Single-Molecule Rapid Imaging of Linear Genomes in Nanochannel Array

Abstract

Human genomic structural variation (SV) is significant factor in genome complexity, and thus has substantial implications to the cause, development and progression of genetic diseases. These SVs, ranging in size of 1kbp-1Mbp, are challenging to assess with current technologies. As such, we have developed a commercial system (nanoAnalyzer® 1000) for the rapid linear analysis of genomes at single-molecule level.The core of our system is a nanofluidic chip consisting of an array of channels with a diameter less than 100 nm, nanofabricated on the surface of a silicon substrate. Thousands of unamplified genomic DNA molecules of 100’s kbps to several Mbps can be isolated and linearly streamed into the array for analysis in a parallel fashion. Fluorescently labeled sequence-specific signatures can then be identified and aligned to reference patterns at high resolution with custom software. This automated, multi-color imaging platform will enable a wide range of applications, such as accurate sequencing assembly, discovering genome structural variations, and uncovering epigenomic content. Nanochannel arrays promise to substantially lower the barriers of entry for single-molecule DNA analysis for scientists and clinicians, greatly impacting the advancement of molecular diagnostics, personalized medicine, and biomedical research.

High-throughput single-molecule mapping links subtelomeric variants and long-range haplotypes with specific telomeres

“…( 35 )). Standard deviations for molecular length measurement of similarly sized single molecules lacking telomeres using single-molecule mapping are typically ±250 bp ( 36 ).…”

Toward Single-Molecule Optical Mapping of the Epigenome

“…Despite the low-throughput of the method, it facilitates imaging on clean surfaces isolated from the sample and allows one to choose the properties of the surface . Approaches involving DNA stretching without fixation include (1) DNA stretching in nanochannels, driven by confinement due to the small dimensions of the channels; , (2) stretching by confinement in nanoslits; − and (3) stretching by stagnation point flow …”

Irys Extract

“…Applying sequence specific fluorescent labeling of the DNA and imaging the stretched molecules, results in an optical map for each DNA molecule reflecting the underlying sequence ( Das et al , 2010 ; Lam et al , 2012 ). This technology is geared toward analysis of DNA ranging in size between 10 kbp and 1 Mbp ( Austin et al , 2011 ), hence providing access to information on the individual gene length scale, with throughput of 200x coverage in about 24 hours ( Pang et al , 2017 ).…”