Jennifer Dasgupta

Principal System Engineer, Roche Sequencing Solutions

Tuesday, February 13 | 8:00 – 8:50 am | Union Suite

Automated Nucleic Acid Extraction for Next-generation Sequencing
Jennifer Dasgupta, Principal System Engineer

Library preparation for next-generation sequencing (NGS) often times requires double-stranded DNA (dsDNA) for adapter ligation. However, many automated extraction methods have not been optimized for such applications and elute at high temperatures, yielding single-stranded DNA. The Roche Sequencing Solutions (RSS) automation team evaluated the MagNA Pure Systems as solutions for NGS workflows. These instruments are designed to extract nucleic acid (NA) mainly for qPCR assays, with less data supporting NGS workflows. Additionally, modifications to workflow parameters, such as elution temperatures, were tested to increase the yield of dsDNA for NGS workflows.

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Dan Klass, PhD

Principal Scientist II, Oncology Applications Lead, Roche Sequencing

Wednesday, February 14 | 8:00 – 8:50 am | Union Suite

The Unique Challenges and Opportunities of Circulating Tumor DNA
Speaker: Dan Klass, PhD, Principal Scientist II | Oncology Applications Lead

The increasing adoption of next generation sequencing in liquid biopsy for clinical research is transforming oncology, yet challenges remain in the application of NGS to circulating tumor DNA (ctDNA). Traditional approaches to sample preparation, sequencing, and analysis are often inadequate to address the difficulties—such as low volume of ctDNA per blood draw, the small fraction that is tumor-derived, and differences in tumor-specific mutation patterns among research subjects. Dr. Klass will discuss these challenges, how AVENIO ctDNA analysis assays can help researchers maximize the information output from a limited source by detecting all four mutation classes in a single workflow.

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Nancy Nabilsi, PhD

Senior Application Scientist, Roche Sequencing

Thursday, February 15 | 8:00 – 8:45 am | Union Suite

SeqCap Epi: Enabling Lower Inputs and New Applications for Targeted Methyl-seq Analysis
Speaker: Nancy Nabilsi, PhD, Sr. Applications Scientist

Aberrant DNA methylation is associated with dysregulated gene expression in multiple disease states. Roche NimbleGen has pioneered target enrichment of bisulfite-treated DNA, enabling the targeting of selected regions from bisulfite treated genomic DNA in a single NGS workflow. Because target enrichment is performed after bisulfite conversion in this workflow, instead of with the conventional capture-then-bisulfite-treat strategies, this technology is better suited for low-input applications such as cfDNA analysis. This session will include workflow modifications that enable targeted DNA methylation analysis from lower input amounts and the application of SeqCap Epi for targeted analysis of 5-hydroxymethylcytosine.

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