The challenges of sequencing by synthesis

Nat Biotechnol. 2009 Nov;27(11):1013-23. doi: 10.1038/nbt.1585. Epub 2009 Nov 6.


DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Animals
  • DNA / biosynthesis*
  • Fluorescent Dyes
  • Humans
  • Optical Phenomena
  • Sequence Analysis, DNA / instrumentation
  • Sequence Analysis, DNA / methods*
  • Substrate Specificity
  • Surface Properties


  • Fluorescent Dyes
  • DNA