Feasibility of Population Scale Comprehensive Identification and Analysis of Complex Structural Variations in Cancer Genome Using Nanochannel Array

Diseases with complex traits such as hematological cancer are known to be associated with large structural variations (SV > 1 kb). Techniques such as karyotyping, FISH and aCGH have been common tools for gross chromosomal lesion analysis. Yet population scale comprehensive SV analysis with these tools remains impractical, tedious or incomplete such as missing balanced lesions by aCGH. Recently, high throughput Next Generation Sequencing (NGS) has generated a large amount of sequencing reads that have rapidly reduced costs and are effective in detection of SNPs and small indels; however, complicated by the fact that large structural variations, often spanning tens to hundreds of thousands of base pairs or involving complex rearrangements throughout the genome, are hard for current short read sequencing technology to assemble or infer. Therefore, there is a blind spot in effectively detecting SVs within this range (1 kb ~ 1 Mb) due to insufficient tools.

Here we demonstrate a technology that rapidly linearizes very long strands of genomic DNA (100 kb to Mbs) through NanoChannels to directly visualize large SVs and rearrangements preserved within intact genomic DNA at the single molecule level. Through specific sequence motif labeling, de novo genome physical maps are assembled within hours and hundreds to thousands of SV events, balanced or imbalanced, are called with no a priori knowledge of the samples. Preliminary testing data from a group of cancer samples and multiple trio families will be shown to demonstrate this highly comprehensive and cost effective approach, with results validated by direct single-molecule images and multiple orthogonal methods. We also show long spanning molecules would provide very valuable information of precise mapping of viral genomic sequence integration in human genomes that are potentially associated with malignant cell transformation. For the first time, it is now feasible to do large population-based comprehensive genome structural variation studies on a single platform. This innovations will transform the biomedical research, diagnosis and treatment of hematological cancers that result from structural variations and chromosomal lesions.