Data Sheet 1_Genomics costing tool: considerations for improving cost-efficiencies through cross scenario comparison.pdf

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.

下一代测序（Next-generation Sequencing, NGS）对于传染病暴发的监测与溯源调查至关重要，可为公共卫生决策提供核心支撑数据。新冠疫情全球大流行显著提升了全球范围内的病原体测序与生物信息学能力，为将这些技术进步应用于其他具备大流行和流行潜力的病原体提供了契机。为满足可持续基因组监测的系统化成本估算需求，尤其是在中低收入国家，五家机构合作开发了基因组成本核算工具（Genomics Costing Tool, GCT），参与合作的机构包括公共卫生实验室协会（Association of Public Health Laboratories, APHL）、创新诊断工具基金会（FIND）、艾滋病、结核病和疟疾全球基金（The Global Fund to Fight AIDS, Tuberculosis and Malaria）、英国卫生安全局（UK Health Security Agency, UKHSA）以及世界卫生组织（World Health Organization, WHO）。为验证该工具的有效性，其在世界卫生组织（WHO）下辖的非洲、东地中海及欧洲三个区域的公共卫生实验室中开展了试点应用，本次试点旨在评估该工具的准确性、实用性与功能完整性，覆盖过往支出验证、常规使用、成本优化及扩大测序服务规模等多种应用场景。试点数据显示，随着样本通量提升，单样本测序成本显著降低，凸显了基于样本通量优化测序平台使用方式所带来的经济效益。该基因组成本核算工具可帮助实验室基于设备采购与预防性维护、试剂与耗材、年度样本通量、人力资源培训、质量保证与管理等要素，估算并可视化测序及生物信息学工作的成本、规划预算，并提升成本效益。本研究分享了试点项目的核心发现，详细剖析了采用短读长或长读长测序技术开展常规下一代测序工作的成本构成，验证了基因组成本核算工具可作为支撑基因组监测领域可持续筹资与战略规划的有效工具。