Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory

Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory Publisher Pubmed

Shahsiah R¹ ; Dekoning J² ; Samie S³ ; Latifzadeh SZ³ ; Kashi ZM²

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1. Cancer Research Center, Tehran University of Medical Sciences, Iran
2. Kashi Clinical Laboratories, United States
3. Pars Hospital Research Center, Iran

Source: Pathology Research and Practice Published:2017

Abstract

Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform. Important parameters for somatic mutations including the threshold for differentiation of a positive and a negative result, coverage, sensitivity, specificity, and limit of detection (LoD) were analyzed. Variant calls with coverage of <100x were found to be inaccurate. The limit of detection for identifying hotspot mutations was determined to be 4.3%. The sensitivity and specificity of the method were 96.1% and 97.8% respectively. No statistically significant difference was found between different gene targets in terms of performance of hotspot frequency measurement for the subset tested. In every validation study, the number of samples, the manner of sample selection, and the number and type of variants play a role in the outcome. Therefore, these parameters should be assessed according to the clinical needs of each laboratory undertaking the validation. © 2016 Elsevier GmbH

Style	Citing Format
MLA	Shahsiah R, et al.. "Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory." Pathology Research and Practice, vol. 213, no. 2, 2017, pp. 98-105.
APA	Shahsiah R, Dekoning J, Samie S, Latifzadeh SZ, Kashi ZM (2017). Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory. Pathology Research and Practice, 213(2), 98-105.
Chicago	Shahsiah R, Dekoning J, Samie S, Latifzadeh SZ, Kashi ZM. "Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory." Pathology Research and Practice 213, no. 2 (2017): 98-105.
Harvard	Shahsiah R et al. (2017) 'Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory', Pathology Research and Practice, 213(2), pp. 98-105.
Vancouver	Shahsiah R, Dekoning J, Samie S, Latifzadeh SZ, Kashi ZM. Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory. Pathology Research and Practice. 2017;213(2):98-105.
BibTex	@article{ author = {Shahsiah R and Dekoning J and Samie S and Latifzadeh SZ and Kashi ZM}, title = {Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory}, journal = {Pathology Research and Practice}, volume = {213}, number = {2}, pages = {98-105}, year = {2017} }
RIS	TY - JOUR AU - Shahsiah R AU - Dekoning J AU - Samie S AU - Latifzadeh SZ AU - Kashi ZM TI - Validation of a Next Generation Sequencing Panel for Detection of Hotspot Cancer Mutations in a Clinical Laboratory JO - Pathology Research and Practice VL - 213 IS - 2 SP - 98 EP - 105 PY - 2017 ER -

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Abstract