Sequencing Core

Contact: Bill Hulme, whulme@med.miami.edu

Current ABI sequencing equipment includes: a) one 3730xl 96 array capillary high-throughput sequencer and one 3130 xl intermediate through-put capillary sequencer and a total of 10 ABI 9700 and 20 ABI 9800 PCR machines. A sequencing center has been set up in room 143 A bldg on South campus and sequencing will be carried out using CGT personnel.

Initial screening for copy number variants can be derived from analysis of the Illumina WGA SNP data. Deletions and/or duplications (in/del) can be detected by signal intensity variation from individual SNPs. Given the standard criteria that 5-6 contiguous SNPs ( on average spaced about every 2.7 kb along a chromosome) with either decreased (putative deletion) or increased signal (putative duplication) intensity relative to control may indicate the presence of a potential in/del.

Gene Expression
For gene expression studies the CGT possesses two primary platforms: the Affymetrix Gene Chip 3000 complete genotyping and expression platforms and a complete Agilent array system provided by the Miller School of Medicine DNA Microarray Core Facility.
All forms of expression array, etc. analysis can be supported by these two platforms. In addition and as outlined above, the CGT is capable of supporting, through existing platforms, both Nimblegen and Illumina gene expression studies

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