Project Goals - Beckman CEQ Collaboration

    Our collaboration with Beckman-Coulter Instruments is to work together to explore the use of the CEQ capillary sequencer for various applications.  This includes investigating the ruggedness of the protocols to reproducibility to new software tools and modifications.

Original Goals:

• Sequence 1 human BAC of ~100kb in size
• Sequence 1 mouse BAC of ~100kb in size
• Develop methods to rapidly process samples
• Investigate performance of CEQ for various samples, contaminates, etc.
• Develop new methods for sample extraction, preparation, handling on the Biomek 2000
• Demonstrate SNP detection on the CEQ
• Use the CEQ to perform various sequencing experiments
• Provide Beckman Coulter with valuable feedback on the instrument, protocols and software

Current Goals:  The primary objectives are to use the CEQ in production experiments, demonstrate its utility in hard to read sequences (repeat expansions and their polymorphisms), and to demonstrate its ease in use in identifying new SNPs with custom software.

• Sequence a collection of mouse BACs.  This 941kb contig is in final finishing.  Done in collaboration with Dr. Ward Wakeland. (~25,000 reads)
• Provide Beckman Coulter with reads of known consensus sequence, in this case, the e. coli contamination reads from all shotgun sequencing projects.  (~10,000 - 15,000 reads)
• To sequence >25 regions in the dog genome.  PCR products are generated from a large number of dog breeds.
• To sequence a large number (~1/week) of human regions with simple sequence repeats.  Each will be done for a matched set of clinical derived DNA samples.
• To write a software package to run on the CEQ NT computer to detect SNPs by identifying high quality discrepancies in a multiple alignment.