Tissue sections (thickness, 8 µm) were prepared from paraffin‐embedded specimens generated before surgery or from diagnostic biopsy specimens obtained before starting clinical therapy. One of two successive sections was stained with hematoxylin and eosin (HE) to assess the cancerous portion. Manual microdissection using a scalpel and microscope was conducted to recover cancerous portions using the HE‐stained slide as a reference.
Chromosomal DNA was isolated from formalin‐fixed paraffin‐embedded (FFPE) tissues of patients (n = 63) with head and neck squamous cell carcinoma (HNSCC) following the instructions from the kit manufacturer (Maxwell RSC DNA FFPE kit; Promega). The concentration of extracted DNA was determined by the fluorometer of the Qubit dsDNA kit (Thermo Fisher Scientific).
The integrity score (ΔΔCq values) and concentration of extracted chromosomal DNA were measured using an Agilent NGS FFPE QC kit (Agilent Technologies) for all samples. As described in the Agilent protocol for HaloPlex HS Target Enrichment, the amount of input DNA was determined based on ΔΔCq values. For ΔΔCq < 1.5, 50 ng was used, and for ΔΔCq > 1.5, 100 ng was used.
Chromosomal DNA was isolated from formalin‐fixed paraffin‐embedded (FFPE) tissues of patients (n = 63) with head and neck squamous cell carcinoma (HNSCC) following the instructions from the kit manufacturer (Maxwell RSC DNA FFPE kit; Promega). The concentration of extracted DNA was determined by the fluorometer of the Qubit dsDNA kit (Thermo Fisher Scientific).
The integrity score (ΔΔCq values) and concentration of extracted chromosomal DNA were measured using an Agilent NGS FFPE QC kit (Agilent Technologies) for all samples. As described in the Agilent protocol for HaloPlex HS Target Enrichment, the amount of input DNA was determined based on ΔΔCq values. For ΔΔCq < 1.5, 50 ng was used, and for ΔΔCq > 1.5, 100 ng was used.