Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

• Published in: Nature biotechnology Vol. 30; no. 8; pp. 771 - 776
• Main Authors: Lam, Ernest T, Hastie, Alex, Lin, Chin, Ehrlich, Dean, Das, Somes K, Austin, Michael D, Deshpande, Paru, Cao, Han, Nagarajan, Niranjan, Xiao, Ming, Kwok, Pui-Yan
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-08-2012; Nature Publishing Group
• Subjects: 631/1647/1513/1382; 631/208/726/649/2157; 631/61/350; 631/61/514/2254; Agriculture; Base Sequence; Bioinformatics; Biological and medical sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Chromosome Mapping - methods; Chromosomes; Chromosomes, Artificial, Bacterial; Copy number variations; Deoxyribonucleic acid; Diverse techniques; DNA; DNA sequencing; Fluorescence; Fluorescent Dyes - chemistry; Fundamental and applied biological sciences. Psychology; Gene mapping; Genomes; Genomics; Haplotypes; Haplotypes - genetics; Humans; Life Sciences; Major histocompatibility complex; Major Histocompatibility Complex - genetics; Microfluidic Analytical Techniques - instrumentation; Molecular and cellular biology; Molecular Sequence Data; Nanotechnology - instrumentation; Nucleotide Motifs; Nucleotide sequencing; Physiological aspects; Scientific imaging; Silicon; United States; Genetic mapping; Technique; Genome; Imagery; Structural analysis
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.2303

Optical maps of a genome, which are generated by imaging labeled single molecules of DNA, facilitate structural variation analysis and sequence assembly. Lam
et al
. immobilize DNA molecules in nanoscale channels, increasing the accuracy and throughput of the mapping process.
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.