Validation of a next generation sequencing panel for detection of hotspot cancer mutations in a clinical laboratory.
作者： Reza Shahsiah , Jenefer DeKoning , Saeed Samie , Seyed Ziaeddin Latifzadeh , Zahra Mehdizadeh Kashi
DOI: 10.1016/J.PRP.2016.11.016
关键词: DNA sequencing 、 Cancer mutations 、 Biology 、 Gene targets 、 Significant difference 、 Sample selection 、 Computational biology 、 Validation study 、 Genetics 、 Hotspot mutation
摘要: Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated is challenging for clinical labs as it involves complex workflows, and requires validation diagnostic purposes. The aim this work towards analytical a next generation (NGS) panel hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens cell-lines were examined by NGS methods utilizing Ion Torrent™ Oncomine™ Focus DNA Assay PGM™ platform. Important parameters somatic mutations threshold differentiation positive negative result, coverage, sensitivity, specificity, limit detection (LoD) analyzed. Variant calls with coverage <100x found be inaccurate. identifying was determined 4.3%. sensitivity specificity method 96.1% 97.8% respectively. No statistically significant difference between different gene targets terms performance frequency measurement subset tested. In every study, number samples, manner sample selection, type variants play role outcome. Therefore, should assessed according needs each laboratory undertaking validation.
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