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Mordaunt DA, Stark Z, Santos Gonzalez F, Dalziel K, Goranitis I. Development of a microcosting protocol to determine the economic cost of diagnostic genomic testing for rare diseases in Australia. BMJ Open 2023; 13:e069441. [PMID: 38030253 PMCID: PMC10689401 DOI: 10.1136/bmjopen-2022-069441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
INTRODUCTION Genomic testing is a relatively new, disruptive and complex health technology with multiple clinical applications in rare diseases, cancer and infection control. Genomic testing is increasingly being implemented into clinical practice, following regulatory approval, funding and adoption in models of care, particularly in the area of rare disease diagnosis. A significant barrier to the adoption and implementation of genomic testing is funding. What remains unclear is what the cost of genomic testing is, what the underlying drivers of cost are and whether policy differences contribute to cost variance in different jurisdictions, such as the requirement to have staff with a medical license involved in testing. This costing study will be useful in future economic evaluations and health technology assessments to inform optimal levels of reimbursement and to support comprehensive and comparable assessment of healthcare resource utilisation in the delivery of genomic testing globally. METHODS A framework is presented that focuses on uncovering the process of genomic testing for any given laboratory, evaluating its utilisation and unit costs, and modelling the cost drivers and overall expenses associated with delivering genomic testing. The goal is to aid in refining and implementing policies regarding both the regulation and funding of genomic testing. A process-focused (activity-based) methodology is outlined, which encompasses resources, assesses individual cost components through a combination of bottom-up and top-down microcosting techniques and allows disaggregation of resource type and process step. ETHICS AND DISSEMINATION The outputs of the study will be reported at relevant regional genetics and health economics conferences, as well as submitted to a peer-reviewed journal focusing on genomics. Human research ethics committee approval is not required for this microcosting study. This study does not involve research on human subjects, and all data used in the analysis are either publicly available.
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Affiliation(s)
- Dylan A Mordaunt
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Women's and Children's Division, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Zornitza Stark
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Australian Genomics Health Alliance, Australia, UK
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Francisco Santos Gonzalez
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kim Dalziel
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
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Oluwole OG, Henry M. Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts. Curr Med Res Opin 2023; 39:141-147. [PMID: 36094413 DOI: 10.1080/03007995.2022.2124072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The large-scale implementation of genomic medicine in Africa has not been actualized. This overview describes how routine molecular genetics and advanced protein engineering/structural biotechnology could accelerate the implementation of genomic medicine. By using data-mining and analysis approaches, we analyzed relevant information obtained from public genomic databases on pharmacogenomics biomarkers and reviewed published studies to discuss the ideas. The results showed that only 68 very important pharmacogenes currently exist, while 867 drug label annotations, 201 curated functional pathways, and 746 annotated drugs have been catalogued on the largest pharmacogenomics database (PharmGKB). Only about 5009 variants of the reported ∼25,000 have been clinically annotated. Predominantly, the genetic variants were derived from 43 genes that contribute to 2318 clinically relevant variations in 57 diseases. Majority (∼60%) of the clinically relevant genetic variations in the pharmacogenes are missense variants (1390). The enrichment analysis showed that 15 pharmacogenes are connected biologically and are involved in the metabolism of cardiovascular and cancer drugs. The review of studies showed that cardiovascular diseases are the most frequent non-communicable diseases responsible for approximately 13% of all deaths in Africa. Also, warfarin pharmacogenomics is the most studied drug on the continent, while CYP2D6, CYP2C9, DPD, and TPMT are the most investigated pharmacogenes with allele activities indicated in African and considered to be intermediate metaboliser for DPD and TPMT (8.4% and 11%). In summary, we highlighted a framework for implementing genomic medicine starting from the available resources on ground.
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Affiliation(s)
- Oluwafemi G Oluwole
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Marc Henry
- Medical Biotechnology and Immunotherapy Unit, Department of Integrative Biomedical Sciences Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Grosse SD, Gudgeon JM. Correspondence on "Cost-effectiveness of exome and genome sequencing for children with rare and undiagnosed conditions" by Lavelle et al. Genet Med 2022; 24:2595-2596. [PMID: 36129466 PMCID: PMC9768457 DOI: 10.1016/j.gim.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Scott D Grosse
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA.
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Nazeha N, Koh AL, Kam S, Lim JY, Goh DLM, Jamuar SS, Graves N. Reduced resource utilization with early use of next-generation sequencing in rare genetic diseases in an Asian cohort. Am J Med Genet A 2022; 188:3482-3491. [PMID: 36156406 DOI: 10.1002/ajmg.a.62974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/22/2022] [Accepted: 09/03/2022] [Indexed: 01/31/2023]
Abstract
Children with genetic diseases endure a prolonged and costly "diagnostic odyssey." The use of whole exome sequencing (WES) and whole genome sequencing (WGS) has improved the diagnosis rate, ending the odyssey. However, the additional costs associated WES/WGS has impeded their adoption in Asian settings. We aim to estimate the expected change to the mean number of diagnostic tests used, and the associated costs from a decision to use WES early in the diagnostic pathways of pediatric phenotypes, as compared to Existing Practice. Retrospective data from a patient cohort recruited under the Singapore Undiagnosed Disease Program from a tertiary hospital in Singapore, for the period October 2004 to September 2020, was analyzed. Four phenotype-specific subgroups were used: multiple congenital anomalies (MCA) without developmental delay; global developmental delay (GDD); neuromuscular disorder (NMD) and primary immunodeficiency disorder (PID). Patients had undergone a traditional diagnostic pathway and received a diagnosis either through clinical exome or WES or WGS. A costs only analysis was performed, by tabulating the outcomes "test quantity" and "test costs" incurred by patients. The outcomes were compared with alternate diagnostic pathways which incorporates the early introduction of WES trio testing. To include uncertainty in cost outcomes, simulation studies were done on uncertain parameters. Cost outcomes are reported in Singapore dollars (S$). The 92 included patients had MCA (n = 48), GDD (n = 29), NMD (n = 10), or PID (n = 5). Patients were aged between 18 days and 26 years, 52.2% were males. The majority were of Chinese ethnicity (81.5%). If patients had access to WES directly, test quantity reduced by 97.38% for MCA, 96.98% for GDD, 96.56% for NMD, and 99.84% for PID. The expected cost savings per patient were $5940 for MCA (US$4433), $5342 for GDD (US$3986), $4622 for NMD (US$3449), and $58,497 for PID (US$43,654). Uncertainty assessment for MCA and GDD patients showed a respective likelihood of 86.9% and 97.4% for cost savings. Adoption of alternate diagnostic pathways with early WES in selected pediatric subgroups are likelt to reduce costs, when compared to Existing Practice. Benefits arising from earlier diagnosis, and the potential cost savings could mitigate the large initial cost of implementing WES in Asian settings.
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Affiliation(s)
- Nuraini Nazeha
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Ai Ling Koh
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Sylvia Kam
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Jiin Ying Lim
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Denise Li Meng Goh
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore.,SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Nicholas Graves
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
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Lavelle TA, Feng X, Keisler M, Cohen JT, Neumann PJ, Prichard D, Schroeder BE, Salyakina D, Espinal PS, Weidner SB, Maron JL. Response to Grosse and Gudgeon. Genet Med 2022; 24:2597-2598. [PMID: 36166002 DOI: 10.1016/j.gim.2022.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA.
| | - Xue Feng
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Marlena Keisler
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Joshua T Cohen
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Peter J Neumann
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | | | | | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Paula S Espinal
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Samuel B Weidner
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Jill L Maron
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI
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Gayduk A, Vlasov Y, Smirnova D. Application of modern approaches in the screening and early diagnosis programs for the orphan diseases. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:30-39. [DOI: 10.17116/jnevro202212206130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Li C, Vandersluis S, Holubowich C, Ungar WJ, Goh ES, Boycott KM, Sikich N, Dhalla I, Ng V. Correspondence on "cost or price of sequencing? implications for economic evaluations in genomic medicine" by Grosse and Gudgeon. Genet Med 2021; 24:251-252. [PMID: 34906460 DOI: 10.1016/j.gim.2021.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Chunmei Li
- Ontario Health (Quality), Toronto, Ontario, Canada.
| | | | | | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada; Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Elaine S Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute (CHEO), University of Ottawa, Ottawa, Ontario, Canada
| | - Nancy Sikich
- Ontario Health (Quality), Toronto, Ontario, Canada
| | - Irfan Dhalla
- Ontario Health (Quality), Toronto, Ontario, Canada; Unity Health Toronto, Toronto, Ontario, Canada
| | - Vivian Ng
- Ontario Health (Quality), Toronto, Ontario, Canada
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