New library construction method for single-cell genomes

PLoS One. 2017 Jul 19;12(7):e0181163. doi: 10.1371/journal.pone.0181163. eCollection 2017.

Abstract

A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments. The library is then amplified by a carefully optimized PCR protocol in a uniform and synchronized fashion for next-generation sequencing. Each step of the protocol can be quantitatively characterized. Our shallow sequencing data show that the library is tightly distributed and is useful for the determination of copy number variations.

MeSH terms

  • DNA Copy Number Variations
  • Gene Library*
  • Genome, Human*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Analysis, DNA / methods*

Grant support

Fluidigm provided financial support in the form of authors' salaries and research materials for the authors, LX, AB, SS, XW, HG, RA, and RF. Fluidigm did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the 'author contributions' section.