The average prescription-grade drug takes a decade of research and billions of dollars in funding in order to reach the market. Combined with the rate at which new and rare diseases continue to be discovered, this leaves pharmaceutical companies (and the clinical researchers they employ) constantly behind the proverbial eight ball. In short, one of the major challenges of drug discovery lies in optimizing the process by which specific treatments are designed, calibrated, and scientifically validated.
The TruSeq Amplicon – Cancer Panel (TSACP) is an example of one technology – targeted sequencing – that stands to significantly aid researchers in this quest for optimization. The TSACP targets variations within 48 specific cancer-related genes (including BRAF, KRAS, and EGFR), and has the unique ability to locate somatic mutations within hundreds of cancer-prone loci using a highly specialized multiplex assay. For cancer researchers, the combined features of the panel represent potentially huge time and cost savings.
Benefitting From the TSACP
TSACP offers extremely high levels of specificity, accuracy, and uniformity, all of which make it ideal for use within the scope of single clinical trials. The panel consistently detects mutations below 5% frequency. A quality control kit can be used to pre-screen and predict performance from fragmented DNA even in FFPE samples, representing a time savings in and of itself. Following pre-screening, the TruSeq Amplicon assay’s bead-to-bead normalization procedure eliminates the need for tedious qPCR. An on-instrument data analysis feature then allows for direct loading of amplicon libraries onto the MiniSeq system, greatly reducing both time spent and potential for user error. Analysis of panel results is also highly efficient, with each MiniSeq run including up to 96 samples with hundreds of amplicons per sample. All this taken together means that TSACP allows for the completion of projects in as little as two days that once took weeks or months.
Effective Clinical Use
The panel can be used to its greatest effect by sequencing genomic data of patients in clinical trials both before and after receiving treatment. Initial pre-treatment sequencing of patients allows the clinician to compare multiple oncogenic loci at once and spot correlations between variations. Instead of relying on the prognostic value of a single locus mutation (such as a TP53 variance in the presence of breast cancer) any additional mutations within in the 48 cancer-related genes targeted by the panel can also be observed, allowing for fine-tuned adjustment of the prognosis. Having the ability to screen multiple loci at once can also help determine the personalized treatment that a patient receives.
By resequencing again post-treatment, researchers can compare and contrast the genomic data to draw conclusions regarding drug efficacy and side effects in the presence of specific mutations. The same results can also be used to screen housekeeping genes for any unexpected changes.
As an aid in minimizing the cost and accelerating the research of a drug, the TSACP acts as a sort of one-stop-shop for sequencing, analyzing, and managing critical cancer-related genomic data. The TSACP is an excellent representation of the type of technology that we at The Sequencing Center hope can be used to forge the future of optimized drug discovery and personalized medicine. Our aim is to fully understand our clients’ goals and help to achieve them by providing the cost-effective technical assistance they need in order to obtain conclusive results that can then be optimized for regulatory body approval.