A CMOS architecture allowing parallel DNA comparison for on-chip assembly

This paper introduces a CMOS based system that has been designed to allow parallel comparison of fragmented DNA sequences for on-chip assembly. The compatibility of different existing PC-based algorithms for implementation in CMOS is compared and the overlap-layout-consensus approach is found to be the most suitable one. The designed system comprises a scalable processing array capable of parallel computation, which allows identification of overlaps in DNA fragments in addition to error tolerance through dynamic programming. Analysis shows that there is a “pixel area vs computation time” trade-off when implementing such a parallel architecture. Results from a hypothetical assembly confirm good overlap detection and error tolerance, with up to 94% similarity in the detected overlaps, when the error is as much as 10%.

[1]  M. Ronaghi.  Pyrosequencing sheds light on DNA sequencing. , 2001, Genome research.

[2]  Eugene W. Myers,et al.  Computability of Models for Sequence Assembly , 2007, WABI.

[3]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[4]  Thomas LaFramboise,et al.  Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing , 2006, Nature Medicine.

[5]  Eugene W. Myers,et al.  The fragment assembly string graph , 2005, ECCB/JBI.

[6]  D. Mccormick.  Sequence the Human Genome , 1986, Bio/Technology.

[7]  Dan Gusfield.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[8]  P. Stankiewicz,et al.  Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. , 2010, The New England journal of medicine.

[9]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[10]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[11]  D. Bentley,et al.  Whole-genome re-sequencing. , 2006, Current opinion in genetics & development.

[12]  E. Mardis.  Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[13]  Piet Bergveld,et al.  Thirty years of ISFETOLOGY ☆: What happened in the past 30 years and what may happen in the next 30 years , 2003 .

[14]  S. Koren,et al.  Assembly algorithms for next-generation sequencing data. , 2010, Genomics.

[15]  Rui Jiang,et al.  Evaluation of next-generation sequencing software in mapping and assembly , 2011, Journal of Human Genetics.

[16]  Haixu Tang,et al.  A new approach to fragment assembly in DNA sequencing , 2001, RECOMB.

[17]  Mihai Pop,et al.  Genome assembly reborn: recent computational challenges , 2009, Briefings Bioinform..