Targeted paired transcriptomic analysis of head and neck carcinoma treated with chemoradiotherapy

We employed contemporary targeted autoimmune RNA sequencing (HTG molecular diagnostics, Precision Immuno-Oncology Panel) to head and neck tissue derived from 30 cancer patients patients before and after chemoradiotherapy. Differential gene expression was calculated and compared to therapy response. Transcriptomic analysis of 60 samples from 30 head and neck cancer patients before and after CRT. ***Please note that raw data is not provided as raw files, basecall and fastq are not meaningful and can't be used by other researchers unless they are demultiplexed, parsed and aligned byt the manufacturer's software. With this technology, thousands of carefully designed probes (covering different isoforms) against thousands of genes were used and then after a Nuclease protection assay, all that is left are probes that are bound to their targets. Then a normal NGS library prep follows and in actuality the probes were sequenced and the number of reads per probe is used as an absolute quantification of mRNA transcripts per target. The produced fastq files are parsed in the manufacturer's software which aligns and counts reads by looking for the sequence of the probes (~100nt).