title: Clinical validation of the 50 gene AmpliSeq Cancer Panel V2 for use on a next generation sequencing platform using formalin fixed, paraffin embedded and fine needle aspiration tumour specimens.
abstract: The advent of massively parallel sequencing has caused a paradigm shift in the ways cancer is treated, as personalised therapy becomes a reality. More and more laboratories are looking to introduce next generation sequencing (NGS) as a tool for mutational analysis, as this technology has many advantages compared to conventional platforms like Sanger sequencing. In Australia all massively parallel sequencing platforms are still considered in-house in vitro diagnostic tools by the National Association of Testing Authorities (NATA) and a comprehensive analytical validation of all assays, and not just mere verification, is a strict requirement before accreditation can be granted for clinical testing on these platforms. Analytical validation of assays on NGS platforms can prove to be extremely challenging for pathology laboratories. Although there are many affordable and easily accessible NGS instruments available, there are no standardised guidelines as yet for clinical validation of NGS assays. We present an accreditation development procedure that was both comprehensive and applicable in a setting of hospital laboratory for NGS services. This approach may also be applied to other NGS applications in service laboratories.
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia; Department of Pathology, The University of Melbourne, Australia. Electronic address: Vivek.Rathi@svha.org.au.
authors.forename: Vivek
authors.initials: V
authors.lastname: Rathi
authors.affiliation: Department of Surgery, St Vincent's Hospital, Fitzroy, Australia.
authors.forename: Gavin
authors.initials: G
authors.lastname: Wright
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Diana
authors.initials: D
authors.lastname: Constantin
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Siok
authors.initials: S
authors.lastname: Chang
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Huong
authors.initials: H
authors.lastname: Pham
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Kerryn
authors.initials: K
authors.lastname: Jones
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Atha
authors.initials: A
authors.lastname: Palios
authors.affiliation: Department of Oncology, St Vincent's Hospital, Fitzroy, Australia.
authors.forename: Sue-Anne
authors.initials: SA
authors.lastname: Mclachlan
authors.affiliation: Department of Respiratory Medicine, St Vincent's Hospital, Fitzroy, Vic, Australia.
authors.forename: Matthew
authors.initials: M
authors.lastname: Conron
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Penny
authors.initials: P
authors.lastname: McKelvie
authors.affiliation: Department of Anatomical Pathology, St Vincent's Hospital Fitzroy, Australia.
authors.forename: Richard
authors.initials: R
authors.lastname: Williams
mesh_terms: D001315:Australia; D044963:Biopsy, Fine-Needle / Q000379:methods; D004252:DNA Mutational Analysis / Q000379:methods; D004273:DNA, Neoplasm / Q000235:genetics*; D020022:Genetic Predisposition to Disease; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009154:Mutation / Q000235:genetics*; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D016707:Tissue Fixation / Q000379:methods
chemical_list: D004273:DNA, Neoplasm
keywords: Validation; formalin fixed paraffin embedded; molecular; mutational analysis; next generation sequencing