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Users Provide Feedback on Performance of Qiagen, Illumina NGS Panels at AMP Corporate Event

NATIONAL HARBOR, Md. (GenomeWeb) — In advance of its annual meeting held here this week, the Association for Molecular Pathology yesterday held a "corporate workshop day," during which clinical researchers shared user experiences and early data regarding a number of recently launched or in-development molecular diagnostic products.

Sequencing technologies were more prevalent than ever at the workshop day, but two presentations in particular drew significant attendance: an early look at the performance of Qiagen's GeneReader targeted next-generation sequencing gene panels, and the recent implementation of Illumina's TruSight One NGS panel for diagnostic testing at a UK hospital.

At the Qiagen-sponsored workshop, Helen Fernandes, laboratory medicine chief for solid tumors and molecular pathology at Weill Cornell Medical College, shared some of the first user feedback about Qiagen's GeneReader DNAseq V2 panels for the detection of cancer-related variants.

Qiagen launched the 14 GeneReader panels, which encompass 570 clinically relevant cancer genes, in July. The panels are customizable to include other genes or gene regions, are compatible with any NGS sequencer, and come in three flavors: focused panels of eight to 25 genes; disease-specific panels of 40 to 50 genes; and comprehensive panels with as many as 160 genes.

Fernandes implemented the GeneReader panels in the context of Qiagen's entire sequencing workflow, which the company calls "sample to insight," and which includes QuantiMize qPCR kits to assess the quantity and quality of DNA amenable to amplification-based target enrichment; GeneReader library preparation; qPCR-based library quantification; and data analysis on the CLC Workbench. Qiagen's workflow now contains everything but the actual sequencing instrument, still under development. In this case Fernandes used Thermo Fisher's Ion PGM instrument, but the GeneReader panels are compatible with any NGS instrument.

Fernandes compared the GeneReader panels to Thermo Fisher's Ion AmpliSeq Hotspot Cancer Panel v2.0, with a workflow consisting of Qubit DNA quality control; AmpliSeq library preparation; library quantification with an Agilent bioanalyzer; Ion PGM sequencing; and data analysis with the Torrent Variant Caller.

On 39 specimens that were previously analyzed using the AmpliSeq panel, the GeneReader workflow showed high analytical performance, with accuracy of greater than 99 percent for 46 EGFR, KRAS, and BRAF variants within the samples, Fernandes said. In addition, she said that the GeneReader workflow had specificity of greater than 95 percent, uniformity of greater than 90 percent, and provided "much better coverage … [which] equates to confidence to call very low-level mutations."

Other pros of the Qiagen workflow, Fernandes said, included an embedded DNA quality assessment step; the ability to adjust first PCR cycles to salvage low-quality DNA, which is a boon for FFPE samples; and compatibility with IonXpress barcodes and multiple sequencers. Compared to the Ion workflow, however, GeneReader had some cons; namely, smaller batch sizes, and the fact that each sample has to be handled separately, which adds to the processing time "and may not be ideal for larger labs," she said. Overall, both workflows had similar turnaround times of between four and five days.

Meantime, in an Illumina-sponsored session, Howard Martin of the Regional Molecular Genetics Laboratory at Addenbrooke’s Hospital, part of the Cambridge University Hospitals system, discussed his laboratory's recent adoption of Illumina's TruSight One sequencing panel.

Launched a little over a year ago, TruSight One targets 4,813 genes with known associated clinical phenotypes. lt specifically focuses on the exonic regions harboring disease-causing mutations, and is designed to cover the most commonly ordered molecular assays, enabling labs to perform these on site with one test, according to the company.

Martin noted that his lab has been employing sequencing-based genetic testing for several years, and was looking to increase its diagnostic yield by sequencing for all relevant genes for a given clinical condition. However, with prior sequencing technologies, such an approach would "send the patient on a diagnostic odyssey of testing over and over again, [which] is very expensive."

As such, last year Martin's lab approached the UK Genetic Testing Network — a UK National Health Service group that evaluates and advises on genetic testing — about developing a new comprehensive gene panel.

Martin noted that Illumina had released the TruSight One Panel right around the same time, and it "ticked off all the boxes" for a comprehensive genetic testing offering. Furthermore, the group already had an Illumina HiSeq instrument in place, so in February the laboratory launched the Genomic Medicine Initiative (GEMINI) with the TruSight One Panel at its core.

The group first technically validated the platform on 200 samples with 244 unique mutations in 74 different genes, and found that it produced results that were 100 percent concordant at 20X coverage with Sanger sequencing results that had been obtained from labs in Europe and the US. Then the lab conducted prospective diagnostic testing on 366 samples targeting 10,000 variants and 650 unique variants per sample, producing a diagnostic yield of approximately 31 percent. Martin also recounted a case study in which the lab was able to use the panel to drill down on a diagnosis of a rare condition called Freeman-Sheldon syndrome in an eight-month-old infant.

Finally, the group conducted an economic evaluation using results from the first 143 diagnostic tests administered using the panel. They found that the average cost per patient of GEMINI testing was $1,000 compared to an average cost of $1,373 per patient when considering the bevy of comparable alternative tests that would be needed.

Martin summarized by noting that the TruSight One Panel allowed his lab to introduce a single test to sequence virtually all clinically relevant genes and to significantly increase the availability of tests for rare genetic diseases. He also noted that the panel has advantages in flexibility and diagnostic yield compared to whole-exome sequencing, and that it is cheaper than most alternatives.

Since the time the group originally launched GEMINI, Illumina commercialized the next-generation NextSeq instrument. Martin said that his team re-validated the GEMINI panel on that instrument and launched the updated testing service in September.