Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison
Next-generation sequencing (NGS) is crucial for monitoring and investigating infectious disease outbreaks, providing essential data for public health decisions. The COVID-19 pandemic has significantly expanded pathogen sequencing and bioinformatics capacities worldwide, creating an opportunity to le...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Public Health |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpubh.2024.1498094/full |
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| author | Marco Marklewitz Alexandr Jaguparov Aude Wilhelm Oluwatosin Wuraola Akande Biran Musul Angela Lee Poates Babak Afrough Ashley Norberg Noah Clayton Hull Soudeh Ehsani Group members of GCT pilot working group Joanna Salvi Le Garrec Toni Whistler |
| author_facet | Marco Marklewitz Alexandr Jaguparov Aude Wilhelm Oluwatosin Wuraola Akande Biran Musul Angela Lee Poates Babak Afrough Ashley Norberg Noah Clayton Hull Soudeh Ehsani Group members of GCT pilot working group Joanna Salvi Le Garrec Toni Whistler |
| author_sort | Marco Marklewitz |
| collection | DOAJ |
| description | Next-generation sequencing (NGS) is crucial for monitoring and investigating infectious disease outbreaks, providing essential data for public health decisions. The COVID-19 pandemic has significantly expanded pathogen sequencing and bioinformatics capacities worldwide, creating an opportunity to leverage these advancements for other pathogens with pandemic and epidemic potential. In response to the need for a systematic cost estimation approach for sustainable genomic surveillance, particularly in low- and middle-income countries, five institutions collaborated to develop the genomics costing tool (GCT). These institutions are the Association of Public Health Laboratories (APHL), FIND, The Global Fund to Fight AIDS, Tuberculosis and Malaria, the UK Health Security Agency (UKHSA), and the World Health Organization (WHO). To validate the GCT, it was piloted in public health laboratories across three WHO regions: African, Eastern Mediterranean, and European. The pilot exercises were intended to assess the tool’s accuracy, utility, and functionality, exploring scenarios for validating past expenditure, routine use, cost optimization, and scaling up sequencing services. Data from these pilots demonstrated significant cost reductions per sample with increased throughput, underscoring the economic benefits of the optimized use of sequencing platforms underpinned by sample throughput. The GCT enables laboratories to estimate and visualize costs, plan budgets, and improve cost-efficiencies for sequencing and bioinformatics based on factors such as equipment purchase and preventative maintenance, reagents and consumables, annual sample throughput, human resources training, quality assurance and management. This publication shares key findings from pilot exercises offering detailed insights into the cost of routine NGS implementation using either short- or long-read sequencing technologies, demonstrating the utility of GCT as an asset to support efforts for sustainable funding and strategic planning in genomic surveillance. |
| format | Article |
| id | doaj-art-0b25ddaeec4c4547938d71614d70e183 |
| institution | Kabale University |
| issn | 2296-2565 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Public Health |
| spelling | doaj-art-0b25ddaeec4c4547938d71614d70e1832025-01-15T13:36:03ZengFrontiers Media S.A.Frontiers in Public Health2296-25652025-01-011210.3389/fpubh.2024.14980941498094Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparisonMarco Marklewitz0Alexandr Jaguparov1Aude Wilhelm2Oluwatosin Wuraola Akande3Biran Musul4Angela Lee Poates5Babak Afrough6Ashley Norberg7Noah Clayton Hull8Soudeh Ehsani9Group members of GCT pilot working groupJoanna Salvi Le Garrec10Toni Whistler11FIND, Geneva, SwitzerlandInfectious Hazard Management, World Health Organization Regional Office for Europe, Copenhagen, DenmarkNew Variant Assessment Platform, UK Health Security Agency, London, United KingdomDepartment of Epidemic and Pandemic Preparedness and Prevention, World Health Organization, Geneva, SwitzerlandInfectious Hazard Management, World Health Organization Regional Office for Europe, Copenhagen, DenmarkGlobal Health, Association of Public Health Laboratories, Bethesda, MD, United StatesNew Variant Assessment Platform, UK Health Security Agency, London, United KingdomGlobal Health, Association of Public Health Laboratories, Bethesda, MD, United StatesGlobal Health, Association of Public Health Laboratories, Bethesda, MD, United StatesJoint Infectious Diseases Unit, World Health Organization Regional Office for Europe, Copenhagen, DenmarkInfectious Hazard Management, World Health Organization Regional Office for Europe, Copenhagen, DenmarkTechnical Advice and Partnership Department, The Global Fund to Fight AIDS, Tuberculosis and Malaria, Geneva, SwitzerlandNext-generation sequencing (NGS) is crucial for monitoring and investigating infectious disease outbreaks, providing essential data for public health decisions. The COVID-19 pandemic has significantly expanded pathogen sequencing and bioinformatics capacities worldwide, creating an opportunity to leverage these advancements for other pathogens with pandemic and epidemic potential. In response to the need for a systematic cost estimation approach for sustainable genomic surveillance, particularly in low- and middle-income countries, five institutions collaborated to develop the genomics costing tool (GCT). These institutions are the Association of Public Health Laboratories (APHL), FIND, The Global Fund to Fight AIDS, Tuberculosis and Malaria, the UK Health Security Agency (UKHSA), and the World Health Organization (WHO). To validate the GCT, it was piloted in public health laboratories across three WHO regions: African, Eastern Mediterranean, and European. The pilot exercises were intended to assess the tool’s accuracy, utility, and functionality, exploring scenarios for validating past expenditure, routine use, cost optimization, and scaling up sequencing services. Data from these pilots demonstrated significant cost reductions per sample with increased throughput, underscoring the economic benefits of the optimized use of sequencing platforms underpinned by sample throughput. The GCT enables laboratories to estimate and visualize costs, plan budgets, and improve cost-efficiencies for sequencing and bioinformatics based on factors such as equipment purchase and preventative maintenance, reagents and consumables, annual sample throughput, human resources training, quality assurance and management. This publication shares key findings from pilot exercises offering detailed insights into the cost of routine NGS implementation using either short- or long-read sequencing technologies, demonstrating the utility of GCT as an asset to support efforts for sustainable funding and strategic planning in genomic surveillance.https://www.frontiersin.org/articles/10.3389/fpubh.2024.1498094/fullnext-generation sequencingcosting toolCOVID-19cost-analysisgenomic surveillance |
| spellingShingle | Marco Marklewitz Alexandr Jaguparov Aude Wilhelm Oluwatosin Wuraola Akande Biran Musul Angela Lee Poates Babak Afrough Ashley Norberg Noah Clayton Hull Soudeh Ehsani Group members of GCT pilot working group Joanna Salvi Le Garrec Toni Whistler Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison Frontiers in Public Health next-generation sequencing costing tool COVID-19 cost-analysis genomic surveillance |
| title | Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison |
| title_full | Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison |
| title_fullStr | Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison |
| title_full_unstemmed | Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison |
| title_short | Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison |
| title_sort | genomics costing tool considerations for improving cost efficiencies through cross scenario comparison |
| topic | next-generation sequencing costing tool COVID-19 cost-analysis genomic surveillance |
| url | https://www.frontiersin.org/articles/10.3389/fpubh.2024.1498094/full |
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