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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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Resolving the complexity of the human genome using single-molecule sequencing.

Mark J P Chaisson1, John Huddleston2, Megan Y Dennis1

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.

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New sequencing technology resolves gaps and reveals complex variations in the human genome. This advancement improves our understanding of repetitive DNA and structural variants, enhancing the human reference genome.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The human genome reference assembly, despite its completeness, contains over 160 euchromatic gaps.
  • Structural variation within the human genome remains incompletely understood a decade after its initial completion.

Purpose of the Study:

  • To identify missing genomic sequences and genetic variations.
  • To leverage long-read sequencing technology for a more comprehensive human genome analysis.

Main Methods:

  • Sequencing and analysis of a haploid human genome (CHM1) using single-molecule, real-time (SMRT) DNA sequencing.
  • Base-pair level resolution of euchromatic structural variants.

Main Results:

  • Closed or extended 55% of remaining interstitial gaps in the GRCh37 reference genome, many containing long, degenerate short tandem repeats within G+C-rich regions.
  • Resolved 26,079 euchromatic structural variants, including inversions, complex insertions, and long tandem repeats, with high sensitivity for events <5 kilobases.
  • Identified a 3:1 insertional bias in regions with complex insertions and long short tandem repeats compared to the human reference.

Conclusions:

  • Longer-read sequencing technology can resolve previously inaccessible complex repetitive DNA.
  • The human genome exhibits greater complexity in its structural variation, particularly concerning longer and more intricate repetitive elements.
  • This study significantly enhances the characterization of the human genome's structural diversity.