1
|
Abbosh C, Hodgson D, Doherty GJ, Gale D, Black JRM, Horn L, Reis-Filho JS, Swanton C. Implementing circulating tumor DNA as a prognostic biomarker in resectable non-small cell lung cancer. Trends Cancer 2024; 10:643-654. [PMID: 38839544 DOI: 10.1016/j.trecan.2024.04.004] [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: 02/28/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Abstract
Systemic treatment of resectable non-small cell lung cancer (NSCLC) is evolving with emerging neoadjuvant, perioperative, and adjuvant immunotherapy approaches. Circulating tumor DNA (ctDNA) detection at clinical diagnosis, during neoadjuvant therapy, or after resection may discern high-risk patients who might benefit from therapy escalation or switch. This Review summarizes translational implications of data supporting ctDNA-based risk determination in NSCLC and outstanding questions regarding ctDNA validity/utility as a prognostic biomarker. We discuss emerging ctDNA capabilities to refine clinical tumor-node-metastasis (TNM) staging in lung adenocarcinoma, ctDNA dynamics during neoadjuvant therapy for identifying patients deriving suboptimal benefit, and postoperative molecular residual disease (MRD) detection to escalate systemic therapy. Considering differential relapse characteristics in landmark MRD-negative/MRD-positive patients, we propose how ctDNA might integrate with pathological response data for optimal postoperative risk stratification.
Collapse
Affiliation(s)
- Chris Abbosh
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - Darren Hodgson
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | | | - Davina Gale
- Cancer Biomarker Development, Early Oncology AstraZeneca, Cambridge, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Leora Horn
- Clinical Development, Late Oncology, AstraZeneca, Nashville, TN, USA
| | - Jorge S Reis-Filho
- Cancer Biomarker Development, Early Oncology, AstraZeneca, Gaithersburg, MD, USA
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
| |
Collapse
|
2
|
Horrow C, Kesselheim AS. Regulating Laboratory Tests: What Framework Would Best Support Safety and Validity? Milbank Q 2024. [PMID: 38738445 DOI: 10.1111/1468-0009.12701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024] Open
Abstract
Policy Points With increasing public attention to cases of inaccurate and misleading laboratory-developed tests, there have been calls for regulatory reform. To protect patients from faulty laboratory tests, we need a framework that balances comprehensive test review with laboratory flexibility. The Verifying Accurate Leading-edge IVCT [In Vitro Clinical Test] Development (VALID) Act would have helped ensure laboratory test safety and validity through a much-needed expansion of Food and Drug Administration (FDA) oversight. However, Congress did not pass the VALID Act in 2022, forcing the FDA to start the regulatory reform process on its own.
Collapse
Affiliation(s)
- Caroline Horrow
- Program on Regulation, Therapeutics, and Law, Brigham and Women's Hospital and Harvard Medical School
| | - Aaron S Kesselheim
- Program on Regulation, Therapeutics, and Law, Brigham and Women's Hospital and Harvard Medical School
| |
Collapse
|
3
|
Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
Collapse
Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| |
Collapse
|
4
|
Seymour H, Feben C, Nevondwe P, Kerr R, Spencer C, Mudau M, Honey E, Lombard Z, Krause A, Carstens N. Mutation profiling in South African patients with Cornelia de Lange syndrome phenotype. Mol Genet Genomic Med 2024; 12:e2342. [PMID: 38284454 PMCID: PMC10785556 DOI: 10.1002/mgg3.2342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Cornelia de Lange Syndrome (CdLS) presents with a variable multi-systemic phenotype and pathogenic variants have been identified in five main genes. This condition has been understudied in African populations with little phenotypic and molecular information available. METHODS AND RESULTS We present a cohort of 14 patients with clinical features suggestive of CdLS. Clinical phenotyping was carried out and cases were classified according to the international consensus criteria. According to this criteria, nine patients had classical CdLS, one had non-classical CdLS and four presented with a phenotype that suggested molecular testing for CdLS. Each patient underwent mutation profiling using a targeted next generation sequencing panel of 18 genes comprising known and suspected CdLS causal genes. Of the 14 patients tested, pathogenic and likely pathogenic variants were identified in nine: eight variants in the NIPBL gene and one in the STAG1 gene. CONCLUSIONS We present the first molecular data for a cohort of South African patients with CdLS. Eight of the nine variants identified were in the NIPBL gene, the most commonly involved gene in cases of CdLS. This is also the first report of a patient of African ancestry presenting with STAG1-related CdLS.
Collapse
Affiliation(s)
- Heather Seymour
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Careni Spencer
- Division of Human Genetics, Department of MedicineUniversity of Cape Town and Groote Schuur HospitalCape TownSouth Africa
| | - Maria Mudau
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Engela Honey
- Department of Biochemistry, Genetics, Microbiology, Faculty of Natural and Agricultural ScienceUniversity of PretoriaPretoriaSouth Africa
| | - Zane Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Genomics Platform, South African Medical Research CouncilCape TownSouth Africa
| |
Collapse
|
5
|
Badrick T, Bowling F. Clinical utility - Information about the usefulness of tests. Clin Biochem 2023; 121-122:110656. [PMID: 37802380 DOI: 10.1016/j.clinbiochem.2023.110656] [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: 07/03/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
The clinical utility of a diagnostic test refers to its usefulness in improving patient outcomes, informing clinical decision-making, and optimizing healthcare resources. A diagnostic test with high clinical utility provides accurate, reliable, and actionable information that can guide appropriate treatment decisions, monitor treatment response, and identify potential adverse events or complications. Ultimately, the clinical utility of a diagnostic test depends on how well it can improve patient outcomes by guiding appropriate treatment decisions, improving clinical outcomes, and optimizing healthcare resource utilization. Healthcare providers need to weigh the benefits and drawbacks of using a particular diagnostic test in their clinical practice to determine its clinical utility.
Collapse
Affiliation(s)
- Tony Badrick
- Royal College of Pathologists of Australasia Quality Assurance Programs, St Leonards, Sydney, Australia.
| | - Francis Bowling
- Walter and Eliza Hall Institute of Medical Research, University of Melbourne, Parkville, Melbourne, Australia
| |
Collapse
|
6
|
Sharma I, Son MJ, Motamedi S, Hoeft A, Teller C, Hamby T, Ray A. Utilization of Genomic Tumor Profiling in Pediatric Liquid Tumors: A Clinical Series. Hematol Rep 2023; 15:256-265. [PMID: 37092520 PMCID: PMC10123750 DOI: 10.3390/hematolrep15020026] [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: 10/29/2022] [Revised: 01/09/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023] Open
Abstract
Hematologic tumors are mostly treated with chemotherapies that have poor toxicity profiles. While molecular tumor profiling can expand therapeutic options, our understanding of potential targetable drivers comes from studies of adult liquid tumors, which does not necessarily translate to efficacious treatment in pediatric liquid tumors. There is also no consensus on when profiling should be performed and its use in guiding therapies. We describe a single institution's experience in integrating profiling for liquid tumors. Pediatric patients diagnosed with leukemia or lymphoma and who underwent tumor profiling were retrospectively reviewed. Ten (83.3%) patients had relapsed disease prior to tumor profiling. Eleven (91.7%) patients had targetable alterations identified on profiling, and three (25%) received targeted therapy based on these variants. Of the three patients that received targeted therapy, two (66.7%) were living, and one (33.3%) decreased. For a portion of our relapsing and/or treatment-refractory patients, genetic profiling was feasible and useful in tailoring therapy to obtain stable or remission states. Practitioners may hesitate to deviate from the 'standard of therapy', resulting in the underutilization of profiling results. Prospective studies should identify actionable genetic variants found more frequently in pediatric liquid tumors and explore the benefits of proactive tumor profiling prior to the first relapse.
Collapse
Affiliation(s)
- Ishna Sharma
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Min Ji Son
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Shoaleh Motamedi
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Alice Hoeft
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
- Department of Research Operations, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Christa Teller
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Tyler Hamby
- Department of Research Operations, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Anish Ray
- Texas College of Osteopathic Medicine, The University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Hematology/Oncology, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| |
Collapse
|
7
|
Halim-Fikri H, Syed-Hassan SNRK, Wan-Juhari WK, Assyuhada MGSN, Hernaningsih Y, Yusoff NM, Merican AF, Zilfalil BA. Central resources of variant discovery and annotation and its role in precision medicine. ASIAN BIOMED 2022; 16:285-298. [PMID: 37551357 PMCID: PMC10392146 DOI: 10.2478/abm-2022-0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Rapid technological advancement in high-throughput genomics, microarray, and deep sequencing technologies has accelerated the possibility of more complex precision medicine research using large amounts of heterogeneous health-related data from patients, including genomic variants. Genomic variants can be identified and annotated based on the reference human genome either within the sequence as a whole or in a putative functional genomic element. The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) mutually created standards and guidelines for the appraisal of proof to expand consistency and straightforwardness in clinical variation interpretations. Various efforts toward precision medicine have been facilitated by many national and international public databases that classify and annotate genomic variation. In the present study, several resources are highlighted with recognition and data spreading of clinically important genetic variations.
Collapse
Affiliation(s)
- Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | | | - Wan-Khairunnisa Wan-Juhari
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Mat Ghani Siti Nor Assyuhada
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| | - Yetti Hernaningsih
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
| | - Narazah Mohd Yusoff
- Department of Clinical Pathology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo Academic General Hospital, Surabaya, Indonesia
- Clinical Diagnostic Laboratory, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Penang13200, Malaysia
| | - Amir Feisal Merican
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur50603, Malaysia
- Center of Research for Computational Sciences and Informatics in Biology, Bio Industry, Environment, Agriculture and Healthcare (CRYSTAL), University of Malaya, Kuala Lumpur50603, Malaysia
| | - Bin Alwi Zilfalil
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kelantan16150, Malaysia
| |
Collapse
|
8
|
Hayeems RZ, Bernier F, Boycott KM, Hartley T, Michaels-Igbokwe C, Marshall DA. Positioning whole exome sequencing in the diagnostic pathway for rare disease to optimise utility: a protocol for an observational cohort study and an economic evaluation. BMJ Open 2022; 12:e061468. [PMID: 36216418 PMCID: PMC9557316 DOI: 10.1136/bmjopen-2022-061468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION Despite the superior diagnostic performance of exome and genome sequencing compared with conventional genetic tests, evidence gaps related to clinical utility and cost effectiveness have limited their availability in routine clinical practice in many jurisdictions. To inform adoption and reimbursement policy, this protocol provides a chain of evidence approach to determining the diagnostic utility, clinical utility and cost-effectiveness of whole exome sequencing (WES) from seven medical genetic centres in two Canadian provinces. METHODS AND ANALYSIS Using a multicentre observational cohort design, we will extract data specific to the pre-WES diagnostic pathway and 1-year post-WES medical management from electronic medical records for 650 patients with rare disease of suspected genetic aetiology who receive WES. The date from the clinical record will be linked to provincial administrative health database to capture healthcare resource use and estimate costs. Our analysis will: (1) define and describe diagnostic testing pathways that occur prior to WES among patients with rare disease, (2) determine the diagnostic utility of WES, characterised as the proportion of patients for whom causative DNA variants are identified, (3) determine the clinical utility of WES, characterised as a change in medical management triggered by WES results, (4) determine the pattern and cost of health service utilisation prior and 1 year following WES among patients who receive a diagnosis, do not receive a diagnosis, or receive an uncertain diagnosis and (5) estimate the cost-effectiveness of WES compared with conventional diagnostic testing pathways, measured by the incremental cost per additional patient diagnosed by WES using simulation modelling. ETHICS AND DISSEMINATION This protocol was approved by Clinical Trials Ontario (CTO-1577) and research ethics boards at the University of Calgary (REB18-0744 and REB20-1449) and University of Alberta (Pro0009156). Findings will be disseminated through academic publications and policy reports.
Collapse
Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Francois Bernier
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Department of Paediatrics, Facuty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Taila Hartley
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Christine Michaels-Igbokwe
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Deborah A Marshall
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O'Brien Institute for Public Health, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
9
|
Hunter JD, Robertson EG, Hetherington K, Ziegler DS, Marshall GM, Kirk J, Marron JM, Denburg AE, Barlow-Stewart K, Warby M, Tucker KM, Lee BM, O’Brien TA, Wakefield CE. What’s in a Name? Parents’ and Healthcare Professionals’ Preferred Terminology for Pathogenic Variants in Childhood Cancer Predisposition Genes. J Pers Med 2022; 12:jpm12081327. [PMID: 36013276 PMCID: PMC9410181 DOI: 10.3390/jpm12081327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Current literature/guidelines regarding the most appropriate term to communicate a cancer-related disease-causing germline variant in childhood cancer lack consensus. Guidelines also rarely address preferences of patients/families. We aimed to assess preferences of parents of children with cancer, genetics professionals, and pediatric oncologists towards terminology to describe a disease-causing germline variant in childhood cancer. Using semi-structured interviews we asked participants their most/least preferred terms from; ‘faulty gene,’ ‘altered gene,’ ‘gene change,’ and ‘genetic variant,’ analyzing responses with directed content analysis. Twenty-five parents, 6 genetics professionals, and 29 oncologists participated. An equal number of parents most preferred ‘gene change,’ ‘altered gene,’ or ‘genetic variant’ (n = 8/25). Parents least preferred ‘faulty gene’ (n = 18/25). Half the genetics professionals most preferred ‘faulty gene’ (n = 3/6); however this was least preferred by the remaining genetics professionals (n = 3/6). Many oncologists most preferred ‘genetic variant’ (n = 11/29) and least preferred ‘faulty gene’ (n = 19/29). Participants across all groups perceived ‘faulty gene’ as having negative connotations, potentially placing blame/guilt on parents/children. Health professionals described challenges selecting a term that was scientifically accurate, easily understood and not distressing to families. Lack of consensus highlights the need to be guided by families’ preferred terminology, while providing accurate explanations regarding implications of genetic findings.
Collapse
Affiliation(s)
- Jacqueline D. Hunter
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
- Correspondence: ; Tel.: +61-4-39-110-680
| | - Eden G. Robertson
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kate Hetherington
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - David S. Ziegler
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children’s Cancer Institute, UNSW Sydney, Kensington, NSW 2750, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Glenn M. Marshall
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children’s Cancer Institute, UNSW Sydney, Kensington, NSW 2750, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Judy Kirk
- The Westmead Institute for Medical Research, Sydney Medical School, University of Sydney, Sydney, NSW 2052, Australia
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW 2145, Australia
| | - Jonathan M. Marron
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, MA 02215, USA
- Center for Bioethics, Harvard Medical School, Boston, MA 02115, USA
| | - Avram E. Denburg
- Division of Haematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kristine Barlow-Stewart
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Children’s Cancer Institute, UNSW Sydney, Kensington, NSW 2750, Australia
- Northern Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2052, Australia
| | - Meera Warby
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Katherine M. Tucker
- Hereditary Cancer Centre, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Brittany M. Lee
- Seattle Children’s Hospital and Research Institute, Seattle, WA 98101, USA
- Division of Hematology/Oncology, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tracey A. O’Brien
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| | - Claire E. Wakefield
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, UNSW Medicine and Health, UNSW Sydney, Sydney, NSW 2052, Australia
- Behavioural Sciences Unit, Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW 2031, Australia
| |
Collapse
|
10
|
Schlaberg R. Clinical Metagenomics-from Proof-of-Concept to Routine Use. Clin Chem 2022; 68:997-999. [PMID: 35714058 DOI: 10.1093/clinchem/hvac091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022]
Affiliation(s)
- Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
11
|
Goddard KAB, Lee K, Buchanan AH, Powell BC, Hunter JE. Establishing the Medical Actionability of Genomic Variants. Annu Rev Genomics Hum Genet 2022; 23:173-192. [PMID: 35363504 PMCID: PMC10184682 DOI: 10.1146/annurev-genom-111021-032401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Actionability is an important concept in medicine that does not have a well-accepted standard definition, nor is there a general consensus on how to establish it. Medical actionability is often conflated with clinical utility, a related but distinct concept. This lack of clarity contributes to practice variation and inconsistent coverage decisions in genomic medicine, leading to the potential for systematic bias in the use of evidence-based interventions. We clarify how medical actionability and clinical utility are distinct and then discuss the spectrum of actionability, including benefits for the person, the family, and society. We also describe applications across the life course, including prediction, diagnosis, and treatment. Current challenges in assessing the medical actionability of identified genomic variants include gaps in the evidence, limited contexts with practice guidelines, and subjective aspects of medical actionability. A standardized and authoritative assessment of medical actionability is critical to implementing genomic medicine in a fashion that improves population health outcomes and reduces health disparities. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Kristy Lee
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Adam H Buchanan
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Bradford C Powell
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA; .,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA; , .,Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA; .,Genomics, Ethics, and Translational Research Program, RTI International, Research Triangle Park, North Carolina, USA;
| |
Collapse
|
12
|
Pritchard D, Goodman C, Nadauld LD. Clinical Utility of Genomic Testing in Cancer Care. JCO Precis Oncol 2022; 6:e2100349. [PMID: 35085005 PMCID: PMC8830511 DOI: 10.1200/po.21.00349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the era of personalized medicine, physicians rely on their understanding of clinical utility to assess the value of rapidly evolving genetic and genomic tests. Current definitions of the clinical utility of genetic testing sufficiently capture a range of benefits and risks that derive from positive and negative results of tests that assess one gene or a few genes. However, these definitions of clinical utility are inadequate to recognize the wider scope of benefits that accrue from more comprehensive genomic tests, which can develop data sets that inform clinical decision making as well as population health and scientific advancement in novel ways.
Collapse
Affiliation(s)
| | | | - Lincoln D Nadauld
- Precision Health and Genomics, Intermountain Healthcare, Salt Lake City, UT
| |
Collapse
|
13
|
Shen EC, Srinivasan S, Passero LE, Allen CG, Dixon M, Foss K, Halliburton B, Milko LV, Smit AK, Carlson R, Roberts MC. Barriers and Facilitators for Population Genetic Screening in Healthy Populations: A Systematic Review. Front Genet 2022; 13:865384. [PMID: 35860476 PMCID: PMC9289280 DOI: 10.3389/fgene.2022.865384] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022] Open
Abstract
Studies suggest that 1-3% of the general population in the United States unknowingly carry a genetic risk factor for a common hereditary disease. Population genetic screening is the process of offering otherwise healthy patients in the general population testing for genomic variants that predispose them to diseases that are clinically actionable, meaning that they can be prevented or mitigated if they are detected early. Population genetic screening may significantly reduce morbidity and mortality from these diseases by informing risk-specific prevention or treatment strategies and facilitating appropriate participation in early detection. To better understand current barriers, facilitators, perceptions, and outcomes related to the implementation of population genetic screening, we conducted a systematic review and searched PubMed, Embase, and Scopus for articles published from date of database inception to May 2020. We included articles that 1) detailed the perspectives of participants in population genetic screening programs and 2) described the barriers, facilitators, perceptions, and outcomes related to population genetic screening programs among patients, healthcare providers, and the public. We excluded articles that 1) focused on direct-to-consumer or risk-based genetic testing and 2) were published before January 2000. Thirty articles met these criteria. Barriers and facilitators to population genetic screening were organized by the Social Ecological Model and further categorized by themes. We found that research in population genetic screening has focused on stakeholder attitudes with all included studies designed to elucidate individuals' perceptions. Additionally, inadequate knowledge and perceived limited clinical utility presented a barrier for healthcare provider uptake. There were very few studies that conducted long-term follow-up and evaluation of population genetic screening. Our findings suggest that these and other factors, such as prescreen counseling and education, may play a role in the adoption and implementation of population genetic screening. Future studies to investigate macro-level determinants, strategies to increase provider buy-in and knowledge, delivery models for prescreen counseling, and long-term outcomes of population genetic screening are needed for the effective design and implementation of such programs. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020198198.
Collapse
Affiliation(s)
- Emily C Shen
- College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Swetha Srinivasan
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Lauren E Passero
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Caitlin G Allen
- Department of Public Health Science, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Madison Dixon
- Department of Behavioral, Social, and Health Education Science, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Kimberly Foss
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Brianna Halliburton
- College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Laura V Milko
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Amelia K Smit
- The Daffodil Centre, University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW, Australia.,Melanoma Institute Australia, University of Sydney, Sydney, NSW, Australia
| | - Rebecca Carlson
- Health Sciences Library, University of North Carolina, Chapel Hill, NC, United States
| | - Megan C Roberts
- Division of Pharmaceutical Outcomes and Policy, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| |
Collapse
|
14
|
Matsui K, Yamamoto K, Tashiro S, Ibuki T. A systematic approach to the disclosure of genomic findings in clinical practice and research: a proposed framework with colored matrix and decision-making pathways. BMC Med Ethics 2021; 22:168. [PMID: 34953504 PMCID: PMC8709972 DOI: 10.1186/s12910-021-00738-9] [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: 09/30/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Whether and how to disclose genomic findings obtained in the course of genomic clinical practice and medical research has been a controversial global bioethical issue over the past two decades. Although several recommendations and judgment tools for the disclosure of genomic findings have been proposed, none are sufficiently systematic or inclusive or even consistent with each other. In order to approach the disclosure/non-disclosure practice in an ethical manner, optimal and easy-to-use tools for supporting the judgment of physicians/researchers in genomic medicine are necessary. Methods The bioethics literature on this topic was analyzed to parse and deconstruct the somewhat overlapping and therefore ill-defined key concepts of genomic findings, such as incidental, primary, secondary, and other findings. Based on the deconstruction and conceptual analyses of these findings, we then defined key parameters from which to identify the strength of duty to disclose (SDD) for a genomic finding. These analyses were then applied to develop a framework with the SDD matrix and systematic decision-making pathways for the disclosure of genomic findings. Results The following six major parameters (axes), along with sub-axes, were identified: Axis 1 (settings and institutions where findings emerge); Axis 2 (presence or absence of intention and anticipatability in discovery); Axis 3 (maximal actionability at the time of discovery); Axis 4 (net medical importance); Axis 5 (expertise of treating physician/researcher); and Axis 6 (preferences of individual patients/research subjects for disclosure). For Axes 1 to 4, a colored SDD matrix for genomic findings was developed in which levels of obligation for disclosing a finding can be categorized. For Axes 5 and 6, systematic decision-making pathways were developed via the SDD matrix. Conclusion We analyzed the SDD of genomic findings and developed subsequent systematic decision-making pathways of whether and how to disclose genomic findings to patients/research subjects and their relatives in an ethical manner. Our comprehensive framework may help physicians and researchers in genomic medicine make consistent ethical judgments regarding the disclosure of genomic findings.
Collapse
Affiliation(s)
- Kenji Matsui
- Division of Bioethics and Healthcare Law, The Institute for Cancer Control, The National Cancer Center Japan, Tsukiji 5-1-1, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Keiichiro Yamamoto
- Office of Bioethics, The Center for Clinical Sciences, The National Center for Global Health and Medicine, Tokyo, Japan
| | - Shimon Tashiro
- Department of Sociology, Graduate School of Arts and Letters, Tohoku University, Sendai, Japan
| | - Tomohide Ibuki
- Institute of Arts and Sciences, Tokyo University of Science, Noda-shi, Japan
| |
Collapse
|
15
|
Lee W, Luca S, Costain G, Snell M, Marano M, Curtis M, Dunsmore K, Veenma D, Walker S, Cohn RD, Marshall CR, Cohen E, Meyn MS, Orkin J, Hayeems RZ. Genome sequencing among children with medical complexity: What constitutes value from parents' perspective? J Genet Couns 2021; 31:523-533. [PMID: 34674352 DOI: 10.1002/jgc4.1522] [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: 04/23/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/06/2022]
Abstract
Genome sequencing (GS) has demonstrated high diagnostic yield in pediatric patients with complex, clinically heterogeneous presentations. Emerging evidence shows generally favorable experiences for patients and families receiving GS. As a result, implementation of GS in pediatrics is gaining momentum. To inform implementation, we conducted a qualitative study to explore the personal utility of GS for parents of children with medical complexity (CMC). GS was performed at an academic tertiary-care center for CMC for whom a genetic etiology was suspected. Following the return of GS results, semi-structured interviews were conducted with 14 parents about their child's diagnostic journey. Of the children whose parents were interviewed, six children received a diagnosis, two received a possible diagnosis, and six did not receive a diagnosis. A predominantly deductive thematic analysis approach to the interview data was used by applying Kohler's personal utility framework to understand affective, cognitive, behavioral and social impacts of GS. Both the diagnosed and undiagnosed groups experienced enhanced emotion-focused coping (affective). The diagnosed group experienced favorable utility related to knowledge of condition (cognitive) and communication with relatives (behavioral). A domain beyond Kohler's framework related to the presence or absence of GS impact on medical management was also described by parents. The deployment of GS late in the diagnostic odyssey and the limited knowledge available for the rare genetic disorders diagnosed in this cohort appeared to diminish the perceived utility of GS. As GS capabilities continue to evolve at a rapid pace and become available earlier in the diagnostic journey, it is important to consider the impact and timing of testing on parents of CMC.
Collapse
Affiliation(s)
- Whiwon Lee
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Stephanie Luca
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meaghan Snell
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Marano
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada.,Service de pédiatrie générale, CHU Sainte-Justine, Montreal, Québec, Canada
| | - Meredith Curtis
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kourtney Dunsmore
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Danielle Veenma
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics: Developmental and Genetics, Erasmus MC Sophia, Rotterdam, Netherlands
| | - Susan Walker
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Genomics England, Queen Mary University of London, London, UK
| | - Ronald D Cohn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Eyal Cohen
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - M Stephen Meyn
- Center for Human Genomics and Precision Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA.,Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Julia Orkin
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
16
|
Nichols ZE, Geddes CD. Sample Preparation and Diagnostic Methods for a Variety of Settings: A Comprehensive Review. Molecules 2021; 26:5666. [PMID: 34577137 PMCID: PMC8470389 DOI: 10.3390/molecules26185666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/16/2022] Open
Abstract
Sample preparation is an essential step for nearly every type of biochemical analysis in use today. Among the most important of these analyses is the diagnosis of diseases, since their treatment may rely greatly on time and, in the case of infectious diseases, containing their spread within a population to prevent outbreaks. To address this, many different methods have been developed for use in the wide variety of settings for which they are needed. In this work, we have reviewed the literature and report on a broad range of methods that have been developed in recent years and their applications to point-of-care (POC), high-throughput screening, and low-resource and traditional clinical settings for diagnosis, including some of those that were developed in response to the coronavirus disease 2019 (COVID-19) pandemic. In addition to covering alternative approaches and improvements to traditional sample preparation techniques such as extractions and separations, techniques that have been developed with focuses on integration with smart devices, laboratory automation, and biosensors are also discussed.
Collapse
Affiliation(s)
- Zach E. Nichols
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| | - Chris D. Geddes
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD 21250, USA;
- Institute of Fluorescence, University of Maryland, Baltimore County, 701 E Pratt Street, Baltimore, MD 21270, USA
| |
Collapse
|
17
|
Lam S, Guthrie KS, Latif MA, Weiss CR. Genetic counseling and testing for hereditary hemorrhagic telangiectasia. Clin Genet 2021; 101:275-284. [PMID: 34415050 DOI: 10.1111/cge.14050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/04/2021] [Accepted: 08/15/2021] [Indexed: 12/13/2022]
Abstract
Genetic counseling is an important means of identifying a patient's genetic risk of hereditary hemorrhagic telangiectasia (HHT) and assisting patients in making informed decisions about their health. With an increase in understanding of the genetic mechanisms underlying HHT over the last decade, genetic counseling is increasingly being incorporated into the care of patients affected by HHT. In addition to refining the diagnosis of symptomatic patients, genetic testing can help to distinguish asymptomatic, at-risk patients from those who are unaffected by HHT. The purpose of this review article is to summarize the current knowledge regarding the role of genetic counseling and genetic testing in identifying and managing HHT in at-risk populations. This article also reviews the guidelines, outcomes, risks, and challenges of genetic counseling and testing for HHT in various patient populations, and provides an algorithm for the use of genetic counseling in symptomatic and asymptomatic patients.
Collapse
Affiliation(s)
- Shravika Lam
- Russel H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kelsey S Guthrie
- Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Muhammad A Latif
- Russel H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Clifford R Weiss
- Russel H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
18
|
Newman S, Nakitandwe J, Kesserwan CA, Azzato EM, Wheeler DA, Rusch M, Shurtleff S, Hedges DJ, Hamilton KV, Foy SG, Edmonson MN, Thrasher A, Bahrami A, Orr BA, Klco JM, Gu J, Harrison LW, Wang L, Clay MR, Ouma A, Silkov A, Liu Y, Zhang Z, Liu Y, Brady SW, Zhou X, Chang TC, Pande M, Davis E, Becksfort J, Patel A, Wilkinson MR, Rahbarinia D, Kubal M, Maciaszek JL, Pastor V, Knight J, Gout AM, Wang J, Gu Z, Mullighan CG, McGee RB, Quinn EA, Nuccio R, Mostafavi R, Gerhardt EL, Taylor LM, Valdez JM, Hines-Dowell SJ, Pappo AS, Robinson G, Johnson LM, Pui CH, Ellison DW, Downing JR, Zhang J, Nichols KE. Genomes for Kids: The scope of pathogenic mutations in pediatric cancer revealed by comprehensive DNA and RNA sequencing. Cancer Discov 2021; 11:3008-3027. [PMID: 34301788 DOI: 10.1158/2159-8290.cd-20-1631] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/21/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022]
Abstract
Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.
Collapse
Affiliation(s)
- Scott Newman
- Computational Biology, St. Jude Children's Research Hospital
| | - Joy Nakitandwe
- Pathology and Laboratory Medicine Institute, Cleveland Clinic
| | | | | | | | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Dale J Hedges
- Computational Biology, St. Jude Children's Research Hospital
| | - Kayla V Hamilton
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Scott G Foy
- Computational Biology, St. Jude Children's Research Hospital
| | | | - Andrew Thrasher
- Computational Biology, St. Jude Children's Research Hospital
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital
| | - Brent A Orr
- Pathology, St. Jude Children's Research Hospital
| | | | - Jiali Gu
- Department of Pathology, St. Jude Children's Research Hospital
| | - Lynn W Harrison
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Lu Wang
- Pathology, St. Jude Children's Research Hospital
| | | | - Annastasia Ouma
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Antonina Silkov
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Yu Liu
- Computational Biology, St. Jude Children's Research Hospital
| | - Samuel W Brady
- Computational Biology, St. Jude Children's Research Hospital
| | - Xin Zhou
- St. Jude Children's Research Hospital
| | - Ti-Cheng Chang
- Computational Biology, St. Jude Children's Research Hospital
| | - Manjusha Pande
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Eric Davis
- Department of Computational Biology, St. Jude Children's Research Hospital
| | - Jared Becksfort
- Computational Biology, St. Jude Children's Research Hospital
| | - Aman Patel
- Computational Biology, St. Jude Children's Research Hospital
| | | | | | - Manish Kubal
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | - Jay Knight
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | - Jian Wang
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | | | | | | - Emily A Quinn
- Pharmacy and Health Sciences, Keck Graduate Institute
| | - Regina Nuccio
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | - Elsie L Gerhardt
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | - Leslie M Taylor
- Division of Cancer Predisposition, St. Jude Children's Research Hospital
| | | | | | | | | | - Liza-Marie Johnson
- Division of Quality of Life and Palliative Care, St. Jude Children's Research Hospital
| | | | | | | | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital
| | | |
Collapse
|
19
|
Hayeems RZ, Luca S, Assamad D, Bhatt A, Ungar WJ. Utility of Genetic Testing from the Perspective of Parents/Caregivers: A Scoping Review. CHILDREN (BASEL, SWITZERLAND) 2021; 8:259. [PMID: 33801725 PMCID: PMC8067127 DOI: 10.3390/children8040259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
In genomics, perceived and personal utility have been proposed as constructs of value that include the subjective meanings and uses of genetic testing. Precisely what constitutes these constructs of utility and how they vary by stakeholder perspective remains unresolved. To advance methods for measuring the value of genetic testing in child health, we conducted a scoping review of the literature to characterize utility from the perspective of parents/caregivers. Peer reviewed literature that included empiric findings from parents/caregivers who received genetic test results for an index child and was written in English from 2016-2020 was included. Identified concepts of utility were coded according to Kohler's construct of personal utility. Of 2142 abstracts screened, 33 met inclusion criteria. Studies reflected a range of genetic test types; the majority of testing was pursued for children with developmental or neurodevelopmental concerns. Coding resulted in 15 elements of utility that mapped to Kohler's four domains of personal utility (affective, cognitive, behavioural and social) and one additional medical management domain. An adapted construct of utility for parents/caregivers may enable specific and standardized strategies for researchers to use to generate evidence of the post-test value of genetic testing. In turn, this will contribute to emerging methods for health technology assessment and policy decision making for genomics in child health.
Collapse
Affiliation(s)
- Robin Z. Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Stephanie Luca
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
| | - Daniel Assamad
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
| | - Ayushi Bhatt
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Wendy J. Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (S.L.); (D.A.); (A.B.); (W.J.U.)
- Institute of Health Policy Management and Evaluation, The University of Toronto, Toronto, ON M5T 3M6, Canada
| |
Collapse
|
20
|
Ginsburg O, Ashton-Prolla P, Cantor A, Mariosa D, Brennan P. The role of genomics in global cancer prevention. Nat Rev Clin Oncol 2021; 18:116-128. [PMID: 32973296 DOI: 10.1038/s41571-020-0428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Despite improvements in the understanding of cancer causation, much remains unknown regarding the mechanisms by which genomic and non-genomic factors initiate carcinogenesis, drive cell invasion and metastasis, and enable cancer to develop. Technological advances have enabled the analysis of whole genomes, comprising thousands of tumours across populations worldwide, with the aim of identifying mutation signatures associated with particular tumour types. Large collaborative efforts have resulted in the identification and improved understanding of causal factors, and have shed light on new opportunities to prevent cancer. In this new era in cancer genomics, discoveries from studies conducted on an international scale can inform evidence-based strategies in cancer control along the cancer care continuum, from prevention to treatment. In this Review, we present the relevant history and emerging frontiers of cancer genetics and genomics from the perspective of global cancer prevention. We highlight the importance of local context in the adoption of new technologies and emergent evidence, with illustrative examples from worldwide. We emphasize the challenges in implementing important genomic findings in clinical settings with disparate resource availability and present a conceptual framework for the translation of such findings into clinical practice, and evidence-based policies in order to maximize the utility for a population.
Collapse
Affiliation(s)
- Ophira Ginsburg
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Section for Global Health, Division of Health and Behavior, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
| | - Patricia Ashton-Prolla
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre and Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anna Cantor
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
21
|
Hayeems RZ, Dimmock D, Bick D, Belmont JW, Green RC, Lanpher B, Jobanputra V, Mendoza R, Kulkarni S, Grove ME, Taylor SL, Ashley E. Clinical utility of genomic sequencing: a measurement toolkit. NPJ Genom Med 2020; 5:56. [PMID: 33319814 PMCID: PMC7738524 DOI: 10.1038/s41525-020-00164-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022] Open
Abstract
Whole-genome sequencing (WGS) is positioned to become one of the most robust strategies for achieving timely diagnosis of rare genomic diseases. Despite its favorable diagnostic performance compared to conventional testing strategies, routine use and reimbursement of WGS are hampered by inconsistencies in the definition and measurement of clinical utility. For example, what constitutes clinical utility for WGS varies by stakeholder's perspective (physicians, patients, families, insurance companies, health-care organizations, and society), clinical context (prenatal, pediatric, critical care, adult medicine), and test purpose (diagnosis, screening, treatment selection). A rapidly evolving technology landscape and challenges associated with robust comparative study design in the context of rare disease further impede progress in this area of empiric research. To address this challenge, an expert working group of the Medical Genome Initiative was formed. Following a consensus-based process, we align with a broad definition of clinical utility and propose a conceptually-grounded and empirically-guided measurement toolkit focused on four domains of utility: diagnostic thinking efficacy, therapeutic efficacy, patient outcome efficacy, and societal efficacy. For each domain of utility, we offer specific indicators and measurement strategies. While we focus on diagnostic applications of WGS for rare germline diseases, this toolkit offers a flexible framework for best practices around measuring clinical utility for a range of WGS applications. While we expect this toolkit to evolve over time, it provides a resource for laboratories, clinicians, and researchers looking to characterize the value of WGS beyond the laboratory.
Collapse
Affiliation(s)
- Robin Z Hayeems
- Program in Child Health Evaluative Sciences, The Hospital for Sick Children and the Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada.
| | - David Dimmock
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, CA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Robert C Green
- Brigham and Women's Hospital Broad Institute and Harvard Medical School, Boston, MA, USA
| | | | - Vaidehi Jobanputra
- New York Genome Center, New York, NY, USA
- Department of Pathology and Cell Biology Columbia University Medical Center, New York, NY, USA
| | - Roberto Mendoza
- The Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Shashi Kulkarni
- Baylor Genetics and Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | |
Collapse
|
22
|
Hsiao SJ, Sireci AN, Pendrick D, Freeman C, Fernandes H, Schwartz GK, Henick BS, Mansukhani MM, Roth KA, Carvajal RD, Oberg JA. Clinical Utilization, Utility, and Reimbursement for Expanded Genomic Panel Testing in Adult Oncology. JCO Precis Oncol 2020; 4:1038-1048. [DOI: 10.1200/po.20.00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The routine use of large next-generation sequencing (NGS) pan-cancer panels is required to identify the increasing number of, but often uncommon, actionable alterations to guide therapy. Inconsistent coverage and variable payment is hindering NGS adoption into clinical practice. A review of test utilization, clinical utility, coverage, and reimbursement was conducted in a cohort of patients diagnosed with high-risk cancer who received pan-cancer panel testing as part of their clinical care. MATERIALS AND METHODS The Columbia Combined Cancer Panel (CCCP), a 467-gene panel designed to detect DNA variations in solid and liquid tumors, was performed in the Laboratory of Personalized Genomic Medicine at Columbia University Irving Medical Center. Utilization was characterized at test order. Results were reviewed by a molecular pathologist, followed by a multidisciplinary molecular tumor board where clinical utility was classified by consensus. Reimbursement was reviewed after payers provided final coverage decisions. RESULTS NGS was performed on 359 high-risk tumors from 349 patients. Reimbursement data were available for 246 cases. The most common reason providers ordered CCCP testing was for patients diagnosed with a treatment-resistant or recurrent tumor (n = 214; 61%). Findings were clinically impactful for 229 cases (64%). Molecular alterations that may inform future therapy in the event of progression or relapse were found in 42% of cases, and a targeted therapy was initiated in 23 cases (6.6%). The majority of tests were denied coverage by payers (n = 190; 77%). On average, insurers reimbursed 10.75% of the total NGS service charge. CONCLUSION CCCP testing identified clinically impactful alterations in 64% of cases. Limited coverage and low reimbursement remain barriers, and broader reimbursement policies are needed to adopt pan-cancer NGS testing that benefits patients into clinical practice.
Collapse
Affiliation(s)
- Susan J. Hsiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Anthony N. Sireci
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Danielle Pendrick
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Christopher Freeman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Gary K. Schwartz
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Brian S. Henick
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Kevin A. Roth
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Richard D. Carvajal
- Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Jennifer A. Oberg
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| |
Collapse
|
23
|
Mighton C, Carlsson L, Clausen M, Casalino S, Shickh S, McCuaig L, Joshi E, Panchal S, Semotiuk K, Ott K, Elser C, Eisen A, Kim RH, Lerner-Ellis J, Carroll JC, Glogowski E, Schrader K, Bombard Y. Quality of life drives patients' preferences for secondary findings from genomic sequencing. Eur J Hum Genet 2020; 28:1178-1186. [PMID: 32424322 PMCID: PMC7609335 DOI: 10.1038/s41431-020-0640-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/31/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023] Open
Abstract
There is growing impetus to include measures of personal utility, the nonmedical value of information, in addition to clinical utility in health technology assessment (HTA) of genomic tests such as genomic sequencing (GS). However, personal utility and clinical utility are challenging to define and measure. This study aimed to explore what drives patients' preferences for hypothetically learning medically actionable and non-medically actionable secondary findings (SF), capturing clinical and personal utility; this may inform development of measures to evaluate patient outcomes following return of SF. Semi-structured interviews were conducted with adults with a personal or family cancer history participating in a trial of a decision aid for selection of SF from genomic sequencing (GS) ( www.GenomicsADvISER.com ). Interviews were analyzed thematically using constant comparison. Preserving health-related and non-health-related quality of life was an overarching motivator for both learning and not learning SF. Some participants perceived that learning SF would help them "have a good quality of life" through informing actions to maintain physical health or leading to psychological benefits such as emotional preparation for disease. Other participants preferred not to learn SF because results "could ruin your quality of life," such as by causing negative psychological impacts. Measuring health-related and non-health-related quality of life may capture outcomes related to clinical and personal utility of GS and SF, which have previously been challenging to measure. Without appropriate measures, generating and synthesizing evidence to evaluate genomic technologies such as GS will continue to be a challenge, and will undervalue potential benefits of GS and SF.
Collapse
Affiliation(s)
- Chloe Mighton
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - Lindsay Carlsson
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | - Marc Clausen
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - Selina Casalino
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - Salma Shickh
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | - Laura McCuaig
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Esha Joshi
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada
| | | | | | - Karen Ott
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Christine Elser
- University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - Andrea Eisen
- Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Raymond H Kim
- University Health Network, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Sinai Health System, Toronto, ON, Canada
| | - Jordan Lerner-Ellis
- Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - June C Carroll
- Sinai Health System, Toronto, ON, Canada
- Department of Family & Community Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Kasmintan Schrader
- BC Cancer Agency, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Unity Health, Toronto, ON, Canada.
| |
Collapse
|
24
|
Peddi VR, Patel PS, Schieve C, Rose S, First MR. Serial Peripheral Blood Gene Expression Profiling to Assess Immune Quiescence in Kidney Transplant Recipients with Stable Renal Function. Ann Transplant 2020; 25:e920839. [PMID: 32341330 PMCID: PMC7204430 DOI: 10.12659/aot.920839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background TruGraf is a blood-based biomarker test that measures differential expression of a collection of genes that have been shown to correlate with surveillance biopsy results. However, in the majority of U.S. transplant centers, surveillance biopsies are not performed. The objectives of this study were to evaluate the clinical validity of TruGraf in stable kidney transplant recipients and to demonstrate the potential clinical utility of serial TruGraf testing in a center not utilizing surveillance biopsies. Material/Methods Serum creatinine levels, TruGraf testing at multiple time points, and subsequent clinical follow-up were obtained for 28 patients. Results Overall concordance of TruGraf results, when compared with independent clinical assessment of testing, was 77% (54/70) for all tests; 79% (22/28) for test 1, 75% (21/28) for test 2, and 79% (11/14) for test 3. The negative predictive value (NPV) was 98.0%. Analysis of clinical utility indicated that 77% of TruGraf results would have been useful in patient management. Conclusions Our results indicate the value of serial TruGraf testing in those transplant centers that do not perform surveillance biopsies as part of their standard of care. The high negative predictive value indicates the ability of TruGraf to confirm immune quiescence with a high degree of probability in patients with a Transplant eXcellence (TX) result, without the need to perform a surveillance biopsy.
Collapse
Affiliation(s)
- V Ram Peddi
- Department of Transplantation, California Pacific Medical Center, San Francisco, CA, USA
| | - Parul S Patel
- Department of Transplantation, California Pacific Medical Center, San Francisco, CA, USA
| | | | - Stan Rose
- Transplant Genomics Inc., Mansfield, MA, USA
| | - M Roy First
- Transplant Genomics Inc., Mansfield, MA, USA
| |
Collapse
|
25
|
Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:46. [PMID: 32127026 PMCID: PMC7055088 DOI: 10.1186/s13046-020-01554-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
The promising expectations about personalized medicine have opened the path to routine large-scale sequencing and increased the importance of genetic counseling for hereditary cancers, among which hereditary breast and ovary cancers (HBOC) have a major impact. High-throughput sequencing, or Next-Generation Sequencing (NGS), has improved cancer patient management, ameliorating diagnosis and treatment decisions. In addition to its undeniable clinical utility, NGS is also unveiling a large number of variants that we are still not able to clearly define and classify, the variants of uncertain significance (VUS), which account for about 40% of total variants. At present, VUS use in the clinical context is challenging. Medical reports may omit this kind of data and, even when included, they limit the clinical utility of genetic information. This has prompted the scientific community to seek easily applicable tests to accurately classify VUS and increase the amount of usable information from NGS data. In this review, we will focus on NGS and classification systems for VUS investigation, with particular attention on HBOC-related genes and in vitro functional tests developed for ameliorating and accelerating variant classification in cancer.
Collapse
|
26
|
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.
Collapse
Affiliation(s)
- Barbara A Zehnbauer
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia (Editor-in-Chief).
| |
Collapse
|
27
|
Lee YJ, Kim D, Kim HS, Na K, Lee JY, Nam EJ, Kim SW, Kim S, Kim YT. Integrating a Next Generation Sequencing Panel into Clinical Practice in Ovarian Cancer. Yonsei Med J 2019; 60:914-923. [PMID: 31538426 PMCID: PMC6753345 DOI: 10.3349/ymj.2019.60.10.914] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
PURPOSE Few efforts have been made to integrate a next generation sequencing (NGS) panel into standard clinical treatment of ovarian cancer. The aim of this study was to investigate the clinical utility of NGS and to identify clinically impactful information beyond targetable alterations. MATERIALS AND METHODS We conducted a retrospective review of 84 patients with ovarian cancer who underwent NGS between March 1, 2017, and July 31, 2018, at the Yonsei Cancer Hospital. We extracted DNA from formalin-fixed, paraffin-embedded tissue samples of ovarian cancer. The TruSight Tumor 170 gene panel was used to prepare libraries, and the MiSeq instrument was used for NGS. RESULTS Of the 84 patients, 55 (65.1%) had high-grade serous carcinomas. Seventy-three (86.7%) patients underwent NGS at the time of diagnosis, and 11 (13.3%) underwent NGS upon relapse. The most common genetic alterations were in TP53 (64%), PIK3CA (15%), and BRCA1/2 (13%), arising as single nucleotide variants and indels. MYC amplification (27%) was the most common copy number variation and fusion. Fifty-seven (67.9%) patients had more than one actionable alteration other than TP53. Seven (8.3%) cases received matched-target therapy based on the following sequencing results: BRCA1 or 2 mutation, poly ADP ribose polymerase inhibitor (n=5); PIK3CA mutation, AKT inhibitor (n=1); and MLH1 mutation, PD-1 inhibitor (n=1). Fifty-three (63.0%) patients had a possibility of treatment change, and 8 (9.5%) patients received genetic counseling. CONCLUSION Implementation of NGS may help in identifying patients who might benefit from targeted treatment therapies and genetic counseling.
Collapse
Affiliation(s)
- Yong Jae Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Dachan Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Soo Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kiyong Na
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jung Yun Lee
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Eun Ji Nam
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Sunghoon Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Young Tae Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| |
Collapse
|
28
|
Abstract
OBJECTIVES To provide a clinical laboratory perspective on the Verifying Accurate Leading-edge IVCT Development Act (VALID) discussion draft. This potential legislative effort, if enacted, would overhaul the regulatory oversight of in vitro diagnostics (IVDs) in the United States and create a single system for regulation of conventional IVDs and laboratory-developed tests (LDTs). METHODS A concise literature-based review of LDT regulation is presented followed by a discussion of key concerns pertinent to clinical laboratories that should be considered in future IVD regulatory reform efforts. RESULTS Key issues identified include the importance of fostering innovation, preserving patient safety, protecting the practice of laboratory medicine, and minimizing undue regulatory burden. Clinical laboratories are not equivalent to manufacturing facilities and would therefore encounter challenges in implementing device-centric regulatory oversight models. CONCLUSIONS It is imperative that a clinical laboratory perspective on LDTs is understood and incorporated prior to advancement of future legislative proposals.
Collapse
Affiliation(s)
- Jonathan R Genzen
- Department of Pathology, University of Utah, Salt Lake City
- ARUP Laboratories, Salt Lake City, UT
| |
Collapse
|
29
|
Clinical utility of custom-designed NGS panel testing in pediatric tumors. Genome Med 2019; 11:32. [PMID: 31133068 PMCID: PMC6537185 DOI: 10.1186/s13073-019-0644-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/07/2019] [Indexed: 02/06/2023] Open
Abstract
Background Somatic genetic testing is rapidly becoming the standard of care in many adult and pediatric cancers. Previously, the standard approach was single-gene or focused multigene testing, but many centers have moved towards broad-based next-generation sequencing (NGS) panels. Here, we report the laboratory validation and clinical utility of a large cohort of clinical NGS somatic sequencing results in diagnosis, prognosis, and treatment of a wide range of pediatric cancers. Methods Subjects were accrued retrospectively at a single pediatric quaternary-care hospital. Sequence analyses were performed on 367 pediatric cancer samples using custom-designed NGS panels over a 15-month period. Cases were profiled for mutations, copy number variations, and fusions identified through sequencing, and their clinical impact on diagnosis, prognosis, and therapy was assessed. Results NGS panel testing was incorporated meaningfully into clinical care in 88.7% of leukemia/lymphomas, 90.6% of central nervous system (CNS) tumors, and 62.6% of non-CNS solid tumors included in this cohort. A change in diagnosis as a result of testing occurred in 3.3% of cases. Additionally, 19.4% of all patients had variants requiring further evaluation for potential germline alteration. Conclusions Use of somatic NGS panel testing resulted in a significant impact on clinical care, including diagnosis, prognosis, and treatment planning in 78.7% of pediatric patients tested in our institution. Somatic NGS tumor testing should be implemented as part of the routine diagnostic workup of newly diagnosed and relapsed pediatric cancer patients. Electronic supplementary material The online version of this article (10.1186/s13073-019-0644-8) contains supplementary material, which is available to authorized users.
Collapse
|
30
|
Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing. J Mol Diagn 2019; 21:3-12. [DOI: 10.1016/j.jmoldx.2018.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/29/2018] [Accepted: 09/17/2018] [Indexed: 01/01/2023] Open
|
31
|
First MR, Peddi VR, Mannon R, Knight R, Marsh CL, Kurian SM, Rice JC, Maluf D, Mandelbrot D, Patel A, David J, Schieve C, Lee D, Lewis P, Friedewald JJ, Abecassis MM, Rose S. Investigator Assessment of the Utility of the TruGraf Molecular Diagnostic Test in Clinical Practice. Transplant Proc 2018; 51:729-733. [PMID: 30979457 DOI: 10.1016/j.transproceed.2018.10.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/14/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND TruGraf v1 is a well-validated DNA microarray-based test that analyzes blood gene expression profiles as an indicator of immune status in kidney transplant recipients with stable renal function. METHODS In this study, investigators assessed clinical utility of the TruGraf test in patient management. In a retrospective study, simultaneous blood tests and clinical assessments were performed in 192 patients at 7 transplant centers, and in a prospective observational study they were performed in 45 subjects at 5 transplant centers. RESULTS When queried regarding whether or not the TruGraf test result impacted their decision regarding patient management, in 168 of 192 (87.5%) cases the investigator responded affirmatively. The prospective study indicated that TruGraf results supported physicians' decisions on patient management 87% (39/45) of the time, and in 93% of cases physicians indicated that they would use serial TruGraf testing in future patient management. A total of 21 of 39 (54%) reported results confirmed their decision that no intervention was needed, and 17 of 39 (44%) reported that results specifically informed them that a decision not to perform a surveillance biopsy was correct. CONCLUSIONS TruGraf is the first and only noninvasive test to be evaluated for clinical utility in determining rejection status of patients with stable renal function and shows promise of providing support for clinical decisions to avoid unnecessary surveillance biopsies with a high degree of confidence. TruGraf is an invaluable addition to the transplant physician's tool kit for managing patient health by avoiding painful and invasive biopsies, reducing health care costs, and enabling frequent assessment of patients with stable renal function to confirm immune quiescence.
Collapse
Affiliation(s)
- M R First
- Transplant Genomics Inc, Mansfield, MA; Comprehensive Transplant Center, Northwestern University, Chicago, IL.
| | - V R Peddi
- California Pacific Medical Center, San Francisco, CA
| | - R Mannon
- University of Alabama at Birmingham, Birmingham, AL
| | - R Knight
- Houston Methodist Hospital, Houston, TX
| | - C L Marsh
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - S M Kurian
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - J C Rice
- Scripps Center for Organ Transplantation, La Jolla, CA
| | - D Maluf
- University of Virginia, Charlottesville, VA
| | | | - A Patel
- Henry Ford Hospital, Detroit, MI
| | - J David
- Transplant Genomics Inc, Mansfield, MA
| | - C Schieve
- Transplant Genomics Inc, Mansfield, MA
| | - D Lee
- Transplant Genomics Inc, Mansfield, MA
| | - P Lewis
- Transplant Genomics Inc, Mansfield, MA
| | - J J Friedewald
- Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - M M Abecassis
- Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - S Rose
- Transplant Genomics Inc, Mansfield, MA
| |
Collapse
|
32
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med 2018; 142:321-346. [PMID: 29355391 DOI: 10.5858/arpa.2017-0388-cp] [Citation(s) in RCA: 515] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
CONTEXT - In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE - To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN - The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS - Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS - The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes ( ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- From the Departments of Pathology (Drs Lindeman and Sholl) and Medicine (Dr Kwiatkowski), Brigham and Women's Hospital, Boston, Massachusetts; the Cancer Center (Dr Bernicker) and the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas (Dr Cagle); the Department of Pathology, University of Colorado School of Medicine, Denver (Dr Aisner); the Diagnostic and Molecular Pathology Laboratory (Dr Arcila) and the Molecular Diagnostics Service (Dr Ladanyi), Memorial Sloan Kettering Cancer Center, New York, New York; the Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York (Dr Beasley); the Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois (Mss Colasacco and Ventura); the Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania (Dr Dacic); the Department of Medicine and Pathology, University of Colorado, Denver (Dr Hirsch); the Department of Pathology, University of Aberdeen, Aberdeen, Scotland (Dr Kerr); the Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York (Dr Nowak); the Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland (Dr Temple-Smolkin); the Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia (Dr Solomon); the Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands (Dr Thunnissen); the Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada (Dr Tsao); Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado (Dr Wynes); and the Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan (Dr Yatabe). Dr Souter is in private practice in Wellanport, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Thorac Oncol 2018; 13:323-358. [PMID: 29396253 DOI: 10.1016/j.jtho.2017.12.001] [Citation(s) in RCA: 329] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 12/15/2022]
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, New York
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | | | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, New York
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| |
Collapse
|
34
|
Lindeman NI, Cagle PT, Aisner DL, Arcila ME, Beasley MB, Bernicker EH, Colasacco C, Dacic S, Hirsch FR, Kerr K, Kwiatkowski DJ, Ladanyi M, Nowak JA, Sholl L, Temple-Smolkin R, Solomon B, Souter LH, Thunnissen E, Tsao MS, Ventura CB, Wynes MW, Yatabe Y. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. J Mol Diagn 2018; 20:129-159. [PMID: 29398453 DOI: 10.1016/j.jmoldx.2017.11.004] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 02/07/2023] Open
Abstract
CONTEXT In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. OBJECTIVE To systematically review and update the 2013 guideline to affirm its validity; to assess the evidence of new genetic discoveries, technologies, and therapies; and to issue an evidence-based update. DESIGN The College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology convened an expert panel to develop an evidence-based guideline to help define the key questions and literature search terms, review abstracts and full articles, and draft recommendations. RESULTS Eighteen new recommendations were drafted. The panel also updated 3 recommendations from the 2013 guideline. CONCLUSIONS The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing. Key new recommendations include ROS1 testing for all adenocarcinoma patients; the inclusion of additional genes (ERBB2, MET, BRAF, KRAS, and RET) for laboratories that perform next-generation sequencing panels; immunohistochemistry as an alternative to fluorescence in situ hybridization for ALK and/or ROS1 testing; use of 5% sensitivity assays for EGFR T790M mutations in patients with secondary resistance to EGFR inhibitors; and the use of cell-free DNA to "rule in" targetable mutations when tissue is limited or hard to obtain.
Collapse
Affiliation(s)
- Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Philip T Cagle
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Dara L Aisner
- Department of Pathology, University of Colorado School of Medicine, Denver, Colorado
| | - Maria E Arcila
- Diagnostic and Molecular Pathology Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Beth Beasley
- Department of Pathology & Medicine, Pulmonary, Critical Care and Sleep Medicine, New York, New York
| | - Eric H Bernicker
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas
| | - Carol Colasacco
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Sanja Dacic
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fred R Hirsch
- Department of Medicine and Pathology, University of Colorado, Denver, Colorado
| | - Keith Kerr
- Department of Pathology, University of Aberdeen, Aberdeen, Scotland
| | | | - Marc Ladanyi
- Molecular Diagnostics Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jan A Nowak
- Department of Molecular Pathology, Roswell Park Cancer Institute, Buffalo, New York
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Robyn Temple-Smolkin
- Clinical and Scientific Affairs Division, Association for Molecular Pathology, Bethesda, Maryland
| | - Benjamin Solomon
- Molecular Therapeutics and Biomarkers Laboratory, Peter Maccallum Cancer Center, Melbourne, Australia
| | | | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ming S Tsao
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Christina B Ventura
- Pathology and Laboratory Quality Center, College of American Pathologists, Northfield, Illinois
| | - Murry W Wynes
- Scientific Affairs, International Association for the Study of Lung Cancer, Aurora, Colorado
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| |
Collapse
|
35
|
Roy S, Coldren C, Karunamurthy A, Kip NS, Klee EW, Lincoln SE, Leon A, Pullambhatla M, Temple-Smolkin RL, Voelkerding KV, Wang C, Carter AB. Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines. J Mol Diagn 2018; 20:4-27. [DOI: 10.1016/j.jmoldx.2017.11.003] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022] Open
|
36
|
Hsiao SJ, Mansukhani MM, Carter MC, Sireci AN. The History and Impact of Molecular Coding Changes on Coverage and Reimbursement of Molecular Diagnostic Tests: Transition from Stacking Codes to the Current Molecular Code Set Including Genomic Sequencing Procedures. J Mol Diagn 2017; 20:177-183. [PMID: 29269278 DOI: 10.1016/j.jmoldx.2017.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/24/2022] Open
Abstract
Changes in coding and coverage generate an uncertain reimbursement environment for molecular pathology laboratories. We analyzed our experience with two representative molecular oncology tests: a T-cell receptor (TCR) β rearrangement test and a large (467-gene) cancer next-generation sequencing panel, the Columbia Combined Cancer Panel (CCCP). Before 2013, the TCR β test was coded using stacked current procedural terminology codes and subsequently transitioned to a tier 1 code. CCCP was coded using a combination of tier 1 and 2 codes until 2015, when a new Genomic Sequencing Procedure code was adopted. A decrease in reimbursement of 61% was observed for the TCR β test on moving from stacking to tier 1 codes. No initial increase in total rejection rate was observed, but a subsequent increase in rejection rates in 2015 and 2016 was noted. The CCCP test showed a similar decrease (48%) in reimbursement after adoption of the new Genomic Sequencing Procedure code and was accompanied by a sharp increase in rejection rates both on implementation of the new code and over time. Changes in coding can result in substantial decreases in reimbursement. This may be a barrier to patient access because of the high cost of molecular diagnostics. Revisions to the molecular code set will continue. These findings help laboratories and manufacturers prepare for the financial impact and advocate appropriately.
Collapse
Affiliation(s)
- Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Melissa C Carter
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Anthony N Sireci
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York.
| |
Collapse
|
37
|
Farkas DH. Clinical Validity and Utility: Putting the Patient Front and Center. J Mol Diagn 2017; 18:635-637. [PMID: 27546311 DOI: 10.1016/j.jmoldx.2016.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/28/2016] [Indexed: 11/27/2022] Open
Abstract
This commentary highlights the article by Joseph et al that provides guidelines for ascribing patient-centric clinical utility and validity parameters.
Collapse
Affiliation(s)
- Daniel H Farkas
- Chief Clinical Laboratory Officer, Celmatix Clinical Laboratories, Brooklyn, New York.
| |
Collapse
|
38
|
Mukherjee S, Sathanoori M, Ma Z, Andreatta M, Lennon PA, Wheeler SR, Prescott JL, Coldren C, Casey T, Rietz H, Fasig K, Woodford R, Hartley T, Spence D, Donnelan W, Berdeja J, Flinn I, Kozyr N, Bouzyk M, Correll M, Ho H, Kravtsov V, Tunnel D, Chandra P. Addition of chromosomal microarray and next generation sequencing to FISH and classical cytogenetics enhances genomic profiling of myeloid malignancies. Cancer Genet 2017; 216-217:128-141. [DOI: 10.1016/j.cancergen.2017.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/28/2017] [Accepted: 07/27/2017] [Indexed: 01/31/2023]
|
39
|
Lemke AA, Hutten Selkirk CG, Glaser NS, Sereika AW, Wake DT, Hulick PJ, Dunnenberger HM. Primary care physician experiences with integrated pharmacogenomic testing in a community health system. Per Med 2017; 14:389-400. [DOI: 10.2217/pme-2017-0036] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aim: To explore primary care physicians’ views of the utility and delivery of direct access to pharmacogenomics (PGx) testing in a community health system. Methods: This descriptive study assessed the perspectives of 15 healthcare providers utilizing qualitative individual interviews. Results: Three main themes emerged: perceived value and utility of PGx testing; challenges to implementation in practice; and provider as well as patient needs. Conclusion: While providers in this study viewed benefits of PGx testing as avoiding side effects, titrating doses more quickly, improving shared decision-making and providing psychological reassurance, challenges will need to be addressed such as privacy concerns, cost, insurance coverage and understanding the complexity of PGx test results.
Collapse
Affiliation(s)
- Amy A Lemke
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Christina G Hutten Selkirk
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Nicole S Glaser
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Annette W Sereika
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Dyson T Wake
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Peter J Hulick
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| | - Henry M Dunnenberger
- Center for Personalized Medicine, NorthShore University HealthSystem, 1001 University Place, Suite 160, Evanston, IL 60201, USA
| |
Collapse
|
40
|
Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn 2017; 19:4-23. [PMID: 27993330 DOI: 10.1016/j.jmoldx.2016.10.002] [Citation(s) in RCA: 1164] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/03/2016] [Accepted: 10/13/2016] [Indexed: 01/01/2023] Open
Abstract
Widespread clinical laboratory implementation of next-generation sequencing-based cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencing-based cancer testing and establish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was convened by the Association for Molecular Pathology with liaison representation from the American College of Medical Genetics and Genomics, American Society of Clinical Oncology, and College of American Pathologists. On the basis of the results of professional surveys, literature review, and the Working Group's subject matter expert consensus, a four-tiered system to categorize somatic sequence variations based on their clinical significances is proposed: tier I, variants with strong clinical significance; tier II, variants with potential clinical significance; tier III, variants of unknown clinical significance; and tier IV, variants deemed benign or likely benign. Cancer genomics is a rapidly evolving field; therefore, the clinical significance of any variant in therapy, diagnosis, or prognosis should be reevaluated on an ongoing basis. Reporting of genomic variants should follow standard nomenclature, with testing method and limitations clearly described. Clinical recommendations should be concise and correlate with histological and clinical findings.
Collapse
Affiliation(s)
- Marilyn M Li
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, the Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Michael Datto
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Duke University School of Medicine, Durham, North Carolina
| | - Eric J Duncavage
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Shashikant Kulkarni
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Baylor Genetics, Houston, Texas
| | - Neal I Lindeman
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Somak Roy
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Apostolia M Tsimberidou
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cindy L Vnencak-Jones
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daynna J Wolff
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Anas Younes
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina N Nikiforova
- Interpretation of Sequence Variants in Somatic Conditions Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| |
Collapse
|
41
|
Lou E, D'Souza D, Nelson AC. Therapeutic Response of Metastatic Colorectal Cancer Harboring a KRAS Missense Mutation After Combination Chemotherapy With the EGFR Inhibitor Panitumumab. J Natl Compr Canc Netw 2017; 15:427-432. [PMID: 28404754 DOI: 10.6004/jnccn.2017.0043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/23/2017] [Indexed: 11/17/2022]
Abstract
Over the past decade, subset analyses of retrospective and prospective clinical studies have determined that KRAS-mutated metastatic colorectal cancers do not respond effectively to inhibition of epidermal growth factor receptor (EGFR) with the EGFR-targeting monoclonal antibodies cetuximab or panitumumab. Within the past few years, the scope of tested variants in the KRAS oncogene has expanded significantly, and testing of all RAS family genes has become more widely available in clinical laboratories. Expert consensus guidelines have recommended not using EGFR inhibitors in patients with KRAS-mutated tumors. However, with increasing identification of low-prevalence variants, it is conceivable that some RAS mutations do not provide equivalent resistance to EGFR inhibition compared with the most prevalent mutations at codons 12, 13, and 61. This report describes a case of a patient with metastatic colon cancer harboring the p.A59T variant of KRAS, with objective radiographic response (36% decrease per RECIST 1.1) and carcinoembryonic antigen biomarker response to panitumumab therapy given with FOLFIRI chemotherapy. We propose that A59T represents one potential exception to the guidelines that KRAS mutant tumors fail to respond to therapy with EGFR inhibitors, altering the paradigm of using this generalized approach.
Collapse
Affiliation(s)
- Emil Lou
- Departments of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, Minnesota
| | - Donna D'Souza
- Departments of Radiology, University of Minnesota, Minneapolis, Minnesota
| | - Andrew C Nelson
- Departments of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
42
|
Preparing pathology for precision medicine: challenges and opportunities. Virchows Arch 2017; 471:141-146. [PMID: 28512674 DOI: 10.1007/s00428-017-2141-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 01/05/2023]
|
43
|
Wolf SM, Thyagarajan B, Fogel BL. The need to develop a patient-centered precision medicine model for adults with chronic disability. Expert Rev Mol Diagn 2017; 17:415-418. [PMID: 28325089 DOI: 10.1080/14737159.2017.1309976] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Susan M Wolf
- a Law School, Medical School, Consortium on Law and Values in Health, Environment & the Life Sciences , University of Minnesota , Minneapolis , MN , USA
| | - Bharat Thyagarajan
- b Department of Laboratory Medicine and Pathology , University of Minnesota , Minneapolis , MN , USA
| | - Brent L Fogel
- c University of California-Los Angeles (UCLA) , Departments of Neurology and Human Genetics , Los Angeles , CA , USA
| |
Collapse
|
44
|
Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV, Nikiforova MN. Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2017; 19:341-365. [PMID: 28341590 DOI: 10.1016/j.jmoldx.2017.01.011] [Citation(s) in RCA: 433] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics. The recommendations emphasize the role of laboratory director in using an error-based approach that identifies potential sources of errors that may occur throughout the analytical process and addressing these potential errors through test design, method validation, or quality controls so that no harm comes to the patient. The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.
Collapse
Affiliation(s)
- Lawrence J Jennings
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, Chicago, Illinois.
| | - Maria E Arcila
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher Corless
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Pathology and Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Suzanne Kamel-Reid
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Department of Clinical Laboratory Genetics, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ira M Lubin
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John Pfeifer
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; Washington University School of Medicine, St. Louis, Missouri
| | | | - Karl V Voelkerding
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; ARUP Laboratories, Salt Lake City, Utah; Department of Pathology, University of Utah, Salt Lake City, Utah
| | - Marina N Nikiforova
- Next-Generation Sequencing Analytical Validation Working Group of the Clinical Practice Committee, Bethesda, Maryland; University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| |
Collapse
|
45
|
Kaul KL, Sabatini LM, Tsongalis GJ, Caliendo AM, Olsen RJ, Ashwood ER, Bale S, Benirschke R, Carlow D, Funke BH, Grody WW, Hayden RT, Hegde M, Lyon E, Murata K, Pessin M, Press RD, Thomson RB. The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Acad Pathol 2017; 4:2374289517708309. [PMID: 28815200 PMCID: PMC5528950 DOI: 10.1177/2374289517708309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022] Open
Abstract
An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories.
Collapse
Affiliation(s)
- Karen L. Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Linda M. Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory J. Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
- Laboratory Medicine, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Angela M. Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | | | | | - Robert Benirschke
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Dean Carlow
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Birgit H. Funke
- Laboratory for Molecular Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wayne W. Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics and Human Genetics, UCLA School of Medicine, Los Angeles, CA, USA
| | - Randall T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elaine Lyon
- Pathology Department, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
| | - Kazunori Murata
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard D. Press
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Richard B. Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| |
Collapse
|
46
|
Marks LJ, Oberg JA, Pendrick D, Sireci AN, Glasser C, Coval C, Zylber RJ, Chung WK, Pang J, Turk AT, Hsiao SJ, Mansukhani MM, Glade Bender JL, Kung AL, Sulis ML. Precision Medicine in Children and Young Adults with Hematologic Malignancies and Blood Disorders: The Columbia University Experience. Front Pediatr 2017; 5:265. [PMID: 29312904 PMCID: PMC5732960 DOI: 10.3389/fped.2017.00265] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 11/28/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The advent of comprehensive genomic profiling has markedly advanced the understanding of the biology of pediatric hematological malignancies, however, its application to clinical care is still unclear. We present our experience integrating genomic data into the clinical management of children with high-risk hematologic malignancies and blood disorders and describe the broad impact that genomic profiling has in multiple aspects of patient care. METHODS The Precision in Pediatric Sequencing Program at Columbia University Medical Center instituted prospective clinical next-generation sequencing (NGS) for high-risk malignancies and blood disorders. Testing included cancer whole exome sequencing (WES) of matched tumor-normal samples or targeted sequencing of 467 cancer-associated genes, when sample adequacy was a concern, and tumor transcriptome (RNA-seq). A multidisciplinary molecular tumor board conducted interpretation of results and final tiered reports were transmitted to the electronic medical record according to patient preferences. RESULTS Sixty-nine samples from 56 patients with high-risk hematologic malignancies and blood disorders were sequenced. Patients carried diagnoses of myeloid malignancy (n = 25), lymphoid malignancy (n = 25), or histiocytic disorder (n = 6). Six patients had only constitutional WES, performed for a suspicion of an inherited predisposition for their disease. For the remaining 50 patients, tumor was sequenced with matched normal tissue when available. The mean number of somatic variants per sample was low across the different disease categories (2.85 variants/sample). Interestingly, a gene fusion was identified by RNA-seq in 58% of samples who had adequate RNA available for testing. Molecular profiling of tumor tissue led to clinically impactful findings in 90% of patients. Forty patients (80%) had at least one targetable gene variant or fusion identified in their tumor tissue; however, only seven received targeted therapy. Importantly, NGS findings contributed to the refinement of diagnosis and prognosis for 34% of patients. Known or likely pathogenic germline alterations were discovered in 24% of patients involving cancer predisposition genes in 12% of cases. CONCLUSION Incorporating whole exome and transcriptome profiling of tumor and normal tissue into clinical practice is feasible, and the value that comprehensive testing provides extends beyond the ability to target-specific mutations.
Collapse
Affiliation(s)
- Lianna J Marks
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jennifer A Oberg
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Danielle Pendrick
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Anthony N Sireci
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Chana Glasser
- Department of Pediatric Hematology/Oncology, NYU Winthrop University Medical Center, Mineola, NY, United States
| | - Carrie Coval
- Department of Pediatrics, Columbia University Medical Center, New York, NY, United States
| | - Rebecca J Zylber
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Jiuhong Pang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Andrew T Turk
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Julia L Glade Bender
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| | - Andrew L Kung
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria Luisa Sulis
- Division of Pediatric Hematology, Oncology and Stem Cell Transplant, Columbia University Medical Center, New York, NY, United States.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, United States
| |
Collapse
|
47
|
Oberg JA, Glade Bender JL, Sulis ML, Pendrick D, Sireci AN, Hsiao SJ, Turk AT, Dela Cruz FS, Hibshoosh H, Remotti H, Zylber RJ, Pang J, Diolaiti D, Koval C, Andrews SJ, Garvin JH, Yamashiro DJ, Chung WK, Emerson SG, Nagy PL, Mansukhani MM, Kung AL. Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations. Genome Med 2016; 8:133. [PMID: 28007021 PMCID: PMC5180407 DOI: 10.1186/s13073-016-0389-6] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. METHODS The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient's electronic medical record. RESULTS NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. CONCLUSIONS Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.
Collapse
Affiliation(s)
- Jennifer A. Oberg
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Julia L. Glade Bender
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Maria Luisa Sulis
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Danielle Pendrick
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Anthony N. Sireci
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Susan J. Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Andrew T. Turk
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Filemon S. Dela Cruz
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Hanina Hibshoosh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Helen Remotti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Rebecca J. Zylber
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
| | - Jiuhong Pang
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - Daniel Diolaiti
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Carrie Koval
- Department of Clinical Genetics, Columbia University Medical Center, New York, NY 10032 USA
| | - Stuart J. Andrews
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
| | - James H. Garvin
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Darrell J. Yamashiro
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Department of Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Stephen G. Emerson
- Department of Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Peter L. Nagy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Present address: MNG Laboratories, 5424 Glenridge Drive, Atlanta, GA 30342 USA
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
| | - Andrew L. Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032 USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032 USA
- Present address: Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| |
Collapse
|
48
|
Sireci AN, Aggarwal VS, Turk AT, Gindin T, Mansukhani MM, Hsiao SJ. Clinical Genomic Profiling of a Diverse Array of Oncology Specimens at a Large Academic Cancer Center: Identification of Targetable Variants and Experience with Reimbursement. J Mol Diagn 2016; 19:277-287. [PMID: 28024947 DOI: 10.1016/j.jmoldx.2016.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/23/2016] [Accepted: 10/05/2016] [Indexed: 12/11/2022] Open
Abstract
Large cancer panels are being increasingly used in the practice of precision medicine to generate genomic profiles of tumors with the goal of identifying targetable variants and guiding eligibility for clinical trials. To facilitate identification of mutations in a broad range of solid and hematological malignancies, a 467-gene oncology panel (Columbia Combined Cancer Panel) was developed in collaboration with pathologists and oncologists and is currently available and in use for clinical diagnostics. Herein, we share our experience with this testing in an academic medical center. Of 255 submitted specimens, which encompassed a diverse range of tumor types, we were able to successfully sequence 92%. The Columbia Combined Cancer Panel assay led to the detection of a targetable variant in 48.7% of cases. However, although we show good clinical performance and diagnostic yield, third-party reimbursement has been poor. Reimbursement from government and third-party payers using the 81455 Current Procedural Terminology code was at 19.4% of billed costs, and 55% of cases were rejected on first submission. Likely contributing factors to this low level of reimbursement are the delays in valuation of the 81455 Current Procedural Terminology code and in establishing national or local coverage determinations. In the absence of additional demonstrations of clinical utility and improved patient outcomes, we expect the reimbursement environment will continue to limit the availability of this testing more broadly.
Collapse
Affiliation(s)
- Anthony N Sireci
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Vimla S Aggarwal
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Andrew T Turk
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Tatyana Gindin
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York.
| |
Collapse
|