Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics.
Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.
Ernest T
ET
Lam
Alex
A
Hastie
Chin
C
Lin
Dean
D
Ehrlich
Somes K
SK
Das
Michael D
MD
Austin
Paru
P
Deshpande
Han
H
Cao
Niranjan
N
Nagarajan
Ming
M
Xiao
Pui-Yan
PY
Kwok
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial; D005456:Fluorescent Dyes / Q000737:chemistry; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics; D046210:Microfluidic Analytical Techniques / Q000295:instrumentation*; D008969:Molecular Sequence Data; D036103:Nanotechnology / Q000295:instrumentation*; D059372:Nucleotide Motifs
D005456:Fluorescent Dyes