Rubicon's ThruPLEX™-FD Prep Kits Enable Study Showing Liquid Biopsy Can Track Cancer Resistance

Rubicon Genomics, Inc, a leader in the development and commercialization of innovative sample-specific nucleic acid library preparation products used in research and clinical testing, has reported that its ThruPLEXTM-FD Prep Kits contributed to the success of a breakthrough study recently published in Nature1 that showed that genomic data extracted from the plasma of cancer patients can be used to track drug resistance and potentially guide treatment.

The proof-of-principle study showed that by sequencing tumor exomes (the “coding” elements of the genome) extracted from patient plasma samples, it is possible to track how metastatic cancer evolves to acquire resistance to cancer therapy. In patients with advanced breast, lung and ovarian cancers, the researchers derived tumor sequences using plasma samples taken during multiple courses of treatment. They were able to identify mutations associated with the emergence of resistance to cancer drugs including cisplatin, tamoxifen and gefitinib. The authors concluded that this non-invasive “liquid biopsy,” based on tumor DNA that is released into the circulation, offers important advantages and could complement current invasive biopsy methods that can be uncomfortable and costly.

ThruPLEX-FD Prep Kits are designed to provide sensitive and consistent sequencing from challenging samples containing small amounts of degraded DNA with minimum hands-on time. They leverage Rubicon’s patented DNA repair and ligation methods to deliver more rapid and sensitive sequencing of plasma, formalin-fixed, ChIP and other fragmented DNA samples with increased throughput.

“This study illustrates how ThruPLEX-FD can be a valuable tool for generating the high quality genomic information that is essential for personalized medicine,” noted Dr. James Koziarz, CEO of Rubicon. Obtaining usable DNA from patient samples can be difficult. ThruPLEX-FD Prep Kits are designed to produce high quality DNA from challenging patient samples, including non-invasive samples such as plasma, and they do so rapidly and efficiently.”

For this study, the scientists used ThruPlex-FD to prepare libraries from very small quantities of circulating DNA extracted from plasma (as small as 2.3 ng of DNA.) After enriching for the exome fraction, pair-end sequencing of the samples were performed on an Illumina HiSeq 2500.

Dr. Koziarz added, “By making it easier to optimize cancer therapy as treatment proceeds, the approach used in this study could produce better outcomes while improving patients’ quality of life and reducing costs. We are proud that our ThruPLEX technology contributed to these important findings, and we expect our ThruPLEX kits will enable other advances as genomic medicine moves from research into clinical practice.”

ThruPLEX-FD is a streamlined single tube, three-step process that eliminates intermediate purifications, transfers, columns or gels. This decreases the likelihood of experimental variability, bias and contamination. DNA is sequencing-ready in two hours with as little as 15 minutes of hands-on time. A technician can prepare 192 ThruPLEX samples per day--a 15-fold increase in productivity compared to other methods. ThruPLEX-FD is designed and validated for use with samples as small as 50 picograms of human DNA and can be used with plasma, FFPE, or fragmented gDNA in FFPE for DNA-seq, RNA-seq and ChIP-seq applications. ThruPLEX-FD is currently available as 12 or 48-reaction, 12-index kits for sequencing on Illumina® HiSeq®, MiSeq® and Genome Analyzer instruments. ThruPLEX-FD kits are being developed for additional formats and platforms.

To learn more about Rubicon’s ThruPLEX technology, visit Booth 418 at the 63rd Annual Meeting of the American Society of Human Genetics in Boston, MA, October 22-26, 2013.