ANN ARBOR (WWJ) — Ann Arbor-based Rubicon Genomics Inc. said its ThruPlex-FD prep kits contributed to the success of a study published in Nature 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 use 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,” said Rubicon CEO James Koziarz. “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 nanograms of DNA. After enriching for the exome fraction, pair-end sequencing of the samples were performed on an Illumina HiSeq 2500.

“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,” Koziarz said. “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.

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 Oct. 22-26.

For more information about ThruPlex-FD, visit .


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