报告题目：Rapid Genome Mapping at Single Molecule Level Using Nanochannel Array for Structural Variation Analysis and de novo Assembly
报告人：Han Cao, PHD,  Founder & Chief Scientific Officer BioNano Genomics, Inc
时间：2013年4月12日，下午2:00
地点：遗传所一号楼210报告厅
联系人：刘铁燕 64806541

摘要：Despite continued cost reduction in raw base generation, improvement in base-calling accuracy, and recent advances in read length, complete de novo assembly and genome wide structural variant analysis of individual large complex genome remains expensive and challenging.

We present here a rapid genome wide analysis method based on the new NanoChannel Array technology (IrysTM System) that dynamically confines and linearizes extremely long DNA molecules for direct image analysis at tens of gigabases per run.  This high-throughput platform automates the imaging of genomic DNA hundreds to thousands of kilobases in length at single molecule level. High-resolution genome maps assembled de novo via unique sequence motif labeling, preserving long-range structural variation information, especially the highly repetitive regions, are intractable by current short read NGS platform. This information is independent of current sequencing biochemistry and algorithm with built-in long range haplotypes and can be very valuable to validate and finish past and future genomic sequencing assembly data. 

Here we report the assembly and analysis of complex regions and whole genome of various model genomes and several human genomes with this approach. Unlike sequence based paired end library approach that is cumbersome and biased towards detecting deletions than insertions, hundreds of large structural variations were uncovered without apparent bias due to its direct view approach.  We have corrected errors in previous assembly, spanned many of the remaining gaps, identified known and novel structural variants and phased haplotype blocks, including in the highly variable MHC region. We also discovered highly complex repetitive patterns previously unknown spanning large regions of genome in and near centromere and telomere regions. The technology and method would open new discoveries and change our view towards understanding genome architecture and functions.