Utility of different massive parallel sequencing platforms for mutation profiling in clinical samples and identification of pitfalls using FFPE tissue

International Journal of Molecular Medicine
Jana FassunkeVolker Endris

Abstract

In the growing field of personalised medicine, the analysis of numerous potential targets is becoming a challenge in terms of work load, tissue availability, as well as costs. The molecular analysis of non-small cell lung cancer (NSCLC) has shifted from the analysis of the epidermal growth factor receptor (EGFR) mutation status to the analysis of different gene regions, including resistance mutations or translocations. Massive parallel sequencing (MPS) allows rapid comprehensive mutation testing in routine molecular pathological diagnostics even on small formalin-fixed, paraffin‑embedded (FFPE) biopsies. In this study, we compared and evaluated currently used MPS platforms for their application in routine pathological diagnostics. We initiated a first round‑robin testing of 30 cases diagnosed with NSCLC and a known EGFR gene mutation status. In this study, three pathology institutes from Germany received FFPE tumour sections that had been individually processed. Fragment libraries were prepared by targeted multiplex PCR using institution‑specific gene panels. Sequencing was carried out using three MPS systems: MiSeq™, GS Junior and PGM Ion Torrent™. In two institutes, data analysis was performed with the platform-specific softw...Continue Reading

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Citations

Dec 4, 2019·Journal of Gynecologic Oncology·Yoonjung KimKyung A Lee
Aug 31, 2016·Annals of Oncology : Official Journal of the European Society for Medical Oncology·C HeydtR Büttner

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Methods Mentioned

BETA
biopsies
electrophoresis
DNA assay
PCR
exome sequencing
dissecting
biopsy
deamination

Software Mentioned

Ion Torrent
FileMaker
IGV browser
AVA
MiSeq
CLC genomics workbench
Integrative Genomics Viewer ( IGV
QIASymphony SP
Torrent Suite

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