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Overview of talks on cfDNA, RNA fusions, and RNA-Seq
  • Circulating tumor cells (CTCs) and cell-free DNA (cfDNA)—learn about an research methodology to quantitatively isolate cells from whole blood samples, useful for detecting genetic mutations
  • Detecting fusions in tumor samples—learn about the importance of focusing on fusion breakpoints to identify novel gene fusions in cancer research using RNA-Seq
  • Targeted transcriptome sequencing—learn about discovering, profiling, and quantifying RNA transcripts

Partial Program

A head-to-head comparison of whole blood derived samples (cfDNA vs CTC DNA) for cancer research using next-generation sequencing

Challenges in biomarker testing in non-small cell lung cancer research

Expanding the scope of RNA-Seq to archival FFPE samples

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Paul W. Dempsey, PhD

Chief Science Officer, Cynvenio

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Nicola Normanno, MD 

Director, Research Department

Centro di Ricerche Oncologiche di Mercogliano (Naples)

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Kelli Bramlett, PhD

Research and Development Scientist

Thermo Fisher Scientific

Both cell-free DNA (cfDNA) and circulating tumor cells (CTCs) represent important possible templates for mutation analysis of research samples. Each template has different theoretical advantages for a test. cfDNA is very easy to access and isolate, while CTCs can provide both DNA as well as RNA for testing. In addition, the templates may reflect different aspects of cancer biology. Cynvenio has tested head-to-head cfDNA and CTC DNA using LiquidBiopsy™ coupled with Ion Torrent™ next-generation sequencing of normal and tumor samples. Both cfDNA and CTC samples provided sufficient quantity and purity of the limited number of tumor genomes for a direct sequencing test. No whole genome amplification was involved. The test for comparison purposes consisted of coupling these CTC and cfDNA purification technologies to an amplicon re-sequencing panel of 50 known cancer-associated genes using a sequencing pipeline for SNV mutations with a sensitivity of 1%. Typically, this pipeline can isolate, extract, sequence, and analyze blood borne cancer cells in 7 days. DNA sequencing process, when applied to breast cancer tumor samples, has demonstrated useful data. The data suggest that cfDNA and DNA recovered from tumor-derived blood cells are complementary and may represent different aspects of cancer biology.

Fusion genes play a central role in many cancer types. Research using gene fusion have been used to classify malignancy, risk factors, disease prognosis, and companion diagnostic biomarkers for certain approved drugs. More than 1500 fusion transcripts have been published to date, but current practices for fusion transcript detection are hampered by high cost and bias. Typically only the top 1–2 commonly observed fusion transcripts are characterized for most samples.

We have developed a next-generation sequencing research solution for highly multiplexed fusion transcript analysis. Using this workflow, hundreds of fusion transcripts can be simultaneously tested in fewer than 24 hours.

In this presentation, Dr Normanno will present an Ion AmpliSeq™ method for fusion detection and analysis from non-small cell lung cancer research samples.

While there are several ways to profile transcripts—including microarrays and whole-transcriptome RNA-Seq—all of these systems require that you have plenty of sample. Realizing that valuable results come from samples that are limited or difficult to work with, the new Ion AmpliSeq™ Transcriptome Human Gene Expression Panel was launched to facilitate and ease the use of precious or degraded samples in critical gene expression studies. The Ion AmpliSeq™ Transcriptome Human Gene Expression Panel requires up to 100-fold less total RNA than other platforms for gene expression profiling experiments.

Dr. Bramlett will discuss the development and verification of the Ion AmpliSeq™ Transcriptome Human Gene Expression Panel.