通过协作解决分歧的方法，对虚拟基因面板进行管理，从而实现国家和国际层面的改善。
Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.
机构信息
Australian Genomics Health Alliance, Melbourne, VIC 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; University of Melbourne, Melbourne, VIC 3010, Australia.
Genomics England, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
出版信息
Am J Hum Genet. 2021 Sep 2;108(9):1551-1557. doi: 10.1016/j.ajhg.2021.06.020. Epub 2021 Jul 29.
Abstract
Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.
摘要
临床有效性评估是基因疾病相关性分析和报告的基础，也是诊断基因组学的关键。然而，在实践中存在广泛的差异，特别是在虚拟基因面板设计和维护中使用这些评估方法。由于缺乏一致的术语、一致的基因管理标准以及可以大规模识别和解决差异的平台，协调工作受到阻碍。我们对英国和澳大利亚的多个诊断服务提供商在两个医疗保健系统中使用的 80 个虚拟基因面板的内容进行了系统比较。这一过程得益于 PanelApp 这一共享管理平台的支持，结果发现并审查了 2144 个不一致的基因评级，这证明了共享结构化的基因疾病有效性评估和协作性差异解决在建立国家和国际共识方面的效用。
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2
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Am J Hum Genet. 2020 Nov 5;107(5):932-941. doi: 10.1016/j.ajhg.2020.09.011. Epub 2020 Oct 26.
3
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4
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Neurogenetics. 2020 Jan;21(1):1-18. doi: 10.1007/s10048-019-00598-x. Epub 2019 Dec 13.
5
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6
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