1
|
Kim SY, Kim JH, Kim TY, Park SR, Yoon S, Lee S, Lee SH, Kim TM, Han SW, Kim HR, Yun H, Lee S, Kim J, Choi YL, Choi KS, Chae H, Ryu H, Lee GW, Zang DY, Ahn JB. Pragmatic nationwide master observational trial based on genomic alterations in advanced solid tumors: KOrean Precision Medicine Networking Group Study of MOlecular profiling guided therapy based on genomic alterations in advanced Solid tumors (KOSMOS)-II study protocol KCSG AL-22-09. BMC Cancer 2024; 24:574. [PMID: 38724991 PMCID: PMC11080169 DOI: 10.1186/s12885-024-12338-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has been introduced to many Korean institutions to support molecular diagnostics in cancer since 2017, when it became eligible for reimbursement by the National Health Insurance Service. However, the uptake of molecularly guided treatment (MGT) based on NGS results has been limited because of stringent regulations regarding prescriptions outside of approved indications, a lack of clinical trial opportunities, and limited access to molecular tumor boards (MTB) at most institutions. The KOSMOS-II study was designed to demonstrate the feasibility and effectiveness of MGT, informed by MTBs, using a nationwide precision medicine platform. METHODS The KOSMOS-II trial is a large-scale nationwide master observational study. It involves a framework for screening patients with metastatic solid tumors for actionable genetic alterations based on local NGS testing. It recommends MGT through a remote and centralized MTB meeting held biweekly. MGT can include one of the following options: Tier 1, the therapeutic use of investigational drugs targeting genetic alterations such as ALK, EGFR, ERBB2, BRAF, FH, ROS1, and RET, or those with high tumor mutational burden; Tier 2, comprising drugs with approved indications or those permitted for treatment outside of the indications approved by the Health Insurance Review and Assessment Service of Korea; Tier 3, involving clinical trials matching the genetic alterations recommended by the MTB. Given the anticipated proportion of patients receiving MGT in the range of 50% ± 3.25%, this study aims to enroll 1,000 patients. Patients must have progressed to one or more lines of therapy and undergone NGS before enrollment. DISCUSSION This pragmatic master protocol provides a mass-screening platform for rare genetic alterations and high-quality real-world data. Collateral clinical trials, translational studies, and clinico-genomic databases will contribute to generating evidence for drug repositioning and the development of new biomarkers. TRIAL REGISTRATION NCT05525858.
Collapse
Grants
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- HA22C0052 Ministry of Health and Welfare, Republic of Korea
- Roche, Basel, Switzerland
- Lunit, Seoul, Republic of Korea
Collapse
Affiliation(s)
- Sun Young Kim
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Jee Hyun Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea.
| | - Tae-Yong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Sook Ryun Park
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Shinkyo Yoon
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Soohyeon Lee
- Department of Internal Medicine, Korea University College of Medicine, Korea University Anam Hospital, Seoul, South Korea
| | - Se-Hoon Lee
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Yonsei Cancer Center, Seoul, South Korea
| | - Hongseok Yun
- Center for Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Sejoon Lee
- Center for Precision Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jihun Kim
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Yoon-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Kui Son Choi
- Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, South Korea
| | - Heejung Chae
- Department of Internal Medicine, National Cancer Center, Goyang, South Korea
| | - Hyewon Ryu
- Division of Hematology and Oncology, Department of Internal Medicine, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, South Korea
| | - Gyeong-Won Lee
- Division of Hematology-Oncology, Department of Internal Medicine, Institute of Health Science, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, South Korea
| | - Dae Young Zang
- Department of Internal Medicine, Hallym University College of Medicine, Hallym University Sacred Heart Hospital, Anyang, South Korea
| | - Joong Bae Ahn
- Division of Medical Oncology, Department of Internal Medicine, Yonsei University College of Medicine, Yonsei Cancer Center, Seoul, South Korea
| |
Collapse
|
2
|
Koh J, Park HY, Bae JM, Kang J, Cho U, Lee SE, Kang H, Hong ME, Won JK, Choi YL, Kim WS, Lee A. Establishing molecular pathology curriculum for pathology trainees and continued medical education: a collaborative work from the Molecular Pathology Study Group of the Korean Society of Pathologists. J Pathol Transl Med 2023; 57:265-272. [PMID: 37735877 PMCID: PMC10518246 DOI: 10.4132/jptm.2023.08.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The importance of molecular pathology tests has increased during the last decade, and there is a great need for efficient training of molecular pathology for pathology trainees and as continued medical education. METHODS The Molecular Pathology Study Group of the Korean Society of Pathologists appointed a task force composed of experienced molecular pathologists to develop a refined educational curriculum of molecular pathology. A 3-day online educational session was held based on the newly established structure of learning objectives; the audience were asked to score their understanding of 22 selected learning objectives before and after the session to assess the effect of structured education. RESULTS The structured objectives and goals of molecular pathology was established and posted as a web-based interface which can serve as a knowledge bank of molecular pathology. A total of 201 pathologists participated in the educational session. For all 22 learning objectives, the scores of self-reported understanding increased after educational session by 9.9 points on average (range, 6.6 to 17.0). The most effectively improved items were objectives from next-generation sequencing (NGS) section: 'NGS library preparation and quality control' (score increased from 51.8 to 68.8), 'NGS interpretation of variants and reference database' (score increased from 54.1 to 68.0), and 'whole genome, whole exome, and targeted gene sequencing' (score increased from 58.2 to 71.2). Qualitative responses regarding the adequacy of refined educational curriculum were collected, where favorable comments dominated. CONCLUSIONS Approach toward the education of molecular pathology was refined, which would greatly benefit the future trainees.
Collapse
Affiliation(s)
- Jiwon Koh
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ha Young Park
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jun Kang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Uiju Cho
- Department of Pathology, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Seung Eun Lee
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Haeyoun Kang
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Min Eui Hong
- Department of Pathology, Chung-Ang University Hospital, Seoul, Korea
| | - Jae Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Youn-La Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Wan-Seop Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - The Molecular Pathology Study Group of the Korean Society of Pathologists
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Department of Pathology, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Pathology, St. Vincent’s Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
- Department of Pathology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
- Department of Pathology, Chung-Ang University Hospital, Seoul, Korea
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Korea
| |
Collapse
|
3
|
Wils G, Helsmoortel C, Volders PJ, Vereecke I, Milazzo M, Vandesompele J, Coppieters F, De Leeneer K, Lefever S. Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow. Mol Diagn Ther 2022; 26:411-419. [PMID: 35633488 DOI: 10.1007/s40291-022-00585-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2022] [Indexed: 12/01/2022]
Abstract
INTRODUCTION Next-generation sequencing applications are becoming indispensable for clinical diagnostics. These experiments require numerous wet- and dry-laboratory steps, each one increasing the probability of a sample swap or contamination. Therefore, identity confirmation at the end of the process is recommended to ensure the right data are used for each patient. METHODS We tested three commercially available, single nucleotide polymorphism (SNP)-based sample tracking kits in a diagnostic workflow to evaluate their ease of use and performance. The coverage uniformity, on-target specificity, sample identification, and genotyping performance were determined to assess the reliability and cost effectiveness of each kit. RESULTS AND DISCUSSION Hands-on time and manual steps are almost identical for the kits from pxlence and Nimagen. The Swift kit has an extra purification step, making it the longest and most demanding protocol. Furthermore, the Swift kit failed to correctly genotype 26 of the 46 samples. The Nimagen kit identified all but one sample and the pxlence kit unambiguously identified all samples, making it the most reliable and robust kit of this evaluation. The Nimagen kit showed poor on-target mapping rates, resulting in deeper sequencing needs and higher sequencing costs compared with the other two kits. CONCLUSION Our conclusion is that the Human Sample ID kit from pxlence is the most cost effective of the three tested tools for DNA sample tracking and identification.
Collapse
Affiliation(s)
| | - Céline Helsmoortel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | | | - Inge Vereecke
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Mauro Milazzo
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- pxlence BVBA, Dendermonde, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- pxlence BVBA, Dendermonde, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kim De Leeneer
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | | |
Collapse
|
4
|
Vanderbilt CM, Bowman AS, Middha S, Petrova-Drus K, Tang YW, Chen X, Wang Y, Chang J, Rekhtman N, Busam KJ, Gupta S, Hameed M, Arcila ME, Ladanyi M, Berger MF, Dogan S, Zehir A. Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data. J Mol Diagn 2022; 24:515-528. [PMID: 35331965 PMCID: PMC9127461 DOI: 10.1016/j.jmoldx.2022.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
This study is the largest analysis of DNA viruses in solid tumors with associated genomics. To achieve this, a novel method for discovery of DNA viruses from matched tumor/normal next-generation sequencing samples was developed and validated. This method performed comparably to reference methods for the detection of high-risk (HR) human papilloma virus (HPV) (area under the receiver operating characteristic curve = 0.953). After virus identification in 48,148 consecutives samples from 42,846 unique patients, novel virus tumor associations were established by segregating tumor types to determine whether each DNA virus was enriched in each of the tumor types compared with the remaining cohort. All firmly established solid tumor-virus associations (eg, HR HPV in cervical cancer) were confirmed, and the novel associations discovered included: human herpes virus 6 in neuroblastoma, human herpes virus 7 in esophagogastric cancer, and HPV42 in digital papillary adenocarcinoma. These associations were confirmed in an independent validation cohort. HR HPV- and Epstein-Barr virus-associated tumors showed newly discovered genomic associations, including a lower tumor mutation burden. The study demonstrated the ability to study the role of DNA viruses in human cancer from clinical genomics data and established the largest cohort that can be utilized as a validation set for future discovery efforts.
Collapse
Affiliation(s)
- Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi-Wei Tang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xin Chen
- Atila Biosystems Inc., Mountain View, California
| | | | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sounak Gupta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
5
|
Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study. PATTERNS (NEW YORK, N.Y.) 2022; 3:100399. [PMID: 35199060 PMCID: PMC8848022 DOI: 10.1016/j.patter.2021.100399] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023]
Abstract
Tumor purity is the percentage of cancer cells within a tissue section. Pathologists estimate tumor purity to select samples for genomic analysis by manually reading hematoxylin-eosin (H&E)-stained slides, which is tedious, time consuming, and prone to inter-observer variability. Besides, pathologists' estimates do not correlate well with genomic tumor purity values, which are inferred from genomic data and accepted as accurate for downstream analysis. We developed a deep multiple instance learning model predicting tumor purity from H&E-stained digital histopathology slides. Our model successfully predicted tumor purity in eight The Cancer Genome Atlas (TCGA) cohorts and a local Singapore cohort. The predictions were highly consistent with genomic tumor purity values. Thus, our model can be utilized to select samples for genomic analysis, which will help reduce pathologists' workload and decrease inter-observer variability. Furthermore, our model provided tumor purity maps showing the spatial variation within sections. They can help better understand the tumor microenvironment. MIL model successfully predicts a sample's tumor purity from histopathology slides MIL model learns to spatially resolve tumor purity from sample-level labels Tumor purity varies spatially within a sample Pathologists’ region selection is vital for correct percentage tumor nuclei estimation
Given some big data and coarse-level labels, extracting fine-level information is a demanding yet rewarding challenge in data science. This study develops a machine learning model utilizing big data and exploiting coarse-level labels to reveal fine-level details within the data. Although it can be applied to different data science tasks with enormous data and coarse labels, we applied it to a computational histopathology task with gigapixel histopathology slides and sample-level labels. Specifically, the model revealed spatial resolution of tumor purity within histopathology slides using only sample-level genomic tumor purity values during training. This can also be extended to other omics features, providing precious information about cancer biology and promising personalized, precision medicine. Such studies are of great clinical importance in discovering imaging biomarkers and better understanding the tumor microenvironment.
Collapse
|
6
|
Sun KH(M, Wong YT(H, Cheung KM(C, Yuen C(M, Chan YT(T, Lai WY(J, Chao C(D, Fan WS(K, Chow YK(K, Law MF, Tam HC(T. Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12020409. [PMID: 35204500 PMCID: PMC8871212 DOI: 10.3390/diagnostics12020409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) infection has long been proposed as the major etiology of lymphomagenesis. The adoption of high-throughput sequencing has allowed us to gain more insight into the molecular mechanisms of ENKTCL, which largely involve chromosome deletion and aberrations in Janus kinase (JAK)-signal transducer and activator of transcription (STAT), programmed cell death protein-1 (PD-1)/PD-ligand 1 (PD-L1) pathways, as well as mutations in tumor suppressor genes. The molecular findings could potentially influence the traditional chemoradiotherapy approach, which is known to be associated with significant toxicity. This article will review the latest molecular findings in NKTCL and recent advances in the field of molecular diagnosis in NKTCL. Issues of quality control and technical difficulties will also be discussed, along with future prospects in the molecular diagnosis and treatment of NKTCL.
Collapse
Affiliation(s)
- Ka-Hei (Murphy) Sun
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | | | - Ka-Man (Carmen) Cheung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Carmen (Michelle) Yuen
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | - Yun-Tat (Ted) Chan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Yan (Jennifer) Lai
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Chun (David) Chao
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Sum (Katie) Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Yuen-Kiu (Karen) Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Man-Fai Law
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
- Correspondence:
| | - Ho-Chi (Tommy) Tam
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| |
Collapse
|
7
|
Rüschoff J, Baretton G, Bläker H, Dietmaier W, Dietel M, Hartmann A, Horn LC, Jöhrens K, Kirchner T, Knüchel R, Mayr D, Merkelbach-Bruse S, Schildhaus HU, Schirmacher P, Tiemann M, Tiemann K, Weichert W, Büttner R. MSI testing : What's new? What should be considered? DER PATHOLOGE 2021; 42:110-118. [PMID: 34477921 DOI: 10.1007/s00292-021-00948-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/12/2022]
Abstract
Based on new trial data regarding immune checkpoint inhibitors (ICIs), the detection of high-grade microsatellite instability (MSI-H) or underlying deficient mismatch repair protein (dMMR) is now becoming increasingly important for predicting treatment response. For the first time, a PD‑1 ICI (pembrolizumab) has been approved by the European Medicines Agency (EMA) for first-line treatment of advanced (stage IV) dMMR/MSI‑H colorectal cancer (CRC). Further indications, such as dMMR/MSI‑H endometrial carcinoma (EC), have already succeeded (Dostarlimab, 2nd line treatment) and others are expected to follow before the end of 2021. The question of optimal testing in routine diagnostics should therefore be re-evaluated. Based on a consideration of the strengths and weaknesses of the widely available methods (immunohistochemistry and PCR), a test algorithm is proposed that allows quality assured, reliable, and cost-effective dMMR/MSI‑H testing. For CRC and EC, testing is therefore already possible at the primary diagnosis stage, in line with international recommendations (NICE, NCCN). The clinician is therefore enabled from the outset to consider not only the predictive but also the prognostic and predispositional implications of such a test when counseling patients and formulating treatment recommendations. As a basis for quality assurance, participation in interlaboratory comparisons and continuous documentation of results (e.g., QuIP Monitor) are strongly recommended.
Collapse
Affiliation(s)
- Josef Rüschoff
- Institute of Pathology, Nordhessen und Targos Molecular Pathology GmbH, Germaniastr. 7, 34119, Kassel, Germany.
| | - Gustavo Baretton
- Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstr. 74, 01307, Dresden, Germany
| | - Hendrik Bläker
- Institute of Pathology, University Hospital Leipzig, Liebigstr. 26, Gebäude G, 04103, Leipzig, Germany
| | - Wolfgang Dietmaier
- Institute of Pathology, Center of Molecular Pathological Diagnostics, Universität Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | - Manfred Dietel
- Institute of Pathology, University Hospital Charité, Campus Mitte, Charitéplatz 1, 10117, Berlin, Germany
| | - Arndt Hartmann
- Pathological Institute, University Erlangen-Nürnberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Lars-Christian Horn
- Institute of Pathology, University Hospital Leipzig, Liebigstr. 26, Gebäude G, 04103, Leipzig, Germany
| | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus, Fetscherstr. 74, 01307, Dresden, Germany
| | - Thomas Kirchner
- Pathological Institute, Ludwig-Maximilians-University Munich, Thalkirchner Str. 36, 80337, München, Germany
| | - Ruth Knüchel
- Institute of Pathology, University Hospital RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Germany
| | - Doris Mayr
- Pathological Institute, Ludwig-Maximilians-University Munich, Thalkirchner Str. 36, 80337, München, Germany
| | | | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Peter Schirmacher
- Pathological Institute, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
| | - Markus Tiemann
- Fangdieckstr. 75a, Institute of Hematopathology Hamburg, 22547, Hamburg, Germany
| | - Katharina Tiemann
- Fangdieckstr. 75a, Institute of Hematopathology Hamburg, 22547, Hamburg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Trogerstr. 18, 81675, München, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Köln, Germany
| |
Collapse
|
8
|
Ménard T, Barros A, Ganter C. Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development. Ther Innov Regul Sci 2021; 55:1066-1074. [PMID: 34046876 PMCID: PMC8332578 DOI: 10.1007/s43441-021-00308-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing (NGS) and decreased costs of genomic testing are changing the paradigm in precision medicine and continue to fuel innovation. Integration of NGS into clinical drug development has the potential to accelerate clinical trial conduct and ultimately will shape the landscape of clinical care by making it easier to identify patients who would benefit from particular therapy(ies) and to monitor treatment outcomes with less invasive tests. This has led to an increased use of NGS service providers by pharmaceutical sponsors: to screen patients for clinical trials eligibility and for patient stratification, expanded Companion Diagnostic (CDx) development for treatment recommendations and Comprehensive Genomic profiling (CGP). These changes are reshaping the face of clinical quality considerations for precision medicine. Although some clinical quality considerations do exist in Health Authorities (HA) guidances and regulations (e.g., International Conference of Harmonization Good Clinical Practices-GCP), there is currently no holistic GxP-like detailed framework for pharmaceutical sponsors using NGS service providers in clinical trials, or for the development of CDx and CGP. In this research, we identified existing and applicable regulations, guidelines and recommendations that could be translated into clinical quality considerations related to technology, data quality, patients and oversight. We propose these considerations as a basis for pharmaceutical sponsors using NGS service providers in clinical drug development to develop a set of guidelines for NGS clinical quality.
Collapse
Affiliation(s)
| | - Alaina Barros
- Genentech Inc. - A Member of the Roche Group, South San Francisco, USA
| | | |
Collapse
|
9
|
Rüschoff J, Baretton G, Bläker H, Dietmaier W, Dietel M, Hartmann A, Horn LC, Jöhrens K, Kirchner T, Knüchel R, Mayr D, Merkelbach-Bruse S, Schildhaus HU, Schirmacher P, Tiemann M, Tiemann K, Weichert W, Büttner R. [MSI testing : What is new? What should be considered? German version]. DER PATHOLOGE 2021; 42:414-423. [PMID: 34043067 DOI: 10.1007/s00292-021-00944-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/25/2021] [Indexed: 12/21/2022]
Abstract
Based on new trial data regarding immune checkpoint inhibitors (ICIs), the detection of high-grade microsatellite instability (MSI-H) or underlying deficient mismatch repair protein (dMMR) is now becoming increasingly important for predicting treatment response. For the first time, a PD‑1 ICI (pembrolizumab) has been approved by the European Medicines Agency (EMA) for first-line treatment of advanced (stage IV) dMMR/MSI‑H colorectal cancer (CRC). Further indications, such as dMMR/MSI‑H endometrial carcinoma (EC), have already succeeded (Dostarlimab, 2nd line treatment) and others are expected to follow before the end of 2021. The question of optimal testing in routine diagnostics should therefore be re-evaluated. Based on a consideration of the strengths and weaknesses of the widely available methods (immunohistochemistry and PCR), a test algorithm is proposed that allows quality assured, reliable, and cost-effective dMMR/MSI‑H testing. For CRC and EC, testing is therefore already possible at the primary diagnosis stage, in line with international recommendations (NICE, NCCN). The clinician is therefore enabled from the outset to consider not only the predictive but also the prognostic and predispositional implications of such a test when counseling patients and formulating treatment recommendations. As a basis for quality assurance, participation in interlaboratory comparisons and continuous documentation of results (e.g., QuIP Monitor) are strongly recommended.
Collapse
Affiliation(s)
- Josef Rüschoff
- Institut für Pathologie Nordhessen, TARGOS Molecular Pathology GmbH, Germaniastr. 7, 34119, Kassel, Deutschland.
| | - Gustavo Baretton
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus, Fetscherstr. 74, 01307, Dresden, Deutschland
| | - Hendrik Bläker
- Institut für Pathologie, Universitätsklinikum Leipzig, Liebigstr. 26, Gebäude G, 04103, Leipzig, Deutschland
| | - Wolfgang Dietmaier
- Institut für Pathologie/Zentrum für molekularpathologische Diagnostik, Universität Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Deutschland
| | - Manfred Dietel
- Institut für Pathologie, Campus Mitte, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland
| | - Arndt Hartmann
- Pathologisches Institut, Universität Erlangen-Nürnberg, Krankenhausstr. 8-10, 91054, Erlangen, Deutschland
| | - Lars-Christian Horn
- Institut für Pathologie, Universitätsklinikum Leipzig, Liebigstr. 26, Gebäude G, 04103, Leipzig, Deutschland
| | - Korinna Jöhrens
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus, Fetscherstr. 74, 01307, Dresden, Deutschland
| | - Thomas Kirchner
- Pathologisches Institut, Ludwig-Maximilians-Universität München, Thalkirchner Str. 36, 80337, München, Deutschland
| | - Ruth Knüchel
- Institut für Pathologie, Universitätsklinikum RWTH Aachen, Pauwelsstr. 30, 52074, Aachen, Deutschland
| | - Doris Mayr
- Pathologisches Institut, Ludwig-Maximilians-Universität München, Thalkirchner Str. 36, 80337, München, Deutschland
| | - Sabine Merkelbach-Bruse
- Institut für Pathologie, Universitätsklinikum Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - Hans-Ulrich Schildhaus
- Institut für Pathologie, Universitätsklinikum Essen, Hufelandstraße 55, 45147, Essen, Deutschland
| | - Peter Schirmacher
- Pathologisches Institut, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Deutschland
| | - Markus Tiemann
- Institut für Hämatopathologie Hamburg, Fangdieckstr. 75a, 22547, Hamburg, Deutschland
| | - Katharina Tiemann
- Institut für Hämatopathologie Hamburg, Fangdieckstr. 75a, 22547, Hamburg, Deutschland
| | - Wilko Weichert
- Institut für Pathologie, Technische Universität München, Trogerstr. 18, 81675, München, Deutschland
| | - Reinhard Büttner
- Institut für Pathologie, Universitätsklinikum Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| |
Collapse
|
10
|
Chang S, Shim HS, Kim TJ, Choi YL, Kim WS, Shin DH, Kim L, Park HS, Lee GK, Lee CH. Molecular biomarker testing for non-small cell lung cancer: consensus statement of the Korean Cardiopulmonary Pathology Study Group. J Pathol Transl Med 2021; 55:181-191. [PMID: 33966368 PMCID: PMC8141968 DOI: 10.4132/jptm.2021.03.23] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular biomarker testing is the standard of care for non–small cell lung cancer (NSCLC) patients. In 2017, the Korean Cardiopulmonary Pathology Study Group and the Korean Molecular Pathology Study Group co-published a molecular testing guideline which contained almost all known genetic changes that aid in treatment decisions or predict prognosis in patients with NSCLC. Since then there have been significant changes in targeted therapies as well as molecular testing including newly approved targeted drugs and liquid biopsy. In order to reflect these changes, the Korean Cardiopulmonary Pathology Study Group developed a consensus statement on molecular biomarker testing. This consensus statement was crafted to provide guidance on what genes should be tested, as well as methodology, samples, patient selection, reporting and quality control.
Collapse
Affiliation(s)
- Sunhee Chang
- Department of Pathology, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Tae Jung Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yoon-La Choi
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Wan Seop Kim
- Department of Pathology, Konkuk University School of Medicine, Seoul, Korea
| | - Dong Hoon Shin
- Department of Pathology, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Lucia Kim
- Department of Pathology, Inha University School of Medicine, Incheon, Korea
| | - Heae Surng Park
- Department of Pathology, Ewha Womans University Seoul Hospital, Seoul, Korea
| | - Geon Kook Lee
- Department of Pathology, National Cancer Center, Goyang, Korea
| | - Chang Hun Lee
- Department of Pathology, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | | |
Collapse
|
11
|
Seong D, Jung S, Bae S, Chung J, Son DS, Yi BK. Fast Healthcare Interoperability Resources (FHIR)-Based Quality Information Exchange for Clinical Next-Generation Sequencing Genomic Testing: Implementation Study. J Med Internet Res 2021; 23:e26261. [PMID: 33908889 PMCID: PMC8116992 DOI: 10.2196/26261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/10/2021] [Accepted: 04/03/2021] [Indexed: 01/23/2023] Open
Abstract
Background Next-generation sequencing (NGS) technology has been rapidly adopted in clinical practice, with the scope extended to early diagnosis, disease classification, and treatment planning. As the number of requests for NGS genomic testing increases, substantial efforts have been made to deliver the testing results clearly and unambiguously. For the legitimacy of clinical NGS genomic testing, quality information from the process of producing genomic data should be included within the results. However, most reports provide insufficient quality information to confirm the reliability of genomic testing owing to the complexity of the NGS process. Objective The goal of this study was to develop a Fast Healthcare Interoperability Resources (FHIR)–based web app, NGS Quality Reporting (NGS-QR), to report and manage the quality of the information obtained from clinical NGS genomic tests. Methods We defined data elements for the exchange of quality information from clinical NGS genomic tests, and profiled a FHIR genomic resource to enable information exchange in a standardized format. We then developed the FHIR-based web app and FHIR server to exchange quality information, along with statistical analysis tools implemented with the R Shiny server. Results Approximately 1000 experimental data entries collected from the targeted sequencing pipeline CancerSCAN designed by Samsung Medical Center were used to validate implementation of the NGS-QR app using real-world data. The user can share the quality information of NGS genomic testing and verify the quality status of individual samples in the overall distribution. Conclusions This study successfully demonstrated how quality information of clinical NGS genomic testing can be exchanged in a standardized format. As the demand for NGS genomic testing in clinical settings increases and genomic data accumulate, quality information can be used as reference material to improve the quality of testing. This app could also motivate laboratories to perform diagnostic tests to provide high-quality genomic data.
Collapse
Affiliation(s)
- Donghyeong Seong
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sungwon Jung
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sungchul Bae
- Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jongsuk Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Dae-Soon Son
- School of Big Data Science, Data Science Convergence Research Center, Hallym University, Chuncheon, Republic of Korea
| | - Byoung-Kee Yi
- Smart Healthcare Research Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Republic of Korea
| |
Collapse
|
12
|
Jung CK, Jung SH, Jeon S, Jeong YM, Kim Y, Lee S, Bae JS, Chung YJ. Risk Stratification Using a Novel Genetic Classifier Including PLEKHS1 Promoter Mutations for Differentiated Thyroid Cancer with Distant Metastasis. Thyroid 2020; 30:1589-1600. [PMID: 32326836 DOI: 10.1089/thy.2019.0459] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background: Although most differentiated thyroid carcinomas (DTCs) have indolent behavior, DTCs with distant metastasis have a poor prognosis. However, there are no validated markers that predict the risk of distant metastasis and the prognosis of DTC. We aimed to develop a genetic classifier for predicting the outcomes of DTC patients with distant metastases. Methods: Targeted deep sequencing of 157 cancer-related genes was performed for 61 DTCs with distant metastases. A candidate mutation was validated with independent thyroid cancer samples using digital polymerase chain reaction. Results: The most frequently mutated gene in the 61 DTCs was BRAF (n = 31, 51%), followed by TERT promoter (n = 28, 46%), NRAS (n = 13, 11%), PLEKHS1 promoter (n = 6, 10%), and STK11 (n = 6, 10%) mutations. PLEKHS1 promoter mutations were more common in the radioactive iodine (RAI)-refractory cases (p = 0.003). Losses of 9q and 11q were associated with RAI-refractory disease (p = 0.002) and cancer-specific mortality (p = 0.028), respectively. In multivariate analysis, bone metastasis (adjusted odds ratio [aOR] = 15.17, 95% confidence interval [CI 3.38-68.06], p < 0.001) and at least one mutation in the TERT promoter, the PLEKHS1 promoter, or TP53 (aOR = 7.64 [CI 1.78-32.76], p = 0.006) remained significant factors associated with RAI-refractoriness. In independently collected papillary thyroid carcinomas without initial distant metastasis (n = 75), a PLEKHS1 promoter mutation was only found in one case that developed distant metastasis during the follow-up period. We developed a genetic classifier consisting of BRAF, RAS, the TERT promoter, the PLEKHS1 promoter, and TP53 for categorizing the prognosis of patients with DTC with distant metastasis. In the poor-prognosis group, 61% of the patients were RAI-refractory and death occurred in 21% during the follow-up. In the intermediate-prognosis group, 29% were RAI-refractory, but no death occurred. In the good-prognosis group, all patients were RAI-responsive and no death occurred. Conclusions: Mutations in the PLEKHS1 promoter are a novel genetic marker of aggressive DTC. Our genetic classifier can be useful for predicting RAI-refractory disease and poor prognosis in DTC patients with distant metastases.
Collapse
Affiliation(s)
- Chan Kwon Jung
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung-Hyun Jung
- Cancer Evolution Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sora Jeon
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Young Mun Jeong
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yourha Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sohee Lee
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ja-Seong Bae
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- IRCGP, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| |
Collapse
|
13
|
SoRelle JA, Wachsmann M, Cantarel BL. Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays. Arch Pathol Lab Med 2020; 144:1118-1130. [PMID: 32045276 DOI: 10.5858/arpa.2019-0476-ra] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Clinical next-generation sequencing (NGS) is being rapidly adopted, but analysis and interpretation of large data sets prompt new challenges for a clinical laboratory setting. Clinical NGS results rely heavily on the bioinformatics pipeline for identifying genetic variation in complex samples. The choice of bioinformatics algorithms, genome assembly, and genetic annotation databases are important for determining genetic alterations associated with disease. The analysis methods are often tuned to the assay to maximize accuracy. Once a pipeline has been developed, it must be validated to determine accuracy and reproducibility for samples similar to real-world cases. In silico proficiency testing or institutional data exchange will ensure consistency among clinical laboratories. OBJECTIVE.— To provide molecular pathologists a step-by-step guide to bioinformatics analysis and validation design in order to navigate the regulatory and validation standards of implementing a bioinformatic pipeline as a part of a new clinical NGS assay. DATA SOURCES.— This guide uses published studies on genomic analysis, bioinformatics methods, and methods comparison studies to inform the reader on what resources, including open source software tools and databases, are available for genetic variant detection and interpretation. CONCLUSIONS.— This review covers 4 key concepts: (1) bioinformatic analysis design for detecting genetic variation, (2) the resources for assessing genetic effects, (3) analysis validation assessment experiments and data sets, including a diverse set of samples to mimic real-world challenges that assess accuracy and reproducibility, and (4) if concordance between clinical laboratories will be improved by proficiency testing designed to test bioinformatic pipelines.
Collapse
Affiliation(s)
- Jeffrey A SoRelle
- Department of Pathology (SoRelle, Wachsmann), University of Texas Southwestern Medical Center, Dallas
| | - Megan Wachsmann
- Department of Pathology (SoRelle, Wachsmann), University of Texas Southwestern Medical Center, Dallas
| | - Brandi L Cantarel
- Bioinformatics Core Facility (Cantarel), University of Texas Southwestern Medical Center, Dallas.,Department of Bioinformatics (Cantarel), University of Texas Southwestern Medical Center, Dallas.,University of Texas Southwestern Medical Center, Dallas
| |
Collapse
|
14
|
Application Areas of Traditional Molecular Genetic Methods and NGS in relation to Hereditary Urological Cancer Diagnosis. JOURNAL OF ONCOLOGY 2020; 2020:7363102. [PMID: 32612654 PMCID: PMC7317306 DOI: 10.1155/2020/7363102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/22/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Next generation sequencing (NGS) is widely used for diagnosing hereditary cancer syndromes. Often, exome sequencing and extended gene panel approaches are the only means that can be used to detect a pathogenic germline mutation in the case of multiple primary tumors, early onset, a family history of cancer, or a lack of specific signs associated with a particular syndrome. Certain germline mutations of oncogenes and tumor suppressor genes that determine specific clinical phenotypes may occur in mutation hot spots. Diagnosis of such cases, which involve hereditary cancer, does not require NGS, but may be made using PCR and Sanger sequencing. Diagnostic criteria and professional community guidelines developed for hereditary cancers of particular organs should be followed when ordering molecular diagnostic tests for a patient. This review focuses on urological oncology associated with germline mutations. Clinical signs and genetic diagnostic laboratory tests for hereditary forms of renal cell cancer, prostate cancer, and bladder cancer are summarized. While exome sequencing, or, conversely, traditional molecular genetic methods are the procedure of choice in some cases, in most situations, sequencing of multigene panels that are specifically aimed at detecting germline mutations in early onset renal cancer, prostate cancer, and bladder cancer seems to be the basic solution for molecular genetic diagnosis of hereditary cancers.
Collapse
|
15
|
Mehta A, Vasudevan S, Sharma SK, Panigrahi M, Suryavanshi M, Saifi M, Batra U. Biomarker testing for advanced lung cancer by next-generation sequencing; a valid method to achieve a comprehensive glimpse at mutational landscape. ACTA ACUST UNITED AC 2020. [DOI: 10.1186/s41241-020-00089-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Background
Next-generation sequencing (NGS) based assay for finding an actionable driver in non-small-cell lung cancer is a less used modality in clinical practice. With a long list of actionable targets, limited tissue, arduous single-gene assays, the alternative of NGS for broad testing in one experiment looks attractive. We report here our experience with NGS for biomarker testing in hundred advanced lung cancer patients.
Methods
Predictive biomarker testing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel V2 (30 tumors) and Oncomine™ Solid Tumor DNA and Oncomine™ Solid Tumor Fusion Transcript kit (70 tumors) on Ion-Torrent sequencing platform.
Results
One-seventeen distinct aberrations were detected across 29 genes in eighty-six tumors. The most commonly mutated genes were TP53 (43% cases), EGFR (23% cases) and KRAS (17% cases). Thirty-four patients presented an actionable genetic variant for which targeted therapy is presently available, and fifty-two cases harbored non-actionable variants with the possibility of recruitment in clinical trials. NGS results were validated by individual tests for detecting EGFR mutation, ALK1 rearrangement, ROS1 fusion, and c-MET amplification. Compared to single test, NGS exhibited good agreement for detecting EGFR mutations and ALK1 fusion (sensitivity- 88.89%, specificity- 100%, Kappa-score 0.92 and sensitivity- 80%, specificity- 100%, Kappa-score 0.88; respectively). Further, the response of patients harboring tyrosine kinase inhibitor (TKI) sensitizing EGFR mutations was assessed. The progression-free-survival of EGFR positive patients on TKI therapy, harboring a concomitant mutation in PIK3CA-mTOR and/or RAS-RAF-MAPK pathway gene and/or TP53 gene was inferior to those with sole-sensitizing EGFR mutation (2 months vs. 9.5 months, P = 0.015).
Conclusions
This is the first study from South Asia looking into the analytical validity of NGS and describing the mutational landscape of lung cancer patients to study the impact of co-mutations on cancer biology and treatment outcome. Our study demonstrates the clinical utility of NGS testing for identifying actionable variants and making treatment decisions in advanced lung cancer.
Collapse
|
16
|
Lee H, Lee HK, Min SK, Lee WH. 16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer. World J Surg Oncol 2020; 18:19. [PMID: 31980025 PMCID: PMC6982396 DOI: 10.1186/s12957-020-1793-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The aim of this study is to investigate the composition of microbiota in biliary tract cancer patients and healthy adults by metagenome analysis and evaluate its potential values as biomarkers for biliary tract cancer. METHODS Patients who were diagnosed with biliary tract cancer or benign inflammation were enrolled in this study. The control group consisted of healthy adults who presented with no history of significant medical issues. We isolated bacteria-derived extracellular vesicles in the plasma. The microbiome composition was investigated with 16S rDNA metagenome analysis. We evaluated each microbiome to ensure suitability for the biliary tract cancer prediction model. RESULTS A total of 155 patients were included in this study: 24 patients with diagnosed biliary tract cancers, 43 diagnosed with cholecystitis or cholangitis, and 88 healthy adults. The microbiome composition pattern of the biliary tract cancer differed from the microbiome composition pattern seen in healthy adult group in beta diversity analysis. The percent composition of microbiota was found to be different from the phylum to genus level. Differences in the composition of the Bifidobacteriaceae and Pseudomonaceae families and Corynebacteriaceae Corynebacterium, Oxalobacteraceae Ralstonia and Comamonadaceae Comamonas species may be used to develop predictive models for biliary tract cancer. CONCLUSION Biliary tract cancer patients have altered microbiome composition, which represents a promising biomarker to differentiate malignant biliary tract disease from normal control group.
Collapse
Affiliation(s)
- Huisong Lee
- Department of Surgery, Ewha Womans University College of Medicine, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, South Korea
| | - Hyeon Kook Lee
- Department of Surgery, Ewha Womans University College of Medicine, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, South Korea.
| | - Seog Ki Min
- Department of Surgery, Ewha Womans University College of Medicine, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, South Korea
| | | |
Collapse
|
17
|
Seong D, Chung J, Lee KW, Kim SY, Kim BS, Song JK, Jung S, Lee T, Park D, Yi BK, Park WY, Son DS. Benchmark Database for Process Optimization and Quality Control of Clinical Cancer Panel Sequencing. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0202-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
18
|
Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA. Diagnostics (Basel) 2019; 9:diagnostics9030117. [PMID: 31547467 PMCID: PMC6787639 DOI: 10.3390/diagnostics9030117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.
Collapse
|
19
|
Kwon D, Kim B, Shin HC, Kim EJ, Ha SY, Jang KT, Kim ST, Lee J, Kang WK, Park JO, Kim KM. Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study. Transl Oncol 2019; 12:1488-1495. [PMID: 31442744 PMCID: PMC6710823 DOI: 10.1016/j.tranon.2019.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing (NGS)-based cancer panel tests are actively being applied in the clinic for precision oncology. Given the importance of NGS panel tests in the palliative clinical setting, it is critical to understand success rates, factors responsible for test failures, and the incidence of clinically meaningful genetic alterations. We performed NGS cancer panel test with tumors from the stomach (n = 234), colorectum (n = 196), and rare tumors (n = 105) from 535 recurrent or metastatic cancer patients for 1 year. Sequencing was successful in 483 (95.3%) archival tumor samples to find single nucleotide variant (SNV), copy number alteration (CNA), and fusion. NGS testing was unsuccessful in 52 (9.7%) specimens due to inadequate tissue (n = 28), low tumor volume (n = 19), and poor quality of nucleic acid (n = 5). According to the Tier system, variants were classified as Tier IA, 0.8%; IIC, 10.3%; IID, 2.0%; III, 66.7% for gastric: Tier IA, 3.6%; IIC, 11.6% for colorectal: Tier IA, 1.6%; IIC, 13.5%; IID, 0.5%; III, 70.8% for melanoma, and Tier IA, 9.1%; IIC, 1.8%; IID, 1.0%; III, 66.4% for GIST. In total, 30.8% of 483 sequenced cases harbored clinically meaningful variants. In Tier IA, KRAS and ERBB2 were the most commonly altered genes. Interestingly, we identified CD274 (PD-L1) amplification, PTPN11 (SHP2) SNV, TPM3-NTRK1 fusion, and FGFR3-TACC3 fusion as a rare (<2%) alteration having therapeutic targets. In conclusion, although small biopsy samples constitute half of cases, informative NGS results were successfully reported in >90% of archival tissue samples, and 30.8% of them harbored clinically meaningful variants.
Collapse
Affiliation(s)
- Dohee Kwon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Binnari Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyeong Chan Shin
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eun Ji Kim
- Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won Ki Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea.
| |
Collapse
|
20
|
Hippman C, Nislow C. Pharmacogenomic Testing: Clinical Evidence and Implementation Challenges. J Pers Med 2019; 9:jpm9030040. [PMID: 31394823 PMCID: PMC6789586 DOI: 10.3390/jpm9030040] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/25/2022] Open
Abstract
Pharmacogenomics can enhance patient care by enabling treatments tailored to genetic make-up and lowering risk of serious adverse events. As of June 2019, there are 132 pharmacogenomic dosing guidelines for 99 drugs and pharmacogenomic information is included in 309 medication labels. Recently, the technology for identifying individual-specific genetic variants (genotyping) has become more accessible. Next generation sequencing (NGS) is a cost-effective option for genotyping patients at many pharmacogenomic loci simultaneously, and guidelines for implementation of these data are available from organizations such as the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the Dutch Pharmacogenetics Working Group (DPWG). NGS and related technologies are increasing knowledge in the research sphere, yet rates of genomic literacy remain low, resulting in a widening gap in knowledge translation to the patient. Multidisciplinary teams—including physicians, nurses, genetic counsellors, and pharmacists—will need to combine their expertise to deliver optimal pharmacogenomically-informed care.
Collapse
Affiliation(s)
- Catriona Hippman
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, BC, V6T 2A1, Canada.
- BC Mental Health and Addictions Research Institute, 3rd Floor - 938 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, 6619-2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
21
|
A DNA pool of FLT3-ITD positive DNA samples can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation - Testing several different ITD sequences and rates, simultaneously. J Biotechnol 2019; 303:25-29. [PMID: 31302157 DOI: 10.1016/j.jbiotec.2019.06.305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
Internal tandem duplication (ITD) in the fms-like tyrosine kinase 3 (FLT3) gene is one of the most frequent genetic alteration in acute myeloid leukemia (AML), and it is associated with worse clinical outcome. Not only the presence but also the size, localization and the rate of this variant or the presence of multiple ITDs has prognostic information. The traditional PCR based diagnostic methods cannot provide information about all of these parameters in one assay, however the application of next generation sequencing (NGS) technique can be a reliable solution for this diagnostic problem. In order to evaluate the analytical properties of an NGS-based FLT3-ITD detection assay a quality control sample was prepared from DNA of AML patients containing 19 different FLT3-ITD variants identified by NGS. The higher the total read count was in a certain sample of the NGS run, the more ITD variant types could be detected. The maximal sensitivity of FLT3-ITD detection by NGS technique was as low as 0.007% FLT3-ITD/total allele rate, however, below 0.1% rate, the reproducibility of the quantitation was poor (CV > 25%). DNA pools with several FLT3-ITDs can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation testing several different ITD sequences and rates, simultaneously.
Collapse
|
22
|
Naugler C, Church DL. Clinical laboratory utilization management and improved healthcare performance. Crit Rev Clin Lab Sci 2019. [DOI: 10.1080/10408363.2018.1526164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christopher Naugler
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Family Medicine, University of Calgary, Calgary, Canada
- Department of Community Health Sciences, University of Calgary, Calgary, Canada
| | - Deirdre L. Church
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
- Department of Medicine, University of Calgary, Calgary, Canada
| |
Collapse
|
23
|
Abstract
During the last decade, ncRNAs have been investigated intensively and revealed their regulatory role in various biological processes. Worldwide research efforts have identified numerous ncRNAs and multiple RNA subtypes, which are attributed to diverse functionalities known to interact with different functional layers, from DNA and RNA to proteins. This makes the prediction of functions for newly identified ncRNAs challenging. Current bioinformatics and systems biology approaches show promising results to facilitate an identification of these diverse ncRNA functionalities. Here, we review (a) current experimental protocols, i.e., for Next Generation Sequencing, for a successful identification of ncRNAs; (b) sequencing data analysis workflows as well as available computational environments; and (c) state-of-the-art approaches to functionally characterize ncRNAs, e.g., by means of transcriptome-wide association studies, molecular network analyses, or artificial intelligence guided prediction. In addition, we present a strategy to cover the identification and functional characterization of unknown transcripts by using connective workflows.
Collapse
|
24
|
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples. Genet Med 2018; 21:972-981. [PMID: 30287923 PMCID: PMC6450397 DOI: 10.1038/s41436-018-0278-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Following automated variant calling, manual review of aligned read sequences is required to identify a high-quality list of somatic variants. Despite widespread use in analyzing sequence data, methods to standardize manual review have not been described, resulting in high inter- and intralab variability. METHODS This manual review standard operating procedure (SOP) consists of methods to annotate variants with four different calls and 19 tags. The calls indicate a reviewer's confidence in each variant and the tags indicate commonly observed sequencing patterns and artifacts that inform the manual review call. Four individuals were asked to classify variants prior to, and after, reading the SOP and accuracy was assessed by comparing reviewer calls with orthogonal validation sequencing. RESULTS After reading the SOP, average accuracy in somatic variant identification increased by 16.7% (p value = 0.0298) and average interreviewer agreement increased by 12.7% (p value < 0.001). Manual review conducted after reading the SOP did not significantly increase reviewer time. CONCLUSION This SOP supports and enhances manual somatic variant detection by improving reviewer accuracy while reducing the interreviewer variability for variant calling and annotation.
Collapse
|
25
|
Bae JM, Won JK, Park SH. Recent Advancement of the Molecular Diagnosis in Pediatric Brain Tumor. J Korean Neurosurg Soc 2018; 61:376-385. [PMID: 29742887 PMCID: PMC5957317 DOI: 10.3340/jkns.2018.0057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 12/11/2022] Open
Abstract
Recent discoveries of brain tumor-related genes and fast advances in genomic testing technologies have led to the era of molecular diagnosis of brain tumor. Molecular profiling of brain tumor became the significant step in the diagnosis, the prediction of prognosis and the treatment of brain tumor. Because traditional molecular testing methods have limitations in time and cost for multiple gene tests, next-generation sequencing technologies are rapidly introduced into clinical practice. Targeted sequencing panels using these technologies have been developed for brain tumors. In this article, focused on pediatric brain tumor, key discoveries of brain tumor-related genes are reviewed and cancer panels used in the molecular profiling of brain tumor are discussed.
Collapse
Affiliation(s)
- Jeong-Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jae-Kyung Won
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Neuroscience Institute, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
26
|
Lee A, Lee SH, Jung CK, Park G, Lee KY, Choi HJ, Min KO, Kim TJ, Lee EJ, Lee YS. Use of the Ion AmpliSeq Cancer Hotspot Panel in clinical molecular pathology laboratories for analysis of solid tumours: With emphasis on validation with relevant single molecular pathology tests and the Oncomine Focus Assay. Pathol Res Pract 2018; 214:713-719. [PMID: 29615338 DOI: 10.1016/j.prp.2018.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/21/2018] [Accepted: 03/05/2018] [Indexed: 11/16/2022]
Abstract
Targeted application of next-generation sequencing (NGS) technology allows detection of specific mutations that can provide treatment opportunities for cancer patients. We evaluated the applicability of the Ion AmpliSeq Cancer Hotspot Panel V2 (CHV2) using formalin-fixed, paraffin-embedded (FFPE) tissue of clinical specimens. Thirty-five FFPE tumour samples with known mutational status were collected from four different hospitals and sequenced with CHV2 using an Ion Chef System and Ion S5 XL system. Out of 35 cases, seven were sequenced with Oncomine focus Assay Panel for comparison. For the limit of detection test, we used an FFPE reference standard, a cell line that included an engineered 50% EGFR T790 M in an RKO cell line background. Coverage analysis results including number of mapped reads, on target percent, mean depth, and uniformity were not different according to hospitals. Sensitivity for mutation detection down to 3% was demonstrated. NGS results showed 100% concordance with the results from single molecular pathology tests Assay in 30 cases with 24 known positive mutations and 14 known negative mutations, and another NGS panel of the Oncomine focus in seven cases. The CHV2 NGS test for solid tumours using Ion chef system and S5 XL system in clinical molecular pathology laboratories for analysis of solid tumours could be routinely used and could replace some single molecular pathology tests after a stringent and thorough validation process.
Collapse
Affiliation(s)
- Ahwon Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung-Hak Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chan Kwon Jung
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gyungsin Park
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyo Young Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyun Joo Choi
- Department of Hospital Pathology, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki Ouk Min
- Department of Hospital Pathology, St. Paul's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tae Jung Kim
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Eun Jung Lee
- Department of Hospital Pathology, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Youn Soo Lee
- Department of Hospital Pathology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| |
Collapse
|
27
|
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.
Collapse
|
28
|
Gong J, Pan K, Fakih M, Pal S, Salgia R. Value-based genomics. Oncotarget 2018; 9:15792-15815. [PMID: 29644010 PMCID: PMC5884665 DOI: 10.18632/oncotarget.24353] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/19/2018] [Indexed: 12/18/2022] Open
Abstract
Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.
Collapse
Affiliation(s)
- Jun Gong
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Kathy Pan
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marwan Fakih
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Sumanta Pal
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| |
Collapse
|
29
|
Fumagalli C, Vacirca D, Rappa A, Passaro A, Guarize J, Rafaniello Raviele P, de Marinis F, Spaggiari L, Casadio C, Viale G, Barberis M, Guerini-Rocco E. The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics. J Clin Pathol 2018. [PMID: 29535211 DOI: 10.1136/jclinpath-2018-205032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Molecular profiling of advanced non-small cell lung cancers (NSCLC) is essential to identify patients who may benefit from targeted treatments. In the last years, the number of potentially actionable molecular alterations has rapidly increased. Next-generation sequencing allows for the analysis of multiple genes simultaneously. AIMS To evaluate the feasibility and the throughput of next-generation sequencing in clinical molecular diagnostics of advanced NSCLC. METHODS A single-institution cohort of 535 non-squamous NSCLC was profiled using a next-generation sequencing panel targeting 22 actionable and cancer-related genes. RESULTS 441 non-squamous NSCLC (82.4%) harboured at least one gene alteration, including 340 cases (63.6%) with clinically relevant molecular aberrations. Mutations have been detected in all but one gene (FGFR1) of the panel. Recurrent alterations were observed in KRAS, TP53, EGFR, STK11 and MET genes, whereas the remaining genes were mutated in <5% of the cases. Concurrent mutations were detected in 183 tumours (34.2%), mostly impairing KRAS or EGFR in association with TP53 alterations. CONCLUSIONS The study highlights the feasibility of targeted next-generation sequencing in clinical setting. The majority of NSCLC harboured mutations in clinically relevant genes, thus identifying patients who might benefit from different targeted therapies.
Collapse
Affiliation(s)
- Caterina Fumagalli
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Davide Vacirca
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology, Milan, Italy
| | - Juliana Guarize
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy
| | | | - Filippo de Marinis
- Division of Thoracic Oncology, European Institute of Oncology, Milan, Italy
| | - Lorenzo Spaggiari
- Division of Thoracic Surgery, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Chiara Casadio
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Massimo Barberis
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| |
Collapse
|