Continuing the sequence?: Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland

Michael Abbott; Lynda McKenzie; Blanca Moran; Sebastian Heidenreich; Rodolfo Hernández; Lynne Hocking- Mennie; Caroline Clark; Caroline Clark; Joana  Gomes; Anne  Lampe; David  Baty; Ruth  McGowan; Zosia Miedzybrodzka; Mandy Ryan

doi:10.1007/s12687-021-00541-4

Continuing the sequence? Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland

Michael Abbott^* (Corresponding Author), Lynda McKenzie, Blanca Moran, Sebastian Heidenreich, Rodolfo Hernández, Lynne Hocking- Mennie, Caroline Clark, Caroline Clark, Joana Gomes, Anne Lampe, David Baty, Ruth McGowan, Zosia Miedzybrodzka, Mandy Ryan

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6,625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued: (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for thebroader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.

Original language	English
Number of pages	15
Journal	Journal of Community Genetics
Early online date	20 Aug 2021
DOIs	https://doi.org/10.1007/s12687-021-00541-4
Publication status	Published - 20 Aug 2021

Keywords

Whole Genome Sequencing
Diagnostic Odyssey
Costs and Benefits
Economic Evaluation
Valuation

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Abbott, M., McKenzie, L., Moran, B., Heidenreich, S., Hernández, R., Hocking- Mennie, L., Clark, C., Clark, C., Gomes, J., Lampe, A., Baty, D., McGowan, R., Miedzybrodzka, Z., & Ryan, M. (2021). Continuing the sequence? Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland. Journal of Community Genetics. https://doi.org/10.1007/s12687-021-00541-4

Abbott, M, McKenzie, L, Moran, B, Heidenreich, S, Hernández, R, Hocking- Mennie, L, Clark, C , Clark, C, Gomes, J, Lampe, A, Baty, D, McGowan, R, Miedzybrodzka, Z & Ryan, M 2021, 'Continuing the sequence? Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland', Journal of Community Genetics. https://doi.org/10.1007/s12687-021-00541-4

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title = "Continuing the sequence?: Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland",

abstract = "Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6,625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued: (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for thebroader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.",

keywords = "Whole Genome Sequencing, Diagnostic Odyssey, Costs and Benefits, Economic Evaluation, Valuation",

author = "Michael Abbott and Lynda McKenzie and Blanca Moran and Sebastian Heidenreich and Rodolfo Hern{\'a}ndez and {Hocking- Mennie}, Lynne and Caroline Clark and Caroline Clark and Joana Gomes and Anne Lampe and David Baty and Ruth McGowan and Zosia Miedzybrodzka and Mandy Ryan",

note = "Funding This research was made possible through access to the data and findings generated by Scotland{\textquoteright}s four regional genetics centres at NHS Grampian, Lothian, Tayside and Greater Glasgow and Clyde. These four centres participated in Scotland{\textquoteright}s involvement in the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health) and funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. Acknowledgements The authors would like to thank the Scottish Genomes Partnership for their support with this work. The Scottish Genomes Partnership is funded by the Chief Scientist Office of the Scottish Government Health Directorates [SGP/1] and The Medical Research Council Whole Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). We are grateful for the contributions of the funding bodies; Scottish Regional Genetics centres at NHS Lothian, Tayside, Grampian and Greater Glasgow and Clyde, clinicians and healthcare teams who contributed to the provision of data as well as the analyses and interpretation of results. We also thank Morad Ansari, Christine Bell, Martin McClatchey, Nicola Williams, Austin Diamond, Jonathan Berg, Jon Warner, Alexis Duncan, Amy Rowlatt, and Tessa Coupar for their help and advice during the SGP Project, and Michael Doherty, Florence Richards and Quinn Heppe for help with costing the standard testing pathway. We thank Professor Tim Aitman for commenting on earlier drafts of the paper. We thank all participants who took part in the valuation study. The University of Aberdeen and the Chief Scientist Office of the Scottish Government Health and Social Care Directorates fund the Health Economics Research Unit (HERU). This study would not be possible without the families, patients, clinicians, nurses, research scientists, laboratory staff, and the wider Scottish Genomes Partnership team to whom we give grateful thanks. ",

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AU - McKenzie, Lynda

AU - Moran, Blanca

AU - Heidenreich, Sebastian

AU - Hernández, Rodolfo

AU - Hocking- Mennie, Lynne

AU - Clark, Caroline

AU - Gomes, Joana

AU - Lampe, Anne

AU - Baty, David

AU - McGowan, Ruth

AU - Miedzybrodzka, Zosia

AU - Ryan, Mandy

N1 - Funding This research was made possible through access to the data and findings generated by Scotland’s four regional genetics centres at NHS Grampian, Lothian, Tayside and Greater Glasgow and Clyde. These four centres participated in Scotland’s involvement in the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health) and funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. Acknowledgements The authors would like to thank the Scottish Genomes Partnership for their support with this work. The Scottish Genomes Partnership is funded by the Chief Scientist Office of the Scottish Government Health Directorates [SGP/1] and The Medical Research Council Whole Genome Sequencing for Health and Wealth Initiative (MC/PC/15080). We are grateful for the contributions of the funding bodies; Scottish Regional Genetics centres at NHS Lothian, Tayside, Grampian and Greater Glasgow and Clyde, clinicians and healthcare teams who contributed to the provision of data as well as the analyses and interpretation of results. We also thank Morad Ansari, Christine Bell, Martin McClatchey, Nicola Williams, Austin Diamond, Jonathan Berg, Jon Warner, Alexis Duncan, Amy Rowlatt, and Tessa Coupar for their help and advice during the SGP Project, and Michael Doherty, Florence Richards and Quinn Heppe for help with costing the standard testing pathway. We thank Professor Tim Aitman for commenting on earlier drafts of the paper. We thank all participants who took part in the valuation study. The University of Aberdeen and the Chief Scientist Office of the Scottish Government Health and Social Care Directorates fund the Health Economics Research Unit (HERU). This study would not be possible without the families, patients, clinicians, nurses, research scientists, laboratory staff, and the wider Scottish Genomes Partnership team to whom we give grateful thanks.

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N2 - Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6,625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued: (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for thebroader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.

AB - Novel developments in genomic medicine may reduce the length of the diagnostic odyssey for patients with rare diseases. Health providers must thus decide whether to offer genome sequencing for the diagnosis of rare conditions in a routine clinical setting. We estimated the costs of singleton standard genetic testing and trio-based whole genome sequencing (WGS), in the context of the Scottish Genomes Partnership (SGP) study. We also explored what users value about genomic sequencing. Insights from the costing and value assessments will inform a subsequent economic evaluation of genomic medicine in Scotland. An average cost of £1,841 per singleton was estimated for the standard genetic testing pathway, with significant variability between phenotypes. WGS cost £6,625 per family trio, but this estimate reflects the use of WGS during the SGP project and large cost savings may be realised if sequencing was scaled up. Patients and families valued: (i) the chance of receiving a diagnosis (and the peace of mind and closure that brings); (ii) the information provided by WGS (including implications for family planning and secondary findings); and (iii) contributions to future research. Our costings will be updated to address limitations of the current study for incorporation in budget impact modelling and cost-effectiveness analysis (cost per diagnostic yield). Our insights into the benefits of WGS will guide the development of a discrete choice experiment valuation study. This will inform a user-perspective cost-benefit analysis of genome-wide sequencing, accounting for thebroader non-health outcomes. Taken together, our research will inform the long-term strategic development of NHS Scotland clinical genetics testing services, and will be of benefit to others seeking to undertake similar evaluations in different contexts.

KW - Whole Genome Sequencing

KW - Diagnostic Odyssey

KW - Costs and Benefits

KW - Economic Evaluation

KW - Valuation

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DO - 10.1007/s12687-021-00541-4

M3 - Article

JO - Journal of Community Genetics

JF - Journal of Community Genetics

SN - 1868-6001

ER -

Continuing the sequence? Towards an Economic Evaluation of Whole Genome Sequencing for the Diagnosis of Rare Diseases in Scotland

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Keywords

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