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Cheng C, Cheng Q, Zhou W, Chen Y, Xiao P. Highly accurate single-color fluorogenic DNA decoding sequencing for mutational genotyping. J Pharm Biomed Anal 2024; 249:116397. [PMID: 39111245 DOI: 10.1016/j.jpba.2024.116397] [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: 04/22/2024] [Revised: 07/30/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024]
Abstract
We proposed a single-color fluorogenic DNA decoding sequencing method designed to improve sequencing accuracy, increase read length and throughput, as well as decrease scanning time. This method involves the incorporation of a mixture of four types of 3'-O-modified nucleotide reversible terminators into each reaction. Among them, two nucleotides are labeled with the same fluorophore, while the remaining two are unlabeled. Only one nucleotide can be extended in each reaction, and an encoding that partially defines base composition can be obtained. Through cyclic interrogation of a template twice with different nucleotide combinations, two sets of encodings are sequentially obtained, enabling the determination of the sequence. We demonstrate the feasibility of this method using established sequencing chemistry, achieving a cycle efficiency of approximately 99.5 %. Notably, this strategy exhibits remarkable efficacy in the detection and correction of sequencing errors, achieving a theoretical error rate of 0.00016 % at a sequencing depth of ×2, which is lower than Sanger sequencing. This method is theoretically compatible with the existing sequencing-by-synthesis (SBS) platforms, and the instrument is simpler, which may facilitate further reductions in sequencing costs, thereby broadening its applications in biology and medicine. Moreover, we demonstrate the capability to detect known mutation sites using information from only a single sequencing run. We validate this approach by accurately identifying a mutation site in the human mitochondrial DNA.
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Affiliation(s)
- Chu Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Qingzhou Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Wei Zhou
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Yulong Chen
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China
| | - Pengfeng Xiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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2
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Cheng C, Cheng Q, Zhou W, Chen Y, Liu W, Zhang Z, Ye J, Xiao P. A correctable decoding DNA sequencing with high accuracy and high throughput. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39171437 DOI: 10.1039/d4ay00831f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Eliminating errors in next-generation sequencing has proven to be challenging. Here we present a novel strategy for DNA sequencing, called correctable two-color fluorogenic DNA decoding sequencing, which can significantly improve sequencing accuracy and throughput by employing a dual-nucleotide addition combined with fluorogenic sequencing-by-synthesis (SBS) chemistry. This sequencing method involves introducing a mixture of natural nucleotide X, labeled unblocked nucleotide X', 3' blocked nucleotide Y*, and labeled 3' blocked nucleotide Y* into each reaction cycle. By cyclically interrogating a template twice with different nucleotide combinations, two sets of base-encoding are sequentially obtained, enabling accurate deduction of base sequence. We demonstrate the remarkable efficacy of this approach in detecting and correcting sequencing errors, achieving a theoretical error rate of 0.0005%, which is twice as accurate as Sanger sequencing. Furthermore, we show the capability to detect known mutation sites using information from only a single sequencing run. The correctable two-color fluorogenic DNA decoding sequencing approach should enable accurate identification of extremely rare genomic variations in diverse applications in biology and medicine.
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Affiliation(s)
- Chu Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Qingzhou Cheng
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Wei Zhou
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Yulong Chen
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | - Wenbin Liu
- College of Medicine and Health Science, Wuhan Polytechnic University, Wuhan, China.
| | | | - Jingsi Ye
- Huaren Technology Co., Ltd, Wuhu, China
| | - Pengfeng Xiao
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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3
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Cheng C, Fei Z, Xiao P. Methods to improve the accuracy of next-generation sequencing. Front Bioeng Biotechnol 2023; 11:982111. [PMID: 36741756 PMCID: PMC9895957 DOI: 10.3389/fbioe.2023.982111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023] Open
Abstract
Next-generation sequencing (NGS) is present in all fields of life science, which has greatly promoted the development of basic research while being gradually applied in clinical diagnosis. However, the cost and throughput advantages of next-generation sequencing are offset by large tradeoffs with respect to read length and accuracy. Specifically, its high error rate makes it extremely difficult to detect SNPs or low-abundance mutations, limiting its clinical applications, such as pharmacogenomics studies primarily based on SNP and early clinical diagnosis primarily based on low abundance mutations. Currently, Sanger sequencing is still considered to be the gold standard due to its high accuracy, so the results of next-generation sequencing require verification by Sanger sequencing in clinical practice. In order to maintain high quality next-generation sequencing data, a variety of improvements at the levels of template preparation, sequencing strategy and data processing have been developed. This study summarized the general procedures of next-generation sequencing platforms, highlighting the improvements involved in eliminating errors at each step. Furthermore, the challenges and future development of next-generation sequencing in clinical application was discussed.
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Cheng C, Fei Z, Xiao P, Huang H, Zhou G, Lu Z. Analysis of mutational genotyping using correctable decoding sequencing with superior specificity. Analyst 2023; 148:402-411. [PMID: 36537878 DOI: 10.1039/d2an01805e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability to accurately identify SNPs or low-abundance mutations is important for early clinical diagnosis of diseases, but the existing high-throughput sequencing platforms are limited in terms of their accuracy. Here, we propose a correctable decoding sequencing strategy that may be used for high-throughput sequencing platforms. This strategy is based on adding a mixture of two types of mononucleotides, natural nucleotide and cyclic reversible termination (CRT), for cyclic sequencing. Using the synthetic characteristic of CRTs, about 75% of the calls are unambiguous for a single sequencing run, and the remaining ambiguous sequence can be accurately deduced by two parallel sequencing runs. We demonstrate the feasibility of this strategy, and its cycle efficiency can reach approximately 99.3%. This strategy is proved to be effective for correcting errors and identifying whether the sequencing information is correct or not. And its conservative theoretical error rate was determined to be 0.0009%, which is lower than that of Sanger sequencing. In addition, we establish that the information of only a single sequencing run can be used to detect samples with known mutation sites. We apply this strategy to accurately identify a mutation site in mitochondrial DNA from human cells.
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Affiliation(s)
- Chu Cheng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Zhongjie Fei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Pengfeng Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Huan Huang
- Department of Obstetrics and Gynecology, The first Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular, Medical School of Nanjing University, Nanjing, 210000, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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Rotondo JC, Martini F, Maritati M, Caselli E, Gallenga CE, Guarino M, De Giorgio R, Mazziotta C, Tramarin ML, Badiale G, Tognon M, Contini C. Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection. Microorganisms 2022; 10:1193. [PMID: 35744711 PMCID: PMC9231257 DOI: 10.3390/microorganisms10061193] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.
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Affiliation(s)
- John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Martina Maritati
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Orthopaedic Ward, Casa di Cura Santa Maria Maddalena, 45030 Occhiobello, Italy
| | - Elisabetta Caselli
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Carla Enrica Gallenga
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Matteo Guarino
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Roberto De Giorgio
- Department of Translational Medicine, St. Anna University Hospital of Ferrara, University of Ferrara, 44124 Ferrara, Italy; (M.G.); (R.D.G.)
| | - Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
- Center for Studies on Gender Medicine, Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Letizia Tramarin
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Giada Badiale
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
| | - Carlo Contini
- Department of Medical Sciences, University of Ferrara, 44121 Ferrara, Italy; (F.M.); (M.M.); (C.E.G.); (C.M.); (M.L.T.); (G.B.); (M.T.)
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Cho JH, Charnot-Katsikas A, Segal J, Pytel P. Identification of Molecular Alterations Challenging Initial Pathologic Classification in Cases of Clinician-Initiated Next-Generation Sequencing Testing. Am J Clin Pathol 2021; 156:1007-1018. [PMID: 34180985 DOI: 10.1093/ajcp/aqab062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Large gene panel next-generation sequencing (NGS) is a powerful tool capable of generating predictive data on cancer prognosis and response to specific therapeutic interventions. The utility of large panel NGS data on tumor classification, however, may be underappreciated because of a workflow that often circumvents the surgical pathologist. We sought to describe cases in which NGS data lead to an unanticipated change in tumor classification and to discuss current workflow practices of NGS testing that limit its use as a diagnostic adjunct. METHODS We performed a retrospective review to identify cases in which NGS testing uncovered data that led to a revision of the initial pathologic diagnosis that an outside or in-house pathologist had made. RESULTS Nine cases are presented in which NGS data provided insights that led to a revision of the original pathologic diagnosis. Distinctive molecular signatures, mutational signatures, fusions, or identification of viral sequencing provided the critical evidence on which these tumors were reclassified. CONCLUSIONS The current workflow of NGS testing should always include the surgical pathologist as an active partner to ensure that the molecular results are fully reflected in the final diagnosis. In some instances, active participation by the surgical pathologist may require amendment of previously issued pathology reports.
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Affiliation(s)
- Joseph H Cho
- Medical Sciences Institute, Versiti Blood Center of Wisconsin, Milwaukee, WI, USA
| | | | - Jeremy Segal
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Peter Pytel
- Department of Pathology, University of Chicago, Chicago, IL, USA
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Lee HF, Chi CS, Tsai CR. Diagnostic yield and treatment impact of whole-genome sequencing in paediatric neurological disorders. Dev Med Child Neurol 2021; 63:934-938. [PMID: 33244750 DOI: 10.1111/dmcn.14722] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/23/2020] [Indexed: 12/19/2022]
Abstract
AIM To investigate the diagnostic yield and treatment impact of whole-genome sequencing (WGS) in patients with paediatric neurological disorders. METHOD From January 2016 to December 2019, paediatric patients who had suspected genetic neurological disorders were assessed using WGS. The phenotypes of eligible patients were divided into four groups: patients with neurodevelopmental disorders; patients with epilepsy; patients with neuromuscular disorders; and patients with movement disorders. RESULTS A total of 214 consecutive patients (128 males, 86 females) underwent WGS. The mean (SD) age of disease onset was 13.8 (27.6) months (range 1d-15y 5mo). The mean (SD) age at which WGS was performed was 71.7 (58.9) months (range 8d-18y). A molecular diagnosis was reported in 43.9% of patients. The highest diagnostic rate was achieved in 62.5% of patients with neuromuscular disorders, 47.5% of patients with epilepsy, 41.1% of patients with neurodevelopment disorders, and 15.4% of patients with movement disorders. All 94 patients with a WGS diagnosis were given access to genetic counselling and 23.4% of patients had immediate changes in treatment strategies after undergoing WGS. INTERPRETATION WGS allows paediatric neurologists to integrate genomic data into their diagnosis and adjust management strategies for a range of clinical and genetically heterogeneous disease entities to improve the clinical outcomes of patients. In our cohort, the diagnosis of a significant proportion of patients was reached through WGS (43.9%). Clinicians could use these results to directly guide the management of their patients and improve their clinical outcomes (23.4%). What this paper adds For selected children in our cohort, the diagnostic yield of whole-genome sequencing (WGS) was 43.9%. WGS can be used to expand our knowledge of phenotype-genotype variations.
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Affiliation(s)
- Hsiu-Fen Lee
- Division of Paediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan
| | - Ching-Shiang Chi
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Division of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli, Taiwan.,Division of Paediatric Neurology, Department of Paediatrics, Tungs' Taichung Metroharbor Hospital, Taichung, Taiwan.,College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Paediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
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Rosenbaum JN, Berry AB, Church AJ, Crooks K, Gagan JR, López-Terrada D, Pfeifer JD, Rennert H, Schrijver I, Snow AN, Wu D, Ewalt MD. A Curriculum for Genomic Education of Molecular Genetic Pathology Fellows: A Report of the Association for Molecular Pathology Training and Education Committee. J Mol Diagn 2021; 23:1218-1240. [PMID: 34245921 DOI: 10.1016/j.jmoldx.2021.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Molecular genetic pathology (MGP) is a subspecialty of pathology and medical genetics and genomics. Genomic testing, which we define as that which generates large data sets and interrogates large segments of the genome in a single assay, is increasingly recognized as essential for optimal patient care through precision medicine. The most common genomic testing technologies in clinical laboratories are next-generation sequencing and microarray. It is essential to train in these methods and to consider the data generated in the context of the diagnosis, medical history, and other clinical findings of individual patients. Accordingly, updating the MGP fellowship curriculum to include genomics is timely, important, and challenging. At the completion of training, an MGP fellow should be capable of independently interpreting and signing out results of a wide range of genomic assays and, given the appropriate context and institutional support, of developing and validating new assays in compliance with applicable regulations. The Genomics Task Force of the MGP Program Directors, a working group of the Association for Molecular Pathology Training and Education Committee, has developed a genomics curriculum framework and recommendations specific to the MGP fellowship. These recommendations are presented for consideration and implementation by MGP fellowship programs with the understanding that MGP programs exist in a diversity of clinical practice environments with a spectrum of available resources.
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Affiliation(s)
- Jason N Rosenbaum
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna B Berry
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Swedish Cancer Institute and Institute of Systems Biology, Seattle, Washington
| | - Alanna J Church
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Kristy Crooks
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jeffrey R Gagan
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Dolores López-Terrada
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Baylor College of Medicine, Houston, Texas
| | - John D Pfeifer
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Hanna Rennert
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Iris Schrijver
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Anthony N Snow
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - David Wu
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Mark D Ewalt
- Molecular Genetic Pathology Fellow Training in Genomics Task Force of the Training and Education Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Min YK, Park KS. The Application of Control Materials for Ongoing Quality Management of Next-Generation Sequencing in a Clinical Genetic Laboratory. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:543. [PMID: 34071304 PMCID: PMC8227145 DOI: 10.3390/medicina57060543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing (NGS) has played an important role in detecting genetic variants with pathologic and therapeutic potential. The advantages of NGS, such as high-throughput sequencing capacity and massively parallel sequencing, have a significant impact on realization of genetic profiling in clinical genetic laboratories. These changes have enabled clinicians to execute precision medicine in diagnosis, prognosis, and treatment for patients. However, to adapt targeted gene panels in diagnostic use, analytical validation and ongoing quality control should be implemented and applied with both practical guidelines and appropriate control materials. Several guidelines for NGS quality control recommend usage of control materials such as HapMap cell lines, synthetic DNA fragments, and genetically characterized cell lines; however, specifications or applications of such usage are insufficient to guideline method development. This review focuses on what factors should be considered before control material selection for NGS assay and practical methods of how they could be developed in clinical genetic laboratories. This review also provides the detailed sources of critical information related to control materials.
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Affiliation(s)
- Young-Kyu Min
- Department of Medical Laser, Dankook University, Chungnam 31116, Korea;
- Department of Laboratory Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyung-Sun Park
- Department of Laboratory Medicine, Kyung Hee University School of Medicine and Kyung Hee University Medical Center, Seoul 02447, Korea
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10
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Implementing Pharmacogenomics Testing: Single Center Experience at Arkansas Children's Hospital. J Pers Med 2021; 11:jpm11050394. [PMID: 34064668 PMCID: PMC8150685 DOI: 10.3390/jpm11050394] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023] Open
Abstract
Pharmacogenomics (PGx) is a growing field within precision medicine. Testing can help predict adverse events and sub-therapeutic response risks of certain medications. To date, the US FDA lists over 280 drugs which provide biomarker-based dosing guidance for adults and children. At Arkansas Children’s Hospital (ACH), a clinical PGx laboratory-based test was developed and implemented to provide guidance on 66 pediatric medications for genotype-guided dosing. This PGx test consists of 174 single nucleotide polymorphisms (SNPs) targeting 23 clinically actionable PGx genes or gene variants. Individual genotypes are processed to provide per-gene discrete results in star-allele and phenotype format. These results are then integrated into EPIC- EHR. Genomic indicators built into EPIC-EHR provide the source for clinical decision support (CDS) for clinicians, providing genotype-guided dosing.
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Cree IA, Indave Ruiz BI, Zavadil J, McKay J, Olivier M, Kozlakidis Z, Lazar AJ, Hyde C, Holdenrieder S, Hastings R, Rajpoot N, de la Fouchardiere A, Rous B, Zenklusen JC, Normanno N, Schilsky RL. The International Collaboration for Cancer Classification and Research. Int J Cancer 2021; 148:560-571. [PMID: 32818326 PMCID: PMC7756795 DOI: 10.1002/ijc.33260] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3 R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3 R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges.
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Affiliation(s)
- Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | | | - Jiri Zavadil
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - James McKay
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Magali Olivier
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Zisis Kozlakidis
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular PathologyThe University of Texas, MD Anderson Cancer CenterHoustonTexasUSA
| | - Chris Hyde
- Exeter Test GroupCollege of Medicine and Health, University of ExeterExeterUK
| | | | - Ros Hastings
- GenQA (Genomics External Quality Assessment)Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation TrustOxfordUK
| | - Nasir Rajpoot
- Department of Computer ScienceUniversity of WarwickCoventryUK
- Alan Turing InstituteLondonUK
- Department of PathologyUniversity Hospitals Coventry & Warwickshire NHS TrustCoventryUK
| | | | - Brian Rous
- National Cancer Registration Service (Eastern Office), Public Health England, Victoria HouseCambridgeUK
| | - Jean Claude Zenklusen
- Center for Cancer GenomicsNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Nicola Normanno
- Cell Biology and Biotherapy UnitIstituto Nazionale Tumori—IRCCS—“Fondazione G. Pascale,” Via M. SemmolaNaplesItaly
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Guelly C, Abilova Z, Nuralinov O, Panzitt K, Akhmetova A, Rakhimova S, Kozhamkulov U, Kairov U, Molkenov A, Seisenova A, Trajanoski S, Abildinova Rashbayeva G, Kaussova G, Windpassinger C, Lee JH, Zhumadilov Z, Bekbossynova M, Akilzhanova A. Patients with coronary heart disease, dilated cardiomyopathy and idiopathic ventricular tachycardia share overlapping patterns of pathogenic variation in cardiac risk genes. PeerJ 2021; 9:e10711. [PMID: 33552729 PMCID: PMC7821765 DOI: 10.7717/peerj.10711] [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: 03/25/2020] [Accepted: 12/15/2020] [Indexed: 12/22/2022] Open
Abstract
Background Ventricular tachycardia (VT) is a major cause of sudden cardiac death (SCD). Clinical investigations can sometimes fail to identify the underlying cause of VT and the event is classified as idiopathic (iVT). VT contributes significantly to the morbidity and mortality in patients with coronary artery disease (CAD) and dilated cardiomyopathy (DCM). Since mutations in arrhythmia-associated genes frequently determine arrhythmia susceptibility screening for disease-predisposing variants could improve VT diagnostics and prevent SCD in patients. Methods Ninety-two patients diagnosed with coronary heart disease (CHD), DCM, or iVT were included in our study. We evaluated genetic profiles and variants in known cardiac risk genes by targeted next generation sequencing (NGS) using a newly designed custom panel of 96 genes. We hypothesized that shared morphological and phenotypical features among these subgroups may have an overlapping molecular base. To our knowledge, this was the first study of the deep sequencing of 96 targeted cardiac genes in Kazakhstan. The clinical significance of the sequence variants was interpreted according to the guidelines developed by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) in 2015. The ClinVar and Varsome databases were used to determine the variant classifications. Results Targeted sequencing and stepwise filtering of the annotated variants identified a total of 307 unique variants in 74 genes, totally 456 variants in the overall study group. We found 168 mutations listed in the Human Genome Mutation Database (HGMD) and another 256 rare/unique variants with elevated pathogenic potential. There was a predominance of high- to intermediate pathogenicity variants in LAMA2, MYBPC3, MYH6, KCNQ1, GAA, and DSG2 in CHD VT patients. Similar frequencies were observed in DCM VT, and iVT patients, pointing to a common molecular disease association. TTN, GAA, LAMA2, and MYBPC3 contained the most variants in the three subgroups which confirm the impact of these genes in the complex pathogenesis of cardiomyopathies and VT. The classification of 307 variants according to ACMG guidelines showed that nine (2.9%) variants could be classified as pathogenic, nine (2.9%) were likely pathogenic, 98 (31.9%) were of uncertain significance, 73 (23.8%) were likely benign, and 118 (38.4%) were benign. CHD VT patients carry rare genetic variants with increased pathogenic potential at a comparable frequency to DCM VT and iVT patients in genes related to sarcomere function, nuclear function, ion flux, and metabolism. Conclusions In this study we showed that in patients with VT secondary to coronary artery disease, DCM, or idiopathic etiology multiple rare mutations and clinically significant sequence variants in classic cardiac risk genes associated with cardiac channelopathies and cardiomyopathies were found in a similar pattern and at a comparable frequency.
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Affiliation(s)
- Christian Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Zhannur Abilova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Katrin Panzitt
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Saule Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ulykbek Kairov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Askhat Molkenov
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Ainur Seisenova
- Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Slave Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | | | | | | | - Joseph H Lee
- Sergievsky Center Taub Institute, Columbia University Medical Center, New York, NY, United States of America
| | - Zhaxybay Zhumadilov
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Science, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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秀芬 李, 上 遲, 啟仁 蔡. 全基因體定序對兒童神經疾病的診斷率和治療影響. Dev Med Child Neurol 2020; 63. [PMID: 33289097 DOI: 10.1111/dmcn.14729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
: (WGS) 。 : 2016 1 2019 12 , 。: 、、。。 : 214 ( 128 , 86 ) , (SD) 13.8 (27.6) , 1 15 5 , (SD) 71.7 (58.9) , 8 18 。 43.9% , 62.5%, 47.5%, 41.1% 15.4%。 94, 23.4% 。 : , , 。, (43.9%), , (23.4%) 。.
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14
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Urban A. "…This Has to Do With My Identity. And I Don't Want to Make it Totally Transparent." Identity Relevance in the Attitudes of Affected People and Laypersons to the Handling of High-Throughput Genomic Data. FRONTIERS IN SOCIOLOGY 2020; 5:532357. [PMID: 33869478 PMCID: PMC8022580 DOI: 10.3389/fsoc.2020.532357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
With the establishment of genome sequencing, the influence of genomic information on self-understanding and identity construction has become increasingly important. New sequencing methods far exceed previous genetic tests in terms of scope and quantity. Despite theoretical approaches, however, there are few empirical findings on the identity-relevant influence of genomic information. The present study examines genomic information's identity-relevant influences and considers whether developments in the field of genome sequencing may generate problems that are not yet addressed by existing identity concepts based on traditional genetic tests. The study is based on 10 partially standardized interviews with personally affected persons and four focus groups with medical laypersons as representatives of the public, which were evaluated on the basis of qualitative content analysis. As a result, this paper presents five thematic areas with identity-relevant references within subjective attitudes toward the handling of genomic information, and also derives two basic identity concepts. The results indicate that the lay discourse is still strongly based on older debates about genetic testing and that the view on the complexity of genomic information established in the scientific context has thus far no influence on the perspectives either of those affected or laypersons.
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Affiliation(s)
- Alexander Urban
- Department of Medical Ethics and History of Medicine, University Medical Center Göttingen, Göttingen, Germany
- Faculty of Social Sciences, Georg-August-University Göttingen, Göttingen, Germany
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15
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Diñeiro M, Capín R, Cifuentes GÁ, Fernández‐Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo‐Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández‐Vega Á, Cabanillas R, Cadiñanos J. Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options. Acta Ophthalmol 2020; 98:e1034-e1048. [PMID: 32483926 PMCID: PMC7754416 DOI: 10.1111/aos.14479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023]
Abstract
PURPOSE In the era of precision medicine, genomic characterization of blind patients is critical. Here, we evaluate the effects of comprehensive genetic analysis on the etiologic diagnosis of potentially hereditary vision loss and its impact on clinical management. METHODS We studied 100 non-syndromic and syndromic Spanish patients with a clinical diagnosis of blindness caused by alterations on the retina, choroid, vitreous and/or optic nerve. We used a next-generation sequencing (NGS) panel (OFTALMOgenics™), developed and validated within this study, including up to 362 genes previously associated with these conditions. RESULTS We identified the genetic cause of blindness in 45% of patients (45/100). A total of 28.9% of genetically diagnosed cases (13/45) were syndromic and, of those, in 30.8% (4/13) extraophthalmic features had been overlooked and/or not related to visual impairment before genetic testing, including cases with Mainzer-Saldino, Bardet-Biedl, mucolipidosis and MLCRD syndromes. In two additional cases-syndromic blindness had been proposed before, but not specifically diagnosed, and one patient with Heimler syndrome had been misdiagnosed as an Usher case before testing. 33.3% of the genetically diagnosed patients (15/45) had causative variants in genes targeted by clinical trials exploring the curative potential of gene therapy approaches. CONCLUSION Comprehensive genomic testing provided clinically relevant insights in a large proportion of blind patients, identifying potential therapeutic opportunities or previously undiagnosed syndromes in 42.2% of the genetically diagnosed cases (19/45).
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Affiliation(s)
- Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Eva Villota
- Instituto Oftalmológico Fernández‐Vega (IOFV)OviedoSpain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Adrián Santiago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.OviedoSpain
| | | | - Inés Hernando
- Hospital Universitario Central de AsturiasOviedoSpain
| | - Noelia S. Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Claudia G. Lago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
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Kalfakakou D, Konstantopoulou I, Yannoukakos D, Fostira F. Pitfalls in variant annotation for hereditary cancer diagnostics: The example of Illumina® VariantStudio®. Genomics 2020; 113:748-754. [PMID: 33053411 DOI: 10.1016/j.ygeno.2020.10.005] [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: 03/23/2020] [Revised: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022]
Abstract
Next Generation Sequencing (NGS), and specifically targeted panel sequencing is the state-of-the-art in clinical genetic diagnosis of Mendelian diseases. However, the bioinformatics analysis and interpretation of the generated data can be challenging. A spotlight on the default transcript selection of a user-friendly, commercially available software that is widely used by genetics professionals, i.e. Illumina® VariantStudio®, is presented. For the sake of comparison, we employed Ensembl VEP, an open-source command-line tool, as it provides flexibility regarding transcript selection. The analysis of NGS data deriving from sequencing of 857 germline DNA samples of cancer patients indicated a concordance of 82.82% between the two software programs. Significantly, using the default transcript configuration of VariantStudio®, we failed to annotate correctly 11.45% of the identified loss-of-function variants. Our results underline the importance of cautious software and transcript selection and the need for reliable, white-box data analysis, along with bioinformatics expertise in clinical diagnostics.
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Affiliation(s)
- Despoina Kalfakakou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos", Greece.
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Jamal L, Schupmann W, Berkman BE. An ethical framework for genetic counseling in the genomic era. J Genet Couns 2020; 29:718-727. [PMID: 31856388 PMCID: PMC7302959 DOI: 10.1002/jgc4.1207] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 01/08/2023]
Abstract
The field of genetic counseling has grown and diversified since the profession emerged in the early 1970s. In the same period, genomic testing has become more complex, profitable, and widespread. With these developments, the scope of ethical considerations relevant to genetic counseling has expanded. In light of this, we find it helpful to revisit how ethical and relational variables are used to inform genetic counseling practice. Our specific focus is on whether, and to what extent, it is ethically acceptable for genetic counselors to make normative recommendations to patients. This article builds on prior literature that has critiqued nondirectiveness, a concept that has influenced and constrained the modern profession of genetic counseling since its origin. In it, we review scholarly efforts to move beyond nondirectiveness, which we believe privilege patient autonomy at the expense of other important values. We then argue that genetic counselors should favor a more explicit commitment to the principles of beneficence and non-maleficence, as well as a broader understanding of autonomy and the relational variables that impact genetic counseling. Finally, to translate our arguments into practice, we present a framework of six considerations that genetic counselors should take into account when deciding whether it is ethically acceptable, or even desirable, to make recommendations to patients in certain areas of their work.
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Affiliation(s)
- Leila Jamal
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD
| | - Will Schupmann
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin E. Berkman
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD
- National Human Genome Research Institute, NIH, Bethesda, MD
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18
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Patient reactions to receiving negative genomic screening results by mail. Genet Med 2020; 22:1994-2002. [PMID: 32669678 DOI: 10.1038/s41436-020-0906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/09/2023] Open
Abstract
PURPOSE As genomic screening is incorporated into a wider array of clinical settings, it is critical that we understand how patients may respond to a various screening results. Although multiple studies have examined how patients understand positive genomic screening results, few data exist regarding patient engagement with negative screening results. METHODS An 82-item survey was administered to 1712 individuals who received negative genomic screening results by mail following evaluation of 109 medically actionable genes. Genetic counselors were available to assist with the interpretation of screening results. RESULTS One thousand four hundred forty-two participants completed the survey (84.2%). The vast majority of respondents valued the information they received, with 98% of respondents reporting that negative genomic screening results were valuable and 72% indicating they would recommend genomic screening to others. Nonetheless, many respondents had questions about their genomic screening results (28%) and would have preferred to receive their screening results in person (18%). CONCLUSION These data suggest most patients value receiving negative genomic screening results and are comfortable receiving their results by mail. Nevertheless, a significant proportion of patients also reported difficulty understanding some aspects of their results. This finding challenges the idea that communicating genomic screening results by mail alone is sufficient to meet patients' needs.
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Stuttgen K, Pacyna J, Kullo I, Sharp R. Neutral, Negative, or Negligible? Changes in Patient Perceptions of Disease Risk Following Receipt of a Negative Genomic Screening Result. J Pers Med 2020; 10:E24. [PMID: 32316380 PMCID: PMC7354612 DOI: 10.3390/jpm10020024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 01/12/2023] Open
Abstract
Most individuals who undergo genomic screening will receive negative results or results not sufficient to warrant a clinical response. Even though a majority of individuals receive negative results, little is known about how negative results may impact individuals' perception of disease risk. Changes in risk perception (specifically reductions in perceived risk) may affect both probands and their family members if inaccurate information is communicated to family members. We surveyed patients who received negative results as part of their participation in a genomic screening study and assessed their perceptions of disease risk following receipt of results. Participants had either hyperlipidemia or colon polyps (or both) and received their negative genomic screening results by mail. Of 1712 total individuals recruited, 1442 completed the survey (84.2% completion rate). Approximately one quarter of individuals believed their risk for heart disease to be lower and approximately one third of individuals believed their risk for colon cancer to be lower after receiving and evaluating their negative genomic screening result. 78% of those who believed their risk for one or both diseases had declined had already shared or intended to share their result with family members. Our study suggests patients may interpret a negative genomic screening result as implying a reduction in their overall disease risk.
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Affiliation(s)
- Kelsey Stuttgen
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55901, USA; (K.S.); (J.P.)
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55901, USA
| | - Joel Pacyna
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55901, USA; (K.S.); (J.P.)
| | - Iftikhar Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55901, USA;
| | - Richard Sharp
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55901, USA; (K.S.); (J.P.)
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55901, USA
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Evans BJ, Javitt G, Hall R, Robertson M, Ossorio P, Wolf SM, Morgan T, Clayton EW. How Can Law and Policy Advance Quality in Genomic Analysis and Interpretation for Clinical Care? THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2020; 48:44-68. [PMID: 32342785 PMCID: PMC7447152 DOI: 10.1177/1073110520916995] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Delivering high quality genomics-informed care to patients requires accurate test results whose clinical implications are understood. While other actors, including state agencies, professional organizations, and clinicians, are involved, this article focuses on the extent to which the federal agencies that play the most prominent roles - the Centers for Medicare and Medicaid Services enforcing CLIA and the FDA - effectively ensure that these elements are met and concludes by suggesting possible ways to improve their oversight of genomic testing.
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Affiliation(s)
- Barbara J Evans
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Gail Javitt
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Ralph Hall
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Megan Robertson
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Pilar Ossorio
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Susan M Wolf
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Thomas Morgan
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
| | - Ellen Wright Clayton
- Barbara J. Evans, Ph.D., J.D., LL.M., is the Mary Ann and Lawrence E. Faust Professor of Law and Professor, Electrical and Computer Engineering at the University of Houston. Gail Javitt, J.D., is a Member of the Firm at Hyman, Phelps, and McNamara, P.C. Ralph Hall, J.D., is a Principal at Leavitt Partners and a Professor of Practice at the University of Minnesota Law School. Megan Robertson, J.D., is an Associate in the Health Care and Life Sciences practice, Epstein Becker & Green, P.C. Pilar Ossorio, Ph.D., J.D., is Professor of Law and Bioethics at the University of Wisconsin Law School and Ethics Scholar-in-Residence at the Morgridge Institute for Research. Susan M. Wolf, J.D., is McKnight Presidential Professor of Law, Medicine & Public Policy; Faegre Baker Daniels Professor of Law; Professor of Medicine; and Chair of the Consortium on Law and Values in Health, Environment & the Life Sciences at the University of Minnesota. Thomas Morgan, M.D., F.A.C.M.G., is Associate Professor of Pediatrics in Medical Genetics at the Vanderbilt University School of Medicine. Ellen W. Clayton, M.D., J.D., is Craig-Weaver Professor of Pediatrics and Professor of Law at Vanderbilt University Medical Center and Vanderbilt University
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Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects. Eur Neuropsychopharmacol 2020; 31:1-15. [PMID: 31866110 DOI: 10.1016/j.euroneuro.2019.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 11/03/2018] [Accepted: 09/20/2019] [Indexed: 12/28/2022]
Abstract
Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.
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22
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Castellani C. Conclusion and Prospects: Genetics of cystic fibrosis – an agenda for the next ten years. Arch Pediatr 2020; 27 Suppl 1:eS45-eS47. [DOI: 10.1016/s0929-693x(20)30051-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Nie Q, Omerza G, Chandok H, Prego M, Hsiao MC, Meyers B, Hesse A, Uvalic J, Soucy M, Bergeron D, Peracchio M, Burns S, Kelly K, Rowe S, Rueter J, Reddi HV. Molecular profiling of gynecologic cancers for treatment and management of disease - demonstrating clinical significance using the AMP/ASCO/CAP guidelines for interpretation and reporting of somatic variants. Cancer Genet 2020; 242:25-34. [PMID: 31992506 DOI: 10.1016/j.cancergen.2019.11.008] [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: 07/04/2019] [Revised: 10/17/2019] [Accepted: 11/02/2019] [Indexed: 10/25/2022]
Abstract
Molecular features of gynecologic cancers have been investigated in comprehensive studies, but correlation of these molecular signatures with clinical significance for precision medicine is yet to be established. Towards this end, we evaluated 95 gynecologic cancer cases submitted for testing using The JAX ActionSeq™ NGS panel. Molecular profiles were studied and compared to TCGA datasets to identify similarities and distinguishing features among subtypes. We identified 146 unique clinically significant variants (Tier I and II) across 45 of the 212 genes (21%), in 87% (83/95) of cases. TP53, PTEN, ARID1A, PIK3CA and ATM were the most commonly mutated genes; CCNE1 and ERBB2 amplifications were the most frequently detected copy-number alterations. PARP inhibitors were among the most commonly reported drug class with clinical trials, consistent with the frequency of DNA damage-response pathway mutations in our cohort. Overall, our study provides additional insight into the molecular profiles of gynecologic cancers, highlighting regulatory pathways involved, raising the potential implications for targeted therapeutic options currently available.
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Affiliation(s)
- Qian Nie
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Gregory Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Harshpreet Chandok
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Matthew Prego
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Meng-Chang Hsiao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Bridgette Meyers
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Andrew Hesse
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Jasmina Uvalic
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Melissa Soucy
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Daniel Bergeron
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Michael Peracchio
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Shelbi Burns
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Shannon Rowe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States
| | - Jens Rueter
- The Maine Cancer Genomics Initiative, The Jackson Laboratory, Augusta, ME 04330, United States.
| | - Honey V Reddi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, United States.
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Abou Tayoun A, Mason-Suares H. Considerations for whole exome sequencing unique to prenatal care. Hum Genet 2019; 139:1149-1159. [PMID: 31701237 DOI: 10.1007/s00439-019-02085-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Whole exome sequencing (WES) is increasingly being used in the prenatal setting. The emerging data support the clinical utility of prenatal WES based on its diagnostic yield, which can be as high as 80% for certain ultrasound findings. However, detailed practice and laboratory guidelines, addressing the indications for prenatal WES and the surrounding technical, interpretation, ethical, and counseling issues, are still lacking. Herein, we review the literature and summarize the most recent findings and applications of prenatal WES. This review offers specialists and clinical genetic laboratorians a body of evidence and expert opinions that can serve as a resource to assist in their practice. Finally, we highlight the emerging technologies that promise a future of prenatal WES without the risks associated with invasive testing.
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Affiliation(s)
| | - Heather Mason-Suares
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Street, Cambridge, MA, 02115, USA.
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Zehnbauer BA. The Journal of Molecular Diagnostics: 20 Years Defining Professional Practice. J Mol Diagn 2019; 21:938-942. [PMID: 31635797 DOI: 10.1016/j.jmoldx.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023] Open
Abstract
This editorial highlights 20 years of JMD defining professional practice.
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Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
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El‐Deiry WS, Goldberg RM, Lenz H, Shields AF, Gibney GT, Tan AR, Brown J, Eisenberg B, Heath EI, Phuphanich S, Kim E, Brenner AJ, Marshall JL. The current state of molecular testing in the treatment of patients with solid tumors, 2019. CA Cancer J Clin 2019; 69:305-343. [PMID: 31116423 PMCID: PMC6767457 DOI: 10.3322/caac.21560] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The world of molecular profiling has undergone revolutionary changes over the last few years as knowledge, technology, and even standard clinical practice have evolved. Broad molecular profiling is now nearly essential for all patients with metastatic solid tumors. New agents have been approved based on molecular testing instead of tumor site of origin. Molecular profiling methodologies have likewise changed such that tests that were performed on patients a few years ago are no longer complete and possibly inaccurate today. As with all rapid change, medical providers can quickly fall behind or struggle to find up-to-date sources to ensure he or she provides optimum care. In this review, the authors provide the current state of the art for molecular profiling/precision medicine, practice standards, and a view into the future ahead.
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Affiliation(s)
- Wafik S. El‐Deiry
- Associate Dean for Oncologic Sciences, Warren Alpert Medical School; Director, Joint Program in Cancer Biology, Brown University and the Lifespan Cancer Institute; Professor of Pathology & Laboratory Medicine and Professor of Medical ScienceBrown UniversityProvidenceRI
| | - Richard M. Goldberg
- Professor of Medicine and DirectorWest Virginia University Cancer InstituteMorgantownWV
| | - Heinz‐Josef Lenz
- Professor of Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCA
| | | | - Geoffrey T. Gibney
- Associate Professor of Medicine, Co‐Leader of the Melanoma Disease GroupLombardi Comprehensive Cancer Institute, MedStar Georgetown Cancer InstituteWashingtonDC
| | - Antoinette R. Tan
- Co‐Director of Phase I Program, Department of Solid Tumor Oncology and Investigational TherapeuticsLevine Cancer Institute, Atrium HealthCharlotteNC
| | - Jubilee Brown
- Professor and Associate Director of Gynecologic OncologyLevine Cancer Institute, Atrium HealthCharlotteNC
| | - Burton Eisenberg
- Professor of Clinical SurgeryUniversity of Southern CaliforniaLos AngelesCA
- Executive Medical DirectorHoag Family Cancer InstituteNewport BeachCA
| | | | - Surasak Phuphanich
- Professor of Neurology, Director, Division of Neuro‐OncologyBarrow Neurological InstitutePhoenixAZ
| | - Edward Kim
- Chair, Solid Tumor Oncology and Investigational TherapeuticsLevine Cancer Institute, Atrium HealthCharlotteNC
| | - Andrew J. Brenner
- Associate Professor of Medicine, Mays Cancer Center at University of Texas Health San Antonio Cancer CenterSan AntonioTX
| | - John L. Marshall
- Professor of Medicine and Oncology, Director, Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer InstituteMedStar Georgetown Cancer InstituteWashingtonDC
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Ragupathy S, Faller AC, Shanmughanandhan D, Kesanakurti P, Shaanker RU, Ravikanth G, Sathishkumar R, Mathivanan N, Song J, Han J, Newmaster S. Exploring DNA quantity and quality from raw materials to botanical extracts. Heliyon 2019; 5:e01935. [PMID: 31245647 PMCID: PMC6582161 DOI: 10.1016/j.heliyon.2019.e01935] [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: 02/02/2019] [Revised: 05/23/2019] [Accepted: 06/06/2019] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES The aim of this study was to explore the variability in DNA quality and quantity along a gradient of industrial processing of botanical ingredients from raw materials to extracts. METHODS A data matrix was assembled for 1242 botanical ingredient samples along a gradient of industrial processing commonly used in the Natural Health Product (NHP) industry. Multivariate statistics was used to explore dependant variables for quality and quantity. The success of attaining a positive DNA test result along a gradient of industrial processing was compared among four biotechnologies: DNA barcoding, NGS, Sanger sequencing and qPCR. RESULTS There was considerable variance in DNA quality and quantity among the samples, which could be interpreted along a gradient from raw materials with greater quantities (50-120 ng/μL) of DNA and longer DNA (400-500bp) sequences to extracts, which were characterized by lower quantities (0.1-10.0 ng/μL) and short fragments (50-150bp). CONCLUSIONS Targeted molecular diagnostic tests for species identity can be used in the NHP industry for raw and processed samples. Non-targeted tests or the use of NGS for any identity test needs considerable research and development and must be validated before it can be used in commercial operations as these methods are subject to considerable risk of false negative and positive results. Proper use of these tools can be used to ensure ingredient authenticity, and to avert adulteration, and contamination with plants that are a health concern. Lastly these tools can be used to prevent the exploitation of rare herbal species and the harvesting of native biodiversity for commercial purposes.
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Affiliation(s)
- Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Adam C. Faller
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Prasad Kesanakurti
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R. Uma Shaanker
- Department of Crop Physiology and School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - Gudasalamani Ravikanth
- Conservation Genetics Lab, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bengaluru, 560064, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
| | - Narayanasamy Mathivanan
- Centre for Advanced Studies in Botany, University of Madras Guindy Campus, Chennai, 600 025, Tamil Nadu, India
| | - Jingyuan Song
- Engineering Research Center of Traditional Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Jianping Han
- Engineering Research Center of Traditional Chinese Medicine Resource, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Steven Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Blais J, Giroux S, Caron A, Clément V, Rousseau F. Development of Reference Materials for Noninvasive Prenatal Aneuploidy Testing by Massively Parallel Sequencing: A Proof-of-Concept Study. J Appl Lab Med 2019; 4:50-60. [PMID: 31639707 DOI: 10.1373/jalm.2018.028100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/02/2019] [Indexed: 11/06/2022]
Abstract
BACKGROUND Noninvasive prenatal aneuploidy testing (NIPT) represents the first large-scale clinical application of massively parallel sequencing technology. However, no NIPT reference material (RM) has yet been widely adopted, impeding the development of quality management systems and standardization. Developing an NIPT RM from a biological sample is complicated by the low concentration of cell-free DNA (cfDNA), which implies pooling specimens and frequent resampling. METHODS We tested the feasibility of using DNA from immortalized cell lines of a woman and her aneuploid offspring to spike an artificial plasma matrix. Enzymatic fragmentation of extracted DNA was optimized to achieve fragment size profiles with a mode of 150 to 200 bp, similar to biological cfDNA. This synthetic material was compared with routine biological samples from pregnant women by a targeted NIPT assay in a multiplex sequencing run on a Proton platform. RESULTS Sequencing statistics were similar between artificially prepared material and routine biological samples, as well as relative chromosomal representation, and no matrix effects could be detected. Estimate of fetal fraction (FF) was within the range of expected value, and aneuploidy detection statistic (z-score) was also comparable between both types of samples. CONCLUSIONS Artificial plasma spiked with DNA from cell lines of mother and offspring is a promising strategy for developing NIPT RM. This type of material would offer the advantage of a constant and stable composition, allowing for greater standardization of NIPT assays. Moreover, it preserves the parental relatedness used by targeted assay to estimate FF by identification of paternal alleles in single-nucleotide polymorphisms or other variable regions.
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Affiliation(s)
- Jonatan Blais
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada; .,Service of Medical Biochemistry, Department of Medical Biology, CHU de Québec, Quebec City, Quebec, Canada.,Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec City, Quebec, Canada.,PEGASUS, Quebec City, Quebec, Canada
| | - Sylvie Giroux
- Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec City, Quebec, Canada.,PEGASUS, Quebec City, Quebec, Canada
| | - André Caron
- Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec City, Quebec, Canada.,PEGASUS, Quebec City, Quebec, Canada
| | - Valérie Clément
- Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec City, Quebec, Canada.,PEGASUS, Quebec City, Quebec, Canada
| | - François Rousseau
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada.,Service of Medical Biochemistry, Department of Medical Biology, CHU de Québec, Quebec City, Quebec, Canada.,Human and Molecular Genetics Research Unit, Research Center, CHU de Québec, Quebec City, Quebec, Canada.,PEGASUS, Quebec City, Quebec, Canada
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Vickers RR, Gibson JS. A Review of the Genomic Analysis of Children Presenting with Developmental Delay/Intellectual Disability and Associated Dysmorphic Features. Cureus 2019; 11:e3873. [PMID: 30899624 PMCID: PMC6420327 DOI: 10.7759/cureus.3873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This review describes the clinical criteria of developmental delay (DD)/intellectual disability (ID) as well as the various techniques that are currently implemented to diagnose neurodevelopmental disorders that typically present with associated dysmorphic features such as Angelman syndrome, Prader-Willi syndrome, and DiGeorge syndrome. These analyses include various forms of chromosomal microarray (CMA), which have proven to be superior to previously implemented techniques such as G-banded karyotyping and fluorescent in situ hybridization (FISH) analysis, as well as whole exome sequencing (WES), which is implemented as a secondary examination when CMA analysis is unrevealing. The clinical significance of identified variants and how it relates to facilitating the management of specific genetic disorders such as the above mentioned is also discussed. In addition, the importance of genomic databases and bioinformatics technologies as they relate to variant classification is also considered. Essentially, the discovery of pathogenic variants allows for enhanced management of a patient’s clinical phenotype, whereas the identification of variants of uncertain significance (VUS) has proven to have an increase in the number of associated conflicts as they typically generate more ambiguity in regard to the clinical manifestations present within the child. As a result, additional procedures need to be implemented to mitigate the issues that surround their identification. The concluding remarks are in regard to both the ethical and legal considerations of genetic testing as they relate to informed consent, testing of minors, how to handle secondary findings, as well as the anticipated future direction of genomic analysis.
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Affiliation(s)
- Ramiah R Vickers
- Genetics, University of Central Florida College of Medicine, Orlando, USA
| | - Jane S Gibson
- Pathology, University of Central Florida College of Medicine, Orlando, USA
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Santani A, Simen BB, Briggs M, Lebo M, Merker JD, Nikiforova M, Vasalos P, Voelkerding K, Pfeifer J, Funke B. Designing and Implementing NGS Tests for Inherited Disorders: A Practical Framework with Step-by-Step Guidance for Clinical Laboratories. J Mol Diagn 2018; 21:369-374. [PMID: 30605766 DOI: 10.1016/j.jmoldx.2018.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/17/2018] [Accepted: 11/17/2018] [Indexed: 11/16/2022] Open
Abstract
Comprehensive next-generation sequencing (NGS) tests are increasingly used as first-line tests in the evaluation of patients with suspected heritable disease. Despite major technical simplifications, these assays still pose significant challenges for molecular testing laboratories. Existing professional guidelines and recommendations provide a framework for laboratories implementing such tests, but in-depth, concrete guidance is generally not provided. Consequently, there is variability in how laboratories interpret and subsequently implement these regulatory frameworks. To address the need for more detailed guidance, the College of American Pathologists with representation from the Association for Molecular Pathologists assembled a working group to create a practical resource for clinical laboratories. This initial work is focused on variant detection in the setting of inherited disease and provides structured worksheets that guide the user through the entire life cycle of an NGS test, including design, optimization, validation, and quality management with additional guidance for clinical bioinformatics. This resource is designed to be a living document that is publicly available and will be updated with user and expert feedback as the wet bench and bioinformatic landscapes continue to evolve. It is intended to facilitate the standardization of NGS testing across laboratories and therefore to improve patient care.
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Affiliation(s)
- Avni Santani
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | | | - Marian Briggs
- Proficiency Testing Department, College of American Pathologists, Northfield, Illinois
| | - Matthew Lebo
- Department of Pathology, Harvard Medical School/Brigham and Women's Hospital, Boston, Massachusetts
| | - Jason D Merker
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Marina Nikiforova
- Department of Molecular & Genomic Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Patricia Vasalos
- Proficiency Testing Department, College of American Pathologists, Northfield, Illinois
| | - Karl Voelkerding
- Department of Pathology, University of Utah School of Medicine/ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - John Pfeifer
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri
| | - Birgit Funke
- Veritas Genetics, Danvers, Massachusetts; Department of Pathology, Harvard Medical School/Massachusetts General Hospital, Boston, Massachusetts.
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Vos S, van Diest PJ, Ausems MGEM, van Dijk MR, de Leng WWJ, Bredenoord AL. Ethical considerations for modern molecular pathology. J Pathol 2018; 246:405-414. [DOI: 10.1002/path.5157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Shoko Vos
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Paul J van Diest
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Margreet GEM Ausems
- Department of Medical Genetics; University Medical Center Utrecht; Utrecht The Netherlands
| | - Marijke R van Dijk
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Wendy WJ de Leng
- Department of Pathology; University Medical Center Utrecht; Utrecht The Netherlands
| | - Annelien L Bredenoord
- Department of Medical Humanities; University Medical Center Utrecht; Utrecht The Netherlands
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Trosman JR, Weldon CB, Gradishar WJ, Benson AB, Cristofanilli M, Kurian AW, Ford JM, Balch A, Watkins J, Phillips KA. From the Past to the Present: Insurer Coverage Frameworks for Next-Generation Tumor Sequencing. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2018; 21:1062-1068. [PMID: 30224110 PMCID: PMC6374027 DOI: 10.1016/j.jval.2018.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/11/2018] [Indexed: 05/16/2023]
Abstract
Next-generation sequencing promises major advancements in precision medicine but faces considerable challenges with insurance coverage. These challenges are especially important to address in oncology in which next-generation tumor sequencing (NGTS) holds a particular promise, guiding the use of life-saving or life-prolonging therapies. Payers' coverage decision making on NGTS is challenging because this revolutionary technology pushes the very boundaries of the underlying framework used in coverage decisions. Some experts have called for the adaptation of the coverage framework to make it better equipped for assessing NGTS. Medicare's recent decision to cover NGTS makes this topic particularly urgent to examine. In this article, we discussed the previously proposed approaches for adaptation of the NGTS coverage framework, highlighted their innovations, and outlined remaining gaps in their ability to assess the features of NGTS. We then compared the three approaches with Medicare's national coverage determination for NGTS and discussed its implications for US private payers as well as for other technologies and clinical areas. We focused on US payers because analyses of coverage approaches and policies in the large and complex US health care system may inform similar efforts in other countries. We concluded that further adaptation of the coverage framework will facilitate a better suited assessment of NGTS and future genomics innovations.
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Affiliation(s)
- Julia R Trosman
- Center for Business Models in Healthcare, Glencoe, IL, USA; Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Christine B Weldon
- Center for Business Models in Healthcare, Glencoe, IL, USA; Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Al B Benson
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - James M Ford
- Stanford University School of Medicine, Stanford, CA, USA
| | - Alan Balch
- Patient Advocate Foundation, Hampton, VA, USA
| | | | - Kathryn A Phillips
- Department of Clinical Pharmacy, UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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Xin T, Xu Z, Jia J, Leon C, Hu S, Lin Y, Ragupathy S, Song J, Newmaster SG. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta Pharm Sin B 2018; 8:488-497. [PMID: 29881688 PMCID: PMC5990340 DOI: 10.1016/j.apsb.2017.10.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/12/2022] Open
Abstract
Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.
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Affiliation(s)
- Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jing Jia
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Christine Leon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Subramanyam Ragupathy
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Steven G. Newmaster
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
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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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Zhang R, Ding J, Han Y, Yi L, Xie J, Yang X, Fan G, Wang G, Hao M, Zhang D, Zhang K, Lin G, Li J. The reliable assurance of detecting somatic mutations in cancer-related genes by next-generation sequencing: the results of external quality assessment in China. Oncotarget 2018; 7:58500-58515. [PMID: 27542269 PMCID: PMC5295447 DOI: 10.18632/oncotarget.11306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/27/2016] [Indexed: 12/14/2022] Open
Abstract
To evaluate the proficiencies of laboratories utilizing next-generation sequencing (NGS) to detect somatic mutations in cancer-related genes, an external quality assessment (EQA) was implemented by the National Center for Clinical Laboratories of China in 2015. We prepared a panel of samples that comprised eight samples made by mixing synthetic mutated DNA fragments with normal human genomic DNA and one reference sample containing only genomic DNA. We validated our sample panel, and then distributed it to laboratories across China. We received complete results from 64 laboratories. The performances of 51.6 % (33/64) respondent labs were acceptable and 26.6 % (17/64) of the labs returned perfect results. In total, 449 mistakes were reported, including 201 false-negatives (201/449, 44.8 %) and 222 false-positives (222/449, 49.4 %) and 26 slightly discordant results (26/449, 5.8 %). We believe these unsatisfactory results and varied performances are mainly due to the enrichment methods used, the diverse sequencing chemistries of the different NGS platforms, and other errors within the sequencing process. The results indicate that our sample panel is suitable for use in EQA studies, and that further laboratory training in targeted NGS testing is urgently required. To address this, we propose a targeted NGS workflow with details on quality assurance procedures according to the current guidelines.
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Affiliation(s)
- Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiansheng Ding
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Xin Yang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Gaowei Fan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Guojing Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Mingju Hao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Dong Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
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36
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Hung SS, Meissner B, Chavez EA, Ben-Neriah S, Ennishi D, Jones MR, Shulha HP, Chan FC, Boyle M, Kridel R, Gascoyne RD, Mungall AJ, Marra MA, Scott DW, Connors JM, Steidl C. Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management. J Mol Diagn 2018; 20:203-214. [PMID: 29429887 DOI: 10.1016/j.jmoldx.2017.11.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/24/2017] [Accepted: 11/03/2017] [Indexed: 01/30/2023] Open
Abstract
Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. Next, we developed a targeted sequencing pipeline using a 32-gene panel for accurate detection of actionable mutations in formalin-fixed, paraffin-embedded tumor samples of the most common lymphocytic malignancies: chronic lymphocytic leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. We show that hybrid capture is superior to amplicon sequencing by providing deep more uniform coverage and yielding higher sensitivity for variant calling. Sanger sequencing of 588 variants identified specificity limits of thresholds for mutation calling, and orthogonal validation on 66 cases indicated 93% concordance with whole-genome sequencing. The developed pipeline and assay identified at least one actionable mutation in 91% of tumors from 219 lymphoma patients and revealed subtype-specific mutation patterns and frequencies consistent with the literature. This pipeline is an accurate and sensitive method for identifying actionable gene mutations in routinely acquired biopsy materials, suggesting further assessment of capture-based assays in the context of personalized lymphoma management.
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Affiliation(s)
- Stacy S Hung
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Martin R Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hennady P Shulha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fong Chun Chan
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Kridel
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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37
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Chen Z, Zhou W, Qiao S, Kang L, Duan H, Xie XS, Huang Y. Highly accurate fluorogenic DNA sequencing with information theory-based error correction. Nat Biotechnol 2017; 35:1170-1178. [PMID: 29106407 DOI: 10.1038/nbt.3982] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 08/30/2017] [Indexed: 11/09/2022]
Abstract
Eliminating errors in next-generation DNA sequencing has proved challenging. Here we present error-correction code (ECC) sequencing, a method to greatly improve sequencing accuracy by combining fluorogenic sequencing-by-synthesis (SBS) with an information theory-based error-correction algorithm. ECC embeds redundancy in sequencing reads by creating three orthogonal degenerate sequences, generated by alternate dual-base reactions. This is similar to encoding and decoding strategies that have proved effective in detecting and correcting errors in information communication and storage. We show that, when combined with a fluorogenic SBS chemistry with raw accuracy of 98.1%, ECC sequencing provides single-end, error-free sequences up to 200 bp. ECC approaches should enable accurate identification of extremely rare genomic variations in various applications in biology and medicine.
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Affiliation(s)
- Zitian Chen
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Wenxiong Zhou
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Shuo Qiao
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Li Kang
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Haifeng Duan
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - X Sunney Xie
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, China.,Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing, China.,College of Engineering, Peking University, Beijing, China.,School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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38
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Zhang YC, Zhou Q, Wu YL. The emerging roles of NGS-based liquid biopsy in non-small cell lung cancer. J Hematol Oncol 2017; 10:167. [PMID: 29061113 PMCID: PMC5654124 DOI: 10.1186/s13045-017-0536-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/17/2017] [Indexed: 12/25/2022] Open
Abstract
The treatment paradigm of non-small cell lung cancer (NSCLC) has evolved into oncogene-directed precision medicine. Identifying actionable genomic alterations is the initial step towards precision medicine. An important scientific progress in molecular profiling of NSCLC over the past decade is the shift from the traditional piecemeal fashion to massively parallel sequencing with the use of next-generation sequencing (NGS). Another technical advance is the development of liquid biopsy with great potential in providing a dynamic and comprehensive genomic profiling of NSCLC in a minimally invasive manner. The integration of NGS with liquid biopsy has been demonstrated to play emerging roles in genomic profiling of NSCLC by increasing evidences. This review summarized the potential applications of NGS-based liquid biopsy in the diagnosis and treatment of NSCLC including identifying actionable genomic alterations, tracking spatiotemporal tumor evolution, dynamically monitoring response and resistance to targeted therapies, and diagnostic value in early-stage NSCLC, and discussed emerging challenges to overcome in order to facilitate clinical translation in future.
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Affiliation(s)
- Yi-Chen Zhang
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan 2nd Road, Guangzhou, Guangdong, 510080, People's Republic of China.
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39
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Abstract
Mutation detection in tumors started with classical cytogenetics as the method of choice more than 50 years ago. Karyotyping proved to be sensitive enough to detect deletions or duplications of large chromosome segments, and translocations. Over time, new techniques were developed to detect mutations that are much smaller in scope. The availability of Sanger sequencing and the invention of the PCR improved the discriminatory power of mutation detection to just one base change in the genomic DNA sequence. Techniques derived from PCR (allele-specific PCR, qPCR) and improved or modified sequencing methods (capillary electrophoresis, pyrosequencing) considerably increased the efficiency and sample throughput of mutation detection assays. With the advent of massive parallel sequencing [also called next-generation sequencing (NGS)] in the past decade, a major shift to even higher sample throughput and a significant decrease in cost per sequenced base occurred. The application of the new technology provided a whole slew of novel biomarkers and potential therapy targets to improve diagnosis and treatment. It even led to changes in cancer classification as new information on the mutation profile of tumors became available that characterizes some disease entities better than morphology. NGS, which usually interrogates multiple genes at once and is a prime example of a multianalyte assay, started to replace older single analyte assays focused on analysis of one target, one gene. However, the transition to these extremely complex NGS-based assays is associated with multiple challenges. There are issues with adequate tissue source of nucleic acids, sequencing library preparation, bioinformatics, government regulations and oversight, reimbursement, and electronic medical records that need to be resolved to successfully implement the new technology in a clinical laboratory.
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40
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Worthey EA. Analysis and Annotation of Whole-Genome or Whole-Exome Sequencing Derived Variants for Clinical Diagnosis. ACTA ACUST UNITED AC 2017; 95:9.24.1-9.24.28. [PMID: 29044471 DOI: 10.1002/cphg.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.
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41
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Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data. Genet Med 2017; 20:329-336. [DOI: 10.1038/gim.2017.153] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022] Open
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42
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Hu Y, Alden RS, Odegaard JI, Fairclough SR, Chen R, Heng J, Feeney N, Nagy RJ, Shah J, Ulrich B, Gutierrez M, Lanman RB, Garber JE, Paweletz CP, Oxnard GR. Discrimination of Germline EGFR T790M Mutations in Plasma Cell-Free DNA Allows Study of Prevalence Across 31,414 Cancer Patients. Clin Cancer Res 2017; 23:7351-7359. [PMID: 28947568 DOI: 10.1158/1078-0432.ccr-17-1745] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/08/2017] [Accepted: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Purpose: Plasma cell-free DNA (cfDNA) analysis is increasingly used clinically for cancer genotyping, but may lead to incidental identification of germline-risk alleles. We studied EGFR T790M mutations in non-small cell lung cancer (NSCLC) toward the aim of discriminating germline and cancer-derived variants within cfDNA.Experimental Design: Patients with EGFR-mutant NSCLC, some with known germline EGFR T790M, underwent plasma genotyping. Separately, deidentified genomic data and buffy coat specimens from a clinical plasma next-generation sequencing (NGS) laboratory were reviewed and tested.Results: In patients with germline T790M mutations, the T790M allelic fraction (AF) in cfDNA approximates 50%, higher than that of EGFR driver mutations. Review of plasma NGS results reveals three groups of variants: a low-AF tumor group, a heterozygous group (∼50% AF), and a homozygous group (∼100% AF). As the EGFR driver mutation AF increases, the distribution of the heterozygous group changes, suggesting increased copy number variation from increased tumor content. Excluding cases with high copy number variation, mutations can be differentiated into somatic variants and incidentally identified germline variants. We then developed a bioinformatic algorithm to distinguish germline and somatic mutations; blinded validation in 21 cases confirmed a 100% positive predictive value for predicting germline T790M. Querying a database of 31,414 patients with plasma NGS, we identified 48 with germline T790M, 43 with nonsquamous NSCLC (P < 0.0001).Conclusions: With appropriate bioinformatics, plasma genotyping can accurately predict the presence of incidentally detected germline risk alleles. This finding in patients indicates a need for genetic counseling and confirmatory germline testing. Clin Cancer Res; 23(23); 7351-9. ©2017 AACR.
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Affiliation(s)
- Yuebi Hu
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ryan S Alden
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Ruthia Chen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Heng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nora Feeney
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Jayshree Shah
- John Theurer Cancer Center, Hackensack Meridian Health, Hackensack, New Jersey
| | - Bryan Ulrich
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Martin Gutierrez
- John Theurer Cancer Center, Hackensack Meridian Health, Hackensack, New Jersey
| | | | - Judy E Garber
- Center for Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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43
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Pan L, Liu G, Lin F, Zhong S, Xia H, Sun X, Liang H. Machine learning applications for prediction of relapse in childhood acute lymphoblastic leukemia. Sci Rep 2017; 7:7402. [PMID: 28784991 PMCID: PMC5547099 DOI: 10.1038/s41598-017-07408-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/23/2017] [Indexed: 01/17/2023] Open
Abstract
The prediction of relapse in childhood acute lymphoblastic leukemia (ALL) is a critical factor for successful treatment and follow-up planning. Our goal was to construct an ALL relapse prediction model based on machine learning algorithms. Monte Carlo cross-validation nested by 10-fold cross-validation was used to rank clinical variables on the randomly split training sets of 336 newly diagnosed ALL children, and a forward feature selection algorithm was employed to find the shortest list of most discriminatory variables. To enable an unbiased estimation of the prediction model to new patients, besides the split test sets of 150 patients, we introduced another independent data set of 84 patients to evaluate the model. The Random Forest model with 14 features achieved a cross-validation accuracy of 0.827 ± 0.031 on one set and an accuracy of 0.798 on the other, with the area under the curve of 0.902 ± 0.027 and 0.904, respectively. The model performed well across different risk-level groups, with the best accuracy of 0.829 in the standard-risk group. To our knowledge, this is the first study to use machine learning models to predict childhood ALL relapse based on medical data from Electronic Medical Record, which will further facilitate stratification treatments.
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Affiliation(s)
- Liyan Pan
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Guangjian Liu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shuling Zhong
- Department of Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Sun
- Department of Hematology and Oncology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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44
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Hardwick SA, Deveson IW, Mercer TR. Reference standards for next-generation sequencing. Nat Rev Genet 2017. [DOI: 10.1038/nrg.2017.44] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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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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Kalman LV, Datta V, Williams M, Zook JM, Salit ML, Han JY. Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships. Ann Lab Med 2017; 36:513-20. [PMID: 27578503 PMCID: PMC5011103 DOI: 10.3343/alm.2016.36.6.513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/08/2016] [Accepted: 07/18/2016] [Indexed: 01/29/2023] Open
Abstract
Characterized reference materials (RMs) are needed for clinical laboratory test development and validation, quality control procedures, and proficiency testing to assure their quality. In this article, we review the development and characterization of RMs for clinical molecular genetic tests. We describe various types of RMs and how to access and utilize them, especially focusing on the Genetic Testing Reference Materials Coordination Program (Get-RM) and the Genome in a Bottle (GIAB) Consortium. This review also reinforces the need for collaborative efforts in the clinical genetic testing community to develop additional RMs.
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Affiliation(s)
- Lisa V Kalman
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivekananda Datta
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Mickey Williams
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Gaithersburg, MD, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Marc L Salit
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jin Yeong Han
- Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea.
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47
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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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48
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Trosman JR, Weldon CB, Douglas MP, Deverka PA, Watkins JB, Phillips KA. Decision Making on Medical Innovations in a Changing Health Care Environment: Insights from Accountable Care Organizations and Payers on Personalized Medicine and Other Technologies. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2017; 20:40-46. [PMID: 28212967 PMCID: PMC5319741 DOI: 10.1016/j.jval.2016.09.2402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND New payment and care organization approaches, such as those of accountable care organizations (ACOs), are reshaping accountability and shifting risk, as well as decision making, from payers to providers, within the Triple Aim context of health reform. The Triple Aim calls for improving experience of care, improving health of populations, and reducing health care costs. OBJECTIVES To understand how the transition to the ACO model impacts decision making on adoption and use of innovative technologies in the era of accelerating scientific advancement of personalized medicine and other innovations. METHODS We interviewed representatives from 10 private payers and 6 provider institutions involved in implementing the ACO model (i.e., ACOs) to understand changes, challenges, and facilitators of decision making on medical innovations, including personalized medicine. We used the framework approach of qualitative research for study design and thematic analysis. RESULTS We found that representatives from the participating payer companies and ACOs perceive similar challenges to ACOs' decision making in terms of achieving a balance between the components of the Triple Aim-improving care experience, improving population health, and reducing costs. The challenges include the prevalence of cost over care quality considerations in ACOs' decisions and ACOs' insufficient analytical and technology assessment capacity to evaluate complex innovations such as personalized medicine. Decision-making facilitators included increased competition across ACOs and patients' interest in personalized medicine. CONCLUSIONS As new payment models evolve, payers, ACOs, and other stakeholders should address challenges and leverage opportunities to arm ACOs with robust, consistent, rigorous, and transparent approaches to decision making on medical innovations.
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Affiliation(s)
- Julia R Trosman
- UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California, San Franscisco, CA, USA; Center for Business Models in Healthcare, Chicago, IL, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Christine B Weldon
- UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California, San Franscisco, CA, USA; Center for Business Models in Healthcare, Chicago, IL, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Michael P Douglas
- UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California, San Franscisco, CA, USA
| | | | | | - Kathryn A Phillips
- UCSF Center for Translational and Policy Research on Personalized Medicine (TRANSPERS), Department of Clinical Pharmacy, University of California, San Franscisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA; Philip R. Lee Institute for Health Policy, University of California, San Francisco, CA, USA
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49
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Masucci GV, Cesano A, Hawtin R, Janetzki S, Zhang J, Kirsch I, Dobbin KK, Alvarez J, Robbins PB, Selvan SR, Streicher HZ, Butterfield LH, Thurin M. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation. J Immunother Cancer 2016; 4:76. [PMID: 27895917 PMCID: PMC5109744 DOI: 10.1186/s40425-016-0178-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/20/2016] [Indexed: 12/31/2022] Open
Abstract
Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
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Affiliation(s)
- Giuseppe V Masucci
- Department of Oncology-Pathology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | | | - Rachael Hawtin
- Nodality, Inc, 170 Harbor Way, South San Francisco, 94080 CA USA
| | - Sylvia Janetzki
- ZellNet Consulting, Inc, 555 North Avenue, Fort Lee, 07024 NJ USA
| | - Jenny Zhang
- Covaris Inc, 14 Gill St, Woburn, MA 01801 USA
| | - Ilan Kirsch
- Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
| | - Kevin K Dobbin
- Department of Epidemiology and Biostatistics, College of Public Health, The University of Georgia, 101 Buck Road, Athens, 30602 GA USA
| | - John Alvarez
- Janssen Research & Development, LLC, Spring House, PA 19477 USA
| | | | - Senthamil R Selvan
- Omni Array Biotechnology, 15601 Crabbs Branch Way, Rockville, 20855 MD USA
| | - Howard Z Streicher
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| | - Magdalena Thurin
- National Cancer Institute, Cancer Diagnosis Program, DCTD, National Institutes of Health, 9609 Medical Center Drive, Bethesda, 20892 MD USA ; Adaptive Biotechnologies, Inc, 1551 Eastlake Ave. E, Seattle, WA 98102 USA
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50
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Kudalkar EM, Almontashiri NA, Huang C, Anekella B, Bowser M, Hynes E, Garlick R, Funke BH. Multiplexed Reference Materials as Controls for Diagnostic Next-Generation Sequencing. J Mol Diagn 2016; 18:882-889. [DOI: 10.1016/j.jmoldx.2016.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 06/20/2016] [Accepted: 07/08/2016] [Indexed: 01/06/2023] Open
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