The Qiagen GeneReader is an NGS platform developed for the clinic and aims to deliver a sample-to-answer solution. I covered the “launch” of the instrument at the end of 2016 and summarised some of the details but there was no public data to take a look at. I just got hold of a paper from JClinPath: Use of the GeneReader NGS System in a clinical pathology laboratory: a comparative study (although this is not up on their website yet).

Researchers from the Institute of Pathology and the Center of Molecular Medicine at the University Hospital of Cologne in Germany (and QIAGEN) evaluated the GeneReader in a path lab for “ease of use, sequencing accuracy and data reproducibility” using clinical samples which were compared to their Sanger and MiSeq platforms. Their experience was good and they said “the GeneReader NGS System is suitable for routine pathology laboratory use”.

FFPE tumour blocks from colorectal and gastric carcinoma, lung cancer, melanoma and gastrointestinal stromal tumours, collected in 2015 & 12016, were processed in two parallel workflows. Mutations and mutant allele frequencies were compared and verified against the Sanger sequencing results (gold standard) and the group reported 100% concordant results from both workflows.

The test used QIAGENs Actionable Insight Tumour Panel which targets 330 amplicons covering 16.7 kb, interrogating 773 unique variant positions in 12 genes of high prognostic and therapeutic relevance (KRAS, NRAS, KIT, BRAF, PDGFRA, ALK, EGFR, ERBB2, PIK3CA, ERBB3, ESR1 and RAF1). The group generated median coverage of 5000x, 95% of amplicons had >500x and 98.58% > 200x.

NGS workflows compared

The QIAGEN Clinical Insight Analyze software was used for analysis. FASTQs were aligned, variants called and an interactive report generated for visualisation and quality control of the sequencing results. Variant cutoff was 5% for FFPE samples, anew pipeline for liquid biopsy (with a variant cutoff of 0.5%) detected a PIK3CA variant (p.E542K) at 2.8%. Very high concordance between  platforms was reported across  a wide range of mutant allele frequencies, <5% to >90%. Qiagen’s interpretations software, which assigns clinical relevance to mutations, correctly identified BRAF and KRAS mutations but also reported an activating p.Y772_A775 duplication in exon 20 of ERBB2 (Her2) for which ther are therapeutic options with ERBB2 inhibitors.

Perhaps most importantly this is the first data comparing Qiagen and Illumina NGS platforms for clinical sequencing directly. Illumina has held top dog spot for a decade now…with Qiagen and Oxford nanopore nibbling at their heels are we about to see a bit more competition in the NGS space?