Automated Sample Handling and QA/QC
Automated DNA/RNA purification from a variety of sample sources is being accomplished with a Qiagen BioRobot Universal system. All Qiagen 96-well format kits (DNAEasy, RNAEasy, PAXGene blood DNA etc) can be automated on this robot to achieve high-quality DNA/RNA extractions and consistent results. BioRobot Universal is also used to perform liquid handling tasks including sample normalization , PCR reaction setup, PCR clean up.. One run ranges from 1 to 5 hours.
AutoPure LS is used for large-scale genomic DNA extraction from clinical samples such as whole blood, buffy coat etc. One run (16 samples) usually requires less than 4 hours.
Agilent Bioanalyzer is used for rapid quantitation and quality assessment on DNA/RNA samples including PCR products.
Multiplex SNP Genotyping
Illumina's BeadXpress reader is supported at the Center for medium-throughput, targeted genotyping projects, allowing 96 or 384 multiplexed SNP assays using GoldenGate chemistry on Veracode beads with samples in the 96-well plate format. One run takes 2-3 days. GoldenGate assays for gene expression, DNA methylation, and protein analysis are also available.
A MAUI hybridization station (Nimblegen) and an Agilent scanner are available in the Center for all microarray application, including gene expression profiling, high-density comparative genomic hybridization (CGH), DNA methylation, and CHIP-chip. The scanner can be used for Agilent and Niblegen microarrays (Illumina and Affymetrix array cannot be read on this scanner). One run takes 2-4 days.
Another recently developed application of the microarray technology is targeted genomic region enrichment for next generation sequencing. The MAUI hybridization station can be used to accomplish this on Nimblegen custom sequence capture arrays. One run takes 3-5 days.
Capillary DNA Sequencing
Capillary DNA sequencing at the Center is carried out on an Applied Biosystems 96-capillary 3730XL DNA analyzer, which is the most advanced capillary sequencing platform available today, using the BigDye Terminator v3.1 cycle sequencing chemistry. High quality reads up to 800 nt can be routinely achieved. One run can usually be finished in 24 hrs.
The Center currently has an Applied Biosystems SOLiD next-generation sequencer which enables highly accurate and massively parallel genomic analysis. Next-generation sequencing holds great promise to facilitate characterization of the entire genome, transcriptome and epigenome, with specific applications including targeted resequencing, whole genome resequencing, small RNA analysis, gene expression analysis, chromatin immunoprecipitation and methylation analysis. One run ranges from 7-14 days.
Genotyping, sequencing, gene expression or next-generation sequencing can be intensive and generate massive amount of data. The Center has its own computer resources and will provide short term data storage and will work with investigators on specific data transfer plans for the projects.