017; 6:170-175. [PMID: 31043270 DOI: 10.1016/j.jasc.2017.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/11/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
Abstract
INTRODUCTION In an era of precision medicine distinguishing pulmonary squamous cell carcinoma (SQCC) from adenocarcinoma (ADC) is vital for treatment. Immunohistochemical (IHC) staining for p40, p63 and Cytokeratin 5 (CK5) are useful for SQCC, while TTF-1 and Napsin-A can be used for confirming ADC. Fine needle aspiration (FNA) cell blocks (CB) have limited tissue, hence, double IHC staining is helpful for tissue conservation for molecular analysis. MATERIALS AND METHODS Thirty six confirmed lung SQCC and 45 ADC CB were selected for IHC. Double staining was performed with p40/CK5 and p63/CK5 on all SQCC, and with TTF-1/Napsin-A on all ADC. Results were positive if at least 5% of malignant cells were immunoreactive for the antigen. RESULTS P40/CK5 had (92%) sensitivity, (100%) specificity, (100%) positive predictive value (PPV), (91%) negative predictive value (NPV) and an overall diagnostic accuracy of (96%). By contrast, P63/CK5 double stains showed (92%) sensitivity, (80%) specificity, (85%) PPV, (89%) NPV and (86%) overall diagnostic accuracy, respectively. TTF-1/Napsin A staining for ADC showed a sensitivity of 80%, specificity of 96%, PPV of 97%, NPV of 71% and accuracy of 85%. CONCLUSION P40/CK5 double stain has higher specificity, PPV, NPV, and overall accuracy than P63/CK5 double stain in the diagnosis of lung SQCC. TTF-1/Napsin-A double staining is a valuable marker with high specificity, PPV, and diagnostic accuracy in diagnosing lung ADC. The usage of P40/CK5 and TTF-1/Napsin-A as a panel can be recommended for characterizing non-small cell carcinoma (NSCC) of the lung and for conserving tissue for molecular testing.
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Affiliation(s)
- Kareem Hosny Mohammed
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia.
| | - Abdulwahab Ewaz
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Cynthia Cohen
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, Georgia
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Abstract
There is great potential for genome sequencing to enhance patient care through improved diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential, genomics strategies that have been developed for genetic discovery - including DNA-sequencing technologies and analysis algorithms - need to be adapted to fit clinical needs. This will require the optimization of alignment algorithms, attention to quality-coverage metrics, tailored solutions for paralogous or low-complexity areas of the genome, and the adoption of consensus standards for variant calling and interpretation. Global sharing of this more accurate genotypic and phenotypic data will accelerate the determination of causality for novel genes or variants. Thus, a deeper understanding of disease will be realized that will allow its targeting with much greater therapeutic precision.
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Affiliation(s)
- Euan A Ashley
- Center for Inherited Cardiovascular Disease, Falk Cardiovascular Research Building, Stanford Medicine, 870 Quarry Road, Stanford, California 94305, USA
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45
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Kim J, Park WY, Kim NKD, Jang SJ, Chun SM, Sung CO, Choi J, Ko YH, Choi YL, Shim HS, Won JK. Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests. J Pathol Transl Med 2017; 51:191-204. [PMID: 28535585 PMCID: PMC5445206 DOI: 10.4132/jptm.2017.03.14] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/14/2017] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.
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Affiliation(s)
- Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nayoung K. D. Kim
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Sung-Min Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Chang-Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
| | - Jene Choi
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Young-Hyeh Ko
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - The Molecular Pathology Study Group of Korean Society of Pathologists
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
- Center for Cancer Genome Discovery, Asan Institute for Life Sciences, Seoul, , Korea
- Samsung Genome Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
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46
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Roukos DH. Spatiotemporal diversification of intrapatient genomic clones and early drug development concepts realize the roadmap of precision cancer medicine. Drug Discov Today 2017; 22:1148-1164. [PMID: 28400153 DOI: 10.1016/j.drudis.2017.03.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 02/21/2017] [Accepted: 03/31/2017] [Indexed: 12/19/2022]
Abstract
The unmet clinical needs of high relapse and cancer-related death rates are reflected by the poor understanding of the genome-wide mutational landscape and molecular mechanisms orchestrating therapeutic resistance. Emerging potential solutions to this challenge include the exploration of cancer genome dynamic evolution in time and space. Breakthrough next-generation sequencing (NGS) applications including multiregional NGS for intratumor heterogeneity identification, repeated cell-free DNA/circulating tumor DNA-NGS for detecting circulating genomic subclones and their comparison to reveal intrapatient heterogeneity (IPH) could identify the dynamic emergence of resistant subclones in the neoadjuvant, adjuvant and metastatic setting. Based on genome-phenotype map, and potential promising findings, rigorous evaluation of IPH spatiotemporal evolution and early drug development concepts in innovative clinical trials could dramatically speed up the translational process to achieve clinical precision oncology.
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Affiliation(s)
- Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, Ioannina, Greece; Department of Surgery, Ioannina University Hospital, Ioannina, Greece.
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47
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Gilbert-Ross M, Konen J, Koo J, Shupe J, Robinson BS, Wiles WG, Huang C, Martin WD, Behera M, Smith GH, Hill CE, Rossi MR, Sica GL, Rupji M, Chen Z, Kowalski J, Kasinski AL, Ramalingam SS, Fu H, Khuri FR, Zhou W, Marcus AI. Targeting adhesion signaling in KRAS, LKB1 mutant lung adenocarcinoma. JCI Insight 2017; 2:e90487. [PMID: 28289710 PMCID: PMC5333956 DOI: 10.1172/jci.insight.90487] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Loss of LKB1 activity is prevalent in KRAS mutant lung adenocarcinoma and promotes aggressive and treatment-resistant tumors. Previous studies have shown that LKB1 is a negative regulator of the focal adhesion kinase (FAK), but in vivo studies testing the efficacy of FAK inhibition in LKB1 mutant cancers are lacking. Here, we took a pharmacologic approach to show that FAK inhibition is an effective early-treatment strategy for this high-risk molecular subtype. We established a lenti-Cre-induced Kras and Lkb1 mutant genetically engineered mouse model (KLLenti) that develops 100% lung adenocarcinoma and showed that high spatiotemporal FAK activation occurs in collective invasive cells that are surrounded by high levels of collagen. Modeling invasion in 3D, loss of Lkb1, but not p53, was sufficient to drive collective invasion and collagen alignment that was highly sensitive to FAK inhibition. Treatment of early, stage-matched KLLenti tumors with FAK inhibitor monotherapy resulted in a striking effect on tumor progression, invasion, and tumor-associated collagen. Chronic treatment extended survival and impeded local lymph node spread. Lastly, we identified focally upregulated FAK and collagen-associated collective invasion in KRAS and LKB1 comutated human lung adenocarcinoma patients. Our results suggest that patients with LKB1 mutant tumors should be stratified for early treatment with FAK inhibitors.
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Affiliation(s)
- Melissa Gilbert-Ross
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - Jessica Konen
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - Junghui Koo
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - John Shupe
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - Brian S Robinson
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine
| | - Walter Guy Wiles
- Winship Cancer Institute of Emory University.,The Cancer Animal Models Shared Resource
| | - Chunzi Huang
- Winship Cancer Institute of Emory University.,The Cancer Animal Models Shared Resource
| | - W David Martin
- Department of Hematology and Medical Oncology, Emory University School of Medicine
| | - Madhusmita Behera
- Winship Research Informatics Shared Resource, Winship Cancer Institute
| | - Geoffrey H Smith
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine
| | - Charles E Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine
| | - Michael R Rossi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine.,Department of Radiation Oncology, Emory University School of Medicine
| | - Gabriel L Sica
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine
| | | | - Zhengjia Chen
- Winship Cancer Institute of Emory University.,Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jeanne Kowalski
- Winship Cancer Institute of Emory University.,Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Andrea L Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - Haian Fu
- Winship Cancer Institute of Emory University.,Department of Pharmacology, Emory University School of Medicine
| | - Fadlo R Khuri
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine.,Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Adam I Marcus
- Department of Hematology and Medical Oncology, Emory University School of Medicine.,Winship Cancer Institute of Emory University
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48
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Emami NC, Leong L, Wan E, Van Blarigan EL, Cooperberg MR, Tenggara I, Carroll PR, Chan JM, Witte JS, Simko JP. Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy. Prostate 2017; 77:425-434. [PMID: 27900799 PMCID: PMC5479703 DOI: 10.1002/pros.23283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/03/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Benign tissue from a tumor-containing organ is commonly the only available source for obtaining a patient's unmutated genome for use in cancer research. While it is critical to identify histologically normal tissue that is independent of the tumor lineage, few additional considerations are applied to the choice of this material for such measurements. METHODS Normal formalin-fixed, paraffin-embedded seminal vesicle, and urethral tissues, in addition to whole blood, were collected from 31 prostate cancer patients having undergone radical prostatectomy. Genotype concordance was evaluated for DNA from each tissue source in relation to whole blood. RESULTS Overall, there was a greater genotype call rate for DNA derived from urethral tissue (97.0%) in comparison with patient-matched seminal vesicle tissues (95.9%, P = 0.0015). Furthermore, with reference to patient-matched whole blood, urethral samples exhibited higher genotype concordance (94.1%) than that of seminal vesicle samples (92.5%, P = 0.035). CONCLUSIONS These findings highlight the heterogeneity between diverse sources of DNA in genotype measurement and motivate the consideration of normal tissue biases in tumor-normal analyses. Prostate 77: 425-434, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nima C. Emami
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Eunice Wan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
| | - Erin L. Van Blarigan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Matthew R. Cooperberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Imelda Tenggara
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Peter R. Carroll
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - June M. Chan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - John S. Witte
- Program in Biological and Medical Informatics, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
| | - Jeffry P. Simko
- Department of Urology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Anatomic Pathology, University of California, San Francisco, San Francisco, California
- Correspondence to: Jeffry P. Simko, 1825 4th St., Room M2360, San Francisco, CA 94158, 415-353-7171 (Phone), 415-353-7094 (Fax), . John S. Witte, 1450 3rd St., San Francisco, CA 94158, 415-502-6882 (Phone), 415-476-1356 (Fax),
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49
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Deans ZC, Costa JL, Cree I, Dequeker E, Edsjö A, Henderson S, Hummel M, Ligtenberg MJ, Loddo M, Machado JC, Marchetti A, Marquis K, Mason J, Normanno N, Rouleau E, Schuuring E, Snelson KM, Thunnissen E, Tops B, Williams G, van Krieken H, Hall JA. Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL. Virchows Arch 2017; 470:5-20. [PMID: 27678269 PMCID: PMC5243883 DOI: 10.1007/s00428-016-2025-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/27/2016] [Accepted: 09/16/2016] [Indexed: 10/31/2022]
Abstract
The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK.
| | - Jose Luis Costa
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ian Cree
- Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Els Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium
| | - Anders Edsjö
- Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden
| | - Shirley Henderson
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Michael Hummel
- Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany
| | - Marjolijn Jl Ligtenberg
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Loddo
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Jose Carlos Machado
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy
| | - Katherine Marquis
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Joanne Mason
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands
| | - Keeda-Marie Snelson
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Erik Thunnissen
- Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Bastiaan Tops
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gareth Williams
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Han van Krieken
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacqueline A Hall
- International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
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50
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Kadri S, Long BC, Mujacic I, Zhen CJ, Wurst MN, Sharma S, McDonald N, Niu N, Benhamed S, Tuteja JH, Seiwert TY, White KP, McNerney ME, Fitzpatrick C, Wang YL, Furtado LV, Segal JP. Clinical Validation of a Next-Generation Sequencing Genomic Oncology Panel via Cross-Platform Benchmarking against Established Amplicon Sequencing Assays. J Mol Diagn 2016; 19:43-56. [PMID: 27836695 DOI: 10.1016/j.jmoldx.2016.07.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/10/2016] [Accepted: 07/19/2016] [Indexed: 10/20/2022] Open
Abstract
Next-generation sequencing (NGS) genomic oncology profiling assays have emerged as key drivers of personalized cancer care and translational research. However, validation of these assays to meet strict clinical standards has been historically problematic because of both significant assay complexity and a scarcity of optimal validation samples. Herein, we present the clinical validation of 76 genes from a novel 1212-gene large-scale hybrid capture cancer sequencing assay (University of Chicago Medicine OncoPlus) using full-data comparisons against multiple clinical NGS amplicon-based assays to yield dramatic increases in per-sample data comparison efficiency compared with previously published validations. Using a sample set of 104 normal, solid tumor, and hematopoietic malignancy specimens, head-to-head NGS data analyses allowed for 6.8 million individual clinical base call comparisons, including 2729 previously confirmed variants, with 100% sensitivity and specificity. University of Chicago Medicine OncoPlus showed excellent performance for detection of single-nucleotide variants, insertions/deletions up to 52 bp, and FLT3 internal tandem duplications of up to 102 bp or larger. Highly concordant copy number variant and ALK/RET/ROS1 gene fusion detection were also observed. In addition to underlining the efficiency of NGS validation via full-data benchmarking against existing clinical NGS assays, this study also highlights the degree of performance similarity between hybrid capture and amplicon assays that is attainable with the application of strict quality control parameters and optimized computational analytics.
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Affiliation(s)
- Sabah Kadri
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Bradley C Long
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Ibro Mujacic
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Chao J Zhen
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Michelle N Wurst
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Shruti Sharma
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nadia McDonald
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Nifang Niu
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Sonia Benhamed
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jigyasa H Tuteja
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Tanguy Y Seiwert
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kevin P White
- Department of Pathology, the Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois
| | - Megan E McNerney
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Carrie Fitzpatrick
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Y Lynn Wang
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Larissa V Furtado
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois
| | - Jeremy P Segal
- Division of Genomic and Molecular Pathology, The University of Chicago, Chicago, Illinois.
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