Abstract 4746: Mapping the “dark matter” of cancer genome - Long repeats, complex structural variations with nanochannel technology
Authors: Cao H. , Hastie A , Pang A. , Andrews W , Anantharaman T. , Chan T. , Saghbini M. , Sadoski H. , Austin M. , Dzakula Z. , Dickinson T. , Holmlin E. , Xun X. , Kwok P. , Rossi M. 
Published: August 2015

Abstract
In spite of advancements in high-throughput short read next-generation sequencing in the past decade, the majority of genome analysis today is limited in exome or transcriptome sequencing, leaving a fair portion of the human genome unresolved or ambiguously characterized. Especially, large genomic structural variations (SV, &gt; 1 kb), known to be associated with complex traits and diseases such as cancer, are found more prevalent than we previously thought. During assembly, they leave gaps and unknown structural or heterozygous information as the “dark matter” of the genome, which is often challenging to detect for short read NGS and conventional labor intensive low resolution cytogenetic techniques. Rapid whole genome mapping in NanoChannel arrays represent a new standard of single-molecule platform independent of yet complementary to DNA sequencing for accurate genome assembly and structural variation analysis in complex cancer genome. Extremely long intact DNA molecules of hundreds to thousands of kilobases, fluorescently labeled at sequence motifs and linearized in true nanofluidic channels, enable direct imaging of comprehensive genome architecture at a high resolution. De novo assembly of these single molecules yields unprecedented long contiguous genome maps, advantageous in spanning over highly repetitive regions and complex structures in their native form. The first hybrid assembly of a diploid human genome combines NGS sequencing with BioNano genome maps, resulting in excellent scaffold N50s exceeding 34 Mb, a step forward towards “medical grade” genome and dramatic improvement upon the current assembly contiguity typically observed in using shotgun sequencing approaches alone.
We present results from analysis on human cancer genome, non-model and large complex genomes. We detected hundreds of large structural variants per genome and haplotype differences in these genomes, revealing the locations, orientations and copy numbers of these complex structural variants often elusive from NGS detection. Using Irys from BioNano, we were able to find and characterize SV and repeat regions in the complex cancer genome that are biologically and clinically relevant, especially able to precisely map viral (oncogene) component integration sites within human genome, believed to be linked to oncogenesis.
Comprehensive genome mapping provides extreme valuable structural information otherwise hard or impossible to decipher with short read sequencing data alone, and paves the road for generating true golden standard in ultimate medical grade and breeding grade genome information. For the first time, population scale comparative genome study to identify comprehensive genomic structural variation on a single platform with a large patient cohorts is feasible due to the standardized high quality data, automated efficiency of data generation and low cost.
Note: This abstract was not presented at the meeting.
Citation Format: H. Cao, A Hastie, A. Pang, W Andrews, T. Anantharaman, T. Chan, M. Saghbini, H. Sadoski, M. Austin, Z. Dzakula, T. Dickinson, E. Holmlin, X. Xun, P. Kwok, M. Rossi. Mapping the “dark matter” of cancer genome - Long repeats, complex structural variations with nanochannel technology. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4746. doi:10.1158/1538-7445.AM2015-4746