Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
| Autor: | Somes K. Das, Pui-Yan Kwok, Han Cao, Michael D. Austin, Ernest T. Lam, Niranjan Nagarajan, Paru Deshpande, Dean Ehrlich, Alex Hastie, Chin Lin, Ming Xiao |
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| Rok vydání: | 2012 |
| Předmět: |
Chromosomes
Artificial Bacterial 1.1 Normal biological development and functioning Molecular Sequence Data Biomedical Engineering Sequence assembly Bioengineering Computational biology Biology Applied Microbiology and Biotechnology Article Chromosomes Structural variation Major Histocompatibility Complex Gene mapping Underpinning research Consensus sequence Genetics Humans Nanotechnology Nucleotide Motifs Fluorescent Dyes Comparative genomics Bacterial artificial chromosome Contig Base Sequence Human Genome Bacterial Chromosome Mapping Microfluidic Analytical Techniques Haplotypes Artificial Molecular Medicine Generic health relevance Sequence motif Biotechnology |
| Zdroj: | Nature biotechnology, vol 30, iss 8 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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