A new class of molecularly targeted cancer drugs promise to greatly improve cancer treatment. The efficiency of such drugs in the individual patients depends on what genes have been mutated and given rise to the tumor. Targeted DNA sequencing of genes frequently involved in specific tumors therefore is a powerful tool to select the optimal therapy for each patient.
The Uppsala team selected 560 genes for analysis in 192 tumor samples from colon cancer patients, and Halo Genomics designed a HaloPlex™ PCR assay covering all these genes.
" Using the HaloPlex PCR Kit, one technician was able to enrich and prepare the 192 samples for sequencing within a week, without the use of dedicated equipment. This increased throughput and productivity up to ten fold compared to conventional approaches. For small to medium sized research laboratories like ours, the simplified workflow and cost reduction really enabled us to perform this project at a scale that have not previously been possible", says Professor Mats Nilsson at the Department of Immunology, Genetics and Pathology at Uppsala University.The samples are now being sequenced at Science for Life Laboratory in Uppsala.
"We expect to identify exactly which molecular pathways are affected in the tumor cells from individual patients, driving their tumors. This will be important for selecting the optimal targeted therapy in future patients, and the approach we are taking is promising for diagnostics due to low cost and high efficiency", says Mats Nilsson.
"This is a great example of how the HaloPlex PCR method can revolutionize the sample preparation workflow for next-generation sequencing" , says Fredrik Dahl, CTO of Halo Genomics.
The study is supported by the Swedish research agency Vinnova.