The use of long-read sequencing to determine the structure of the Her2 amplicon in breast cancer

Rosenfeld, Jeffrey, Goodwin, Sara, Ganesan, Shridar (2017) The use of long-read sequencing to determine the structure of the Her2 amplicon in breast cancer. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017, 2017 Apr 1-5, Washington, DC..

DOI: 10.1158/1538-7445.AM2017-3373


HER2 amplification is present in ~15% of breast cancers, and is present in small subsets of other cancer types including gastric and lung cancers. Therapy targeting HER2 is now routinely used in treatment of HER2-amplificed breast cancer and has changed the natural history of this disease. The region of chromosome 17q12 containing Her2 contains many genes, and little is known about the actual genomic alterations that underlie the amplification event. While it is known that parts of the amplicon exist in multiple copies in a tumor, the exact structure of the duplicated region is not known and their relative orientation and positions in the genome is not clear. There is the potential for rearrangements between the genes and for different segments of the amplicon to exist and varied copy numbers. There is no clear way to assemble the complete structure of this region using short reads, as they cannot resolve repetitive regions and identify junction reads. Long read sequencing has the potential to overcome these limitations, however the sequencing depth is limited and difficult to apply to large genomes. To apply long read sequencing to a limited part of the cancer genome, we have used Nimblegen target enrichment coupled with Oxford Nanopore and Pacific Bioscience sequencing in an attempt to sequence and assemble the Her2 amplicon. The error rate of the sequencers are not of concern since we are not looking at base-pair level variation. Instead, our need is for long reads that can span the gene boundaries and repetitive elements to give complete structure of the amplicon. Nimblegen custom capture probes were designed for the 2mb chromosomal region containing Her2. DNA was extracted from 3 breast cancer cell lines and enriched using the Nimblegen kit. This DNA was then sequenced with long reads on the MinIon and the PacBio to allow for complete assembly of the region. The DNA was assembled to determine the structure of the HER2 amplicon in each cell line. These results may give new insight into the molecular events that led to formation of the HER2 amplicon.

Item Type: Conference or Workshop Item (Poster)
Subjects: bioinformatics
diseases & disorders > cancer
diseases & disorders
bioinformatics > genomics and proteomics
diseases & disorders > cancer > cancer types > breast cancer
diseases & disorders > cancer > cancer types
CSHL Authors:
Communities: CSHL labs > McCombie lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 2017
Date Deposited: 22 Jan 2024 20:49
Last Modified: 22 Jan 2024 20:49
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