NEW YORK (GenomeWeb) – Researchers and clinicians in Heldelberg, Germany, are participating in a large, ongoing study that they said highlights the utility of comprehensive NGS-based genetic profiling in a routine clinical setting.
In a study published this month in the International Journal of Cancer, the multidisciplinary and multi-institutional team provided an assessment of clinical data from 3,000 late-stage non-small cell lung cancer patients after performing DNA and RNA sequencing on their tissue samples.
The patients had been identified to receive novel therapies based on the detection of specific biomarkers in their tumor biopsies.
The Heidelberg report is unique because of its parallel NGS assessment of DNA and RNA from formalin-fixed, paraffin-embedded tissue samples, allowing for the assessment of mutations as well as gene fusions and rearrangements "in an accurate, comprehensive, and discovery fashion," said Solange Peters, president of the European Society for Medical Oncology, who was not involved in the study.
"Exceptional features of this [study] are the number of samples analyzed — the largest using DNA/RNA [through] this integrated approach — as well as the description of a minimal dropout rate and extremely short turnaround times," said Peters, who is also head of medical oncology at the Lausanne University Hospital,
The Heidelberg team reported achieving reliable results and low rates of dropout, which occurs when an insufficient quantity of tumor material is available and the quantity and quality of DNA or RNA does not match what is needed by the assay.
They kept the dropout rate to less than 4 percent for more than 3,000 patients, which contributes to clinicians' goals of obtaining suitable diagnostic information for as many patients as possible, said Albrecht Stenzinger, a professor at the Institute of Pathology at Heidelberg University Hospital.
The researchers also conducted comprehensive profiling using minimal amounts of tissue and realized faster turnaround times and lower costs compared to single-gene sequencing, a competing diagnostic approach for evaluating NSCLC tumors, he said.
These combined benefits highlight the practicability of applying the method in a routine clinical setting to support individual decisions in patient care and clinical and translational research, Stenzinger said.
A growing demand for more comprehensive genetic assays and a limit to the amount of tissue available from small biopsies are among the drivers for use of NGS, the Heidelberg researchers said. Cancer center guidelines are moving toward upfront profiling with NGS of all advanced lung cancers, but there are still practical issues with this testing method that can limit clinical testing and prevent or delay patients being started on targeted therapies. Barriers to therapy include assay failure due to insufficient sampling, cost, and increased turnaround times, and as a result, clinicians sometimes opt for single-gene testing.
Tyrosine kinase inhibitors currently confer the greatest survival gain for NSCLC patients with actionable genetic alterations. However, the increasing number of targets and compounds poses the challenge of obtaining reliable, broad, and timely molecular assays for the identification of patients likely to benefit from novel treatments, the Heidelberg researchers noted.
Their study, which began in 2014, is continuing and adding 1,000 samples per year to the existing cohort.
The Heidelberg team had previously described the development of their approach in the Journal of Molecular Diagnostics and Genes, Chromosomes, & Cancer.
In particular, they had validated the Thermo Fisher Scientific Ion Torrent sequencing system for detecting mutations in DNA derived from FFPE lung cancer specimens that were previously detected by Sanger sequencing.
They also evaluated the performance of a one-step approach for parallel DNA and RNA extraction and preparation from single tumor specimens, using Thermo Fisher AmpliSeq library prep for both nucleic acids.
Subsequently, they implemented a custom-designed lung cancer sequencing panel and the Thermo Fisher AmpliSeq RNA Lung Cancer fusion panel designed for the detection of ALK, ROS1, RET, and NTRK1 gene rearrangements.
The AmpliSeq technology uses proprietary algorithms and primer modifications for multiplex PCR enrichment of up to several hundred target regions in a single reaction that are tailored for the needs of bench top sequencers, including the Ion Torrent PGM and the Illumina MiSeq.
In the current study, the group found that 807 of the 3,000 patients were eligible for currently approved EGFR-/BRAF-/ALK- and ROS1-directed therapies and that 218 additional patients with MET, ERBB2 (HER2) or RET alterations could potentially profit from off-label treatments.
"[Stenzinger] and his clinical research team’s analysis strongly supports growing evidence that a combined approach to DNA and RNA targeted sequencing on the Ion Torrent platform can provide significant advantages in the accurate and dependable determination of the molecular signature of a tumor," said Joydeep Goswami, president of clinical next-generation sequencing and oncology for Thermo Fisher Scientific. The ability to mine more meaningful genomic data with faster turnaround times, minimal dropout rates, and using smaller samples creates a perfect trifecta, he said.
The current approach can be scaled up and is adaptable to clinical requirements, such as evaluating tumor mutational burden, Stenzinger said.
"For tumor mutational burden testing, you need a gene panel that's sufficiently large, and we are therefore increasing the size of our gene panel," he said, adding that the group anticipates launching the new panel in the second quarter to interrogate additional immuno-oncology biomarkers and provide assessments of tumor mutational burden.
The work conducted by the Heidelberg team illustrates what can be achieved with data obtained from routine diagnostics and is similar to the use of such diagnostic datasets by others, such as Memorial Sloan Kettering Cancer Center in the US, Stenzinger noted.
Researchers at MSKCC reported in Nature Genetics this month that cancer patients with high tumor mutational burden who were treated with immunotherapy tended to live longer than those with fewer mutations.
Stenzinger and his colleagues are also developing their NGS approach for assessment of cancers other than NSCLC, such as melanomas, colorectal cancer, and cancers of unknown primary origin, he said.