Broadcast Date: July 1, 2020
Time: 8:00 am PT, 11:00 am ET, 17:00 CET

Oncogene amplification, a significant driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA)—enabling gene amplification, rapid tumor evolution, and the rewiring of regulatory circuitry. Resolving an fCNA’s structure is a first step in deciphering the mechanisms of its genesis and the fCNA’s subsequent biological consequences.

In this Clinical OMICs webinar, we will hear about a powerful new computational method, AmpliconReconstructor (AR), for integrating optical mapping (OM) of long DNA fragments (>150kb) with next-generation sequencing (NGS) to resolve fCNAs at single-nucleotide resolution. AR uses an NGS-derived breakpoint graph alongside OM scaffolds to produce high-fidelity reconstructions. After validating its performance by extensive simulations, AR was used to reconstruct fCNAs in seven cancer cell lines to reveal the complex architecture of ecDNA, breakage-fusion-bridge cycles, and other complex rearrangements. By distinguishing between chromosomal and extrachromosomal origins, and by reconstructing the rearrangement signatures associated with a given fCNA’s generative mechanism, AR enables a more thorough understanding of the origins of fCNAs and their functional consequences.

 

A live Q&A session will follow the presentation, offering you a chance to pose questions to our expert panelist.

 

Produced with support from:

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Vineet Bafna, PhDVineet Bafna, PhD
Professor of Computer Science
Institute for Genomic Medicine
University of California, San Diego