NEW YORK (GenomeWeb) – Biomarker screening is becoming an essential part of oncology treatment, but the cost and flexibility of molecular and companion diagnostics have been a barrier to uptake.
For patients with metastatic colorectal cancer, physicians can use KRAS mutation assays to guide certain therapies. The Therascreen KRAS RGQ PCR kit from Qiagen was approved by the US Food and Drug Administration as a companion diagnostic for Lilly's drug Erbitux (cetuximab) in 2012, and for Amgen's colorectal cancer drug Vectibix (panitumumab) last May.
A study published this month in PLoS One now demonstrates that a test developed using Thermo Fisher Scientific brand Life Technologies' competitive allele-specific TaqMan PCR, or castPCR, is essentially equivalent to Therascreen for KRAS mutation detection. The castPCR customizable plates potentially have the advantage of a less complicated workflow with flexible biomarker selection, and may be cheaper, according to one of the study's authors.
Also, whereas the Therascreen assay is locked in at seven mutations, user-customized castPCR plates "allow larger numbers of clinically relevant mutations to be included … providing a real alternative to next generaltion sequencing, particularly for laboratories without this facility," according to the study.
"We wanted a simpler method with less pipetting steps," Ian Cree, professor of pathology at Warwick Medical School in Coventry, UK and author on the study, wrote in an email to GenomeWeb. "One of the major costs in diagnostic laboratories is staff time, and a manufactured plate was therefore likely to be a good solution," he said. "It is important to validate diagnostics adequately against existing methods, and we felt that castPCR might have some advantages for us in our laboratory," Cree said.
Funding for the research came from Merck Serono, while Life Tech provided discounted reagents and castPCR plates. Cree has also lectured on behalf of Life Tech regarding use of Ion Torrent next-generation sequencing arrays in its network of European pathology laboratories, OncoNetwork.
The study aimed to assess the status of seven KRAS mutations in codon 12 and 13 from 99 formalin-fixed, paraffin-embeded colorectal cancer biopsies.
The customized castPCR plates, which are sold containing pre-dispensed reagents, used a panel that included the same markers as the Therascreen KRAS assay, plus six additional KRAS mutations. They also included an assay for the V600E BRAF mutation, which the authors maintained will likely be a part of future colorectal cancer companion diagnostics testing based on an analysis published in The Lancet Oncology.
Customizing the castPCR plates is "really very simple," Cree said. "If you know the genes you want to look at, and the mutations required, then it is possible to choose these from a list of mutations on the Life Technologies website," he noted, adding that customer support for the plates can help resolve any issues.
For cancer mutation detection, the castPCR plates can be customized using 586 different mutations in 45 different genes, according to Life Tech's website. The reagents are available in 96- or 384-well plates, and can be provided wet or lyophilized.
The research was done at both Queen Alexandra Hospital in Portsmouth, and the Warwick Medical School in Coventry, UK. Both sites used the Maxwell DNA extraction platform and reagents from Promega. Each site tested the full set of 99 samples. One site processed all samples in 96-well plates using the Applied Biosystems 7500 Fast Dx real-time PCR machine. The other site processed the Therascreen assays in tubes using Qiagen's Rotor-Gene platform and ran the castPCR on the Life Tech ViiA7. Overall, with three exceptions, Therascreen and castPCR called the samples identically. After re-testing, however, the three discrepant results were reconciled.
There has been some discussion of the lack of adoption of the Therascreen KRAS test as a companion diagnostic, as previously reported. Merck Serono surveyed a group of UK oncologists in 2012 and found that cost was a barrier to biomarker testing.
Cree noted that the Royal College of Pathologists recently launched a project to help laboratories better assess the costs of molecular pathology services. The business planning tool comprises a spreadsheet which populates a form letter that labs can use for funding applications to demonstrate the "value and rationale to investing in further diagnostics tests."
Merck Serono and Life Tech have been collaborating to co-develop pharmaceuticals and companion diagnostics since mid-2013. Merck also recently signed a deal with Sysmex Inostics to develop a circulating tumor DNA biomarker for metastatic colorectal cancer, estimating a CE mark some time in 2015.
The number of FDA-approved drugs with pharmacogenomic information in their labeling has quadrupled in the past four years, as has the list of approved companion diagnostics, despite apparent hesitation on the part of big pharma firms toward investing, as recently covered by GenomeWeb. Firms such as Illumina, Transgenomic, and Trovagene are also pursuing KRAS biomarker tests, while Qiagen's Therascreen EGFR test was recently approved as a companion diagnostic for Boehringer Ingelheim's metastatic non-small cell lung cancer, Gilotrif (afatinib).