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Journal article
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
Nature biotechnology, v 30(8), pp 771-776
01 Aug 2012
PMID: 22797562
Abstract
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 114x 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.
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Details
- Title
- Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly
- Creators
- Ernest T. Lam - University of California, San FranciscoAlex Hastie - BioNano Genomics (United States)Chin Lin - University of California, San FranciscoDean Ehrlich - University of California, San FranciscoSomes K. Das - BioNano Genomics (United States)Michael D. Austin - BioNano Genomics (United States)Paru Deshpande - BioNano Genomics (United States)Han Cao - BioNano Genomics (United States)Niranjan Nagarajan - Genome Institute of SingaporeMing Xiao - BioNano Genomics (United States)Pui-Yan Kwok - University of California, San Francisco
- Publication Details
- Nature biotechnology, v 30(8), pp 771-776
- Publisher
- Springer Nature
- Number of pages
- 6
- Grant note
- T32 GM007175 / NIH Training Grant; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA T32GM007175 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) R01 HG005946 / US National Institutes of Health (NIH) award R01HG005946 / NATIONAL HUMAN GENOME RESEARCH INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Human Genome Research Institute (NHGRI)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000307416900020
- Scopus ID
- 2-s2.0-84864883566
- Other Identifier
- 991019167747904721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biotechnology & Applied Microbiology