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Diagnostics Genetics and epigenetics, Biochemistry and molecular biology, Oncology

Covering All Bases

sponsored by QIAGEN

Why is it important to test for EGFR and KRAS in non-small cell lung cancer patients?
 

EGFR and KRAS represent about 40 percent of all driver mutations within non- small cell lung cancer (NSCLC). Multiple therapies are now approved in the US to target specific driver mutations for patients whose tumors harbor these alterations, but molecular testing is required to guide appropriate, targeted use of these drugs.

Why is molecular testing underperformed in NSCLC patients?
 

A recent publication suggests that about 23 percent of NSCLC patients in western Europe are not tested for the most clinically relevant biomarkers (1), a statement that was consistently reiterated at the 2022 European Society of Medical Oncology (ESMO) conference. Missed opportunities for testing are likely multifactorial, but one key challenge is the turnaround time of results relative to the need to rapidly initiate treatment – causing some patients to miss out on precision therapy due to access issues or lack of relevant information.

Implementing a user-friendly testing platform that offers a wide menu for oncology testing would facilitate efficient workflows and enable rapid turnaround times with certified diagnostic products that require minimal in-house validation.

Increasing knowledge and access by introducing tests that can use either tissue or liquid biopsies could also help overcome some of the challenges. Tissue remains the primary material for testing, but NSCLC guidelines are constantly evolving to include liquid biopsy when tissue sampling is not possible, which would increase the number of patients tested and allow for routine monitoring where appropriate. Recent approvals of new therapies may also provide additional opportunities for patients once tested, such as newly approved drugs that target previously “untargetable mutations.” For example, the KRAS G12C mutation represents 13 percent of all KRAS mutations. Identifying KRAS G12C using molecular testing is of paramount importance to guiding treatment – and makes the mutation a key target for precision medicine.

Tell me about QIAGEN’s genomic testing solutions...
 

Our third-generation therascreen EGFR Plus RGQ Kit tests for key EGFR treatment resistance biomarkers T790M and C797S and supports testing with either FFPE or plasma samples. therascreen EGFR Plus is a certified diagnostic tool within the EU and approved as “Research Use Only” in the US. Important clinical trials using the therascreen KRAS RGQ PCR Kit have also led to the approval of the kit as a companion diagnostic. Now, the therascreen KRAS RGQ PCR Kit has an approved extension for NSCLC, as well as its original indication in colorectal cancer testing. By combining QIAGEN’s EGFR Plus and KRAS kits, pathologists can test NSCLC FFPE samples viaqPCR for the two most frequently mutated genes in NSCLC.

For customers who wish to conduct deeper testing with next-generation sequencing (NGS), QIAGEN enables comprehensive oncology profiling with a number of targeted library prep solutions. Our QIAseq Targeted NGS portfolio facilitates ultrasensitive variant and fusion detection using integrated unique molecular indices and highly optimized target enrichment technology.

QIAGEN’s newly launched QIAseq Targeted DNA Pro Panel allows labs to expand variant analysis to reveal structural variants with breakpoints defined at the nucleotide level across multiple exons. Another QIAGEN product – the QIAseq RNA Fusion XP – enables the combined analysis of RNA fusion with single- nucleotide variants and gene expression from a single sample, allowing customers to gain complex RNA-seq insights.

Finally, QIAseq Multimodal Panels enable the simultaneous enrichment and profiling of DNA variants, RNA fusions, and gene expression levels from one sample input. Our NGS solutions are molecular biologic applications that are not certified for diagnostic use.

How do clinical and research labs benefit from these solutions?
 

Our therascreen kits are accredited as diagnostic tests, having been both analytically and clinically validated; therefore, a clinical lab can use them confidently without the need for additional validation. EGFR Plus is validated with QIAsymphony extraction and Rotor-Gene AssayManager software to allow the user to automate sample extraction and data analysis. Furthermore, therascreen KRAS and EGFR are part of a much wider portfolio of oncology biomarker testing kits that run on the QIAGEN Rotor-Gene Q platform. Any lab adopting this platform can therefore test for multiple indications in both solid tumors and oncohematology.

Users can easily automate our NGS panels, which come with various levels of automated analysis to reduce the need for costly or time-consuming bioinformatics. The new QIAseq Targeted DNA Pro Panel reduces library preparation time to as little as six hours and requires only two hours of hands-on operator time – allowing highly trained staff to repurpose their time for other tasks.

What sets QIAGEN’s genomic testing solutions apart from competitors?
 

QIAGEN has been providing products in this space for many years and is a trusted supplier of both qPCR and NGS testing solutions. The therascreen EGFR and KRAS kits have both been thoroughly validated and registered as in vitro diagnostics – inspiring user confidence that third-party clinical trials have produced reliable data. The sheer breadth of QIAGEN’s portfolio is attractive and allows labs to set up for multiple indications with a single, small-footprint system. With EGFR Plus, labs can test liquid biopsy samples for resistance biomarkers T790M and C797S – one of the only qPCR kits on the market to enable this.

The sheer breadth of QIAGEN’s portfolio is attractive and allows labs to set up for multiple indications with a single, small-footprint system.

Due to the fragmented and modified nature of FFPE DNA samples, many NGS library construction workflows have a low recovery rate from FFPE DNA, but the QIAseq Targeted DNA Pro incorporates a seamless FFPE DNA repair step before library construction. The specially formulated chemistry achieves highly efficient enrichment even in GC- rich regions. In addition, QIAseq Targeted DNA Pro libraries can be sequenced with Illumina default sequencing primers and are compatible with most mid- to high-throughput sequencers. Alternative targeted DNA library construction methods have multiple bead cleanup steps that are labor- intensive and result in inconsistent library yield; by replacing the bead cleanup steps with enzymatic processes after ligation and target enrichment, QIAseq Targeted DNA Pro enables an efficient, automation-friendly workflow.

The QIAseq Targeted NGS portfolio comes with a number of catalog panels that have preconfigured workflows for seamless variant calling; however, QIAGEN also offers its customers the flexibility to customize their NGS panels without compromising on data quality.

What’s your one key message to laboratory medicine professionals about molecular testing in NSCLC?
 

“Test your patients” – which was also the main message running throughout ESMO 2022. Molecular diagnosis is required to identify specific alterations that can inform the clinician and enable the initiation of targeted therapy. Genomic testing for NSCLC has provided huge benefits in the past decade and improved patient outcomes by allowing more targeted therapies for their individual disease. I believe the importance of genomic testing will increase alongside our understanding of disease drivers and resistance mechanisms within cancer cells. There will be many opportunities for labs of all sizes to continue to test patients for optimal therapies with qPCR and NGS solutions – and with QIAGEN’s comprehensive portfolio in qPCR, dPCR, and NGS, customers can easily access relevant genomic information in a faster, simpler, and more efficient manner.

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  1. J Mateo et al., “Delivering precision oncology to patients with cancer,” Nat Med, 28, 658 (2022). PMID: 35440717.
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