WHOLE GENOME PROFILING & MAPPING

Whole Genome Profiling (WGP) is a technology invented and developed in partnership with Amplicon Express and KeyGene NV. This exciting technology was announced at the Plant & Animal Genome meetings in January 2009.


Basic overview of Whole Genome Profiling:

  1. Starting with a custom BAC library or BAC library clones you supply.
  2. Amplicon pools BAC clones in a systematic manner.
  3. Highly purified BAC DNA is prepared then digested with endonuclease enzyme and tags/labels are added to the ends of the fragments.
  4. These pools of labeled BAC DNA are run on Illumina-Solexa GA II instruments, generating giga-bases of DNA sequence data of ~30 bp reads every ~4 to 6 Kb across all the BAC clones.
  5. The sequence data are processed and analyzed by an optimized FPC software program to build BAC contigs across the entire genome.
  6. The BAC contigs are linked by the DNA Sequence tags, with very stringent parameters, so you can trust the ultra high density Physical Map is accurate and reliable.
  7. Because the WGP data are sequence based, they can be combine with existing Whole Genome Sequencing data. Thus giving super structure of contigs for random reads to align.

The final WGP deliverables are: a data carrier (disk or laptop) with all the WGP sequence data loaded, the FPC program is installed/optimized and ready to analyze the data (in addition to the living BAC clones on 384-well plates- if a custom BAC library is made).


WHY WGP IS BETTER than SnapShot or other mapping/fingerprinting technologies: the BAC clones are assembled into contigs which are linked together by SEQUENCES! Not by fragment lengths as with other fingerprinting technologies. Fragment length data are not sequence based, so they cannot be added directly to existing whole genome sequencing project.


With WGP- when a region of interest if found in the sequence data, then you immediately have the BAC clone address (for deep sequencing or down stream experiments).


COMPLETED WGP PROJECTS: In summer 2008, we validated WGP on Arabidopsis (as a proof of principle), then a few months later de novo sequenced a 450 Mbp melon genome using WGP. Since then we have completed, or are in the process of finishing genomes as large as 4,000 Mbp


WGP is the perfect technology to accompany/augment a Whole Genome Sequencing project or WGP data can stand alone as an ultra accurate high density physical map


Whole Genome Profiling and Whole Genome Sequencing

Restriction fragments with 30 bp reads on each end whole genome profiling