Qiaamp generead dna ffpe tissue kit

Formalin-Fixed, Paraffin Embedded (FFPE) blocks of the primary tumour were obtained. Following Haematoxylin-Eosin staining (H&E), a Consultant Pathologist marked a high density area of tumour and a 1.5mm core biopsy was performed. DNA was extracted using the QIAamp Generead DNA FFPE Tissue Kit (Qiagen) as per manufacturer’s instructions.

FFPE tissues were macrodissected after hematoxylin–eosin slide examination and determination of tumour content by an experienced pathologist.
For NGS and ddPCR assays, DNA was extracted using the QIAamp Generead DNA FFPE tissue kit (Qiagen, Hilden, Germany) and DNA concentrations were measured using the Qubit dsDNA HS assay kit and Qubit 3.0 Fluorometer instrument according to the manufacturer's recommendations (ThermoFisher Scientific, Courtaboeuf, France).
For Promega MSI Analysis System, DNA was extracted using the NucleoSpin DNA FFPE XS kit (Macherey–Nagel, Hoerdt, France) and DNA were quantified by spectrophotometry using NanoDrop instrument (ThermoFisher Scientific).
DNA quality was determined by a qPCR-based quality control assay using the TruSeq FFPE DNA Library Prep QC kit (Illumina, San Diego, USA) and the LightCycler 480 Software W UDF 2.0.0 (Roche Diagnostics, Meylan, France). For each sample, Delta-Cq ( $\mathrm{\Delta }$ Cq) were calculated as follows: Cq value of the sample − Cq value of the internal control included in the kit. Samples with $\mathrm{\Delta }$ Cq ≤ 0 are characterized by a high DNA quality, those with $\mathrm{\Delta }$ Cq between 0 and 6 are of intermediate DNA quality, and those with $\mathrm{\Delta }$ Cq ≥ 6 are of poor DNA quality.