The primary responsibility of the Genomic Core will be to provide high-throughput sequencing support to the program using the Roche/454 Genome Sequencer FLX Titanium platform to determine the sequence variability in Human Leukocyte Antigen related genes (HLA/MIC) and to interrogate the repertoire of rearranged immunoglobulin (Ig) and T cell receptor (TcR) loci in samples isolated from the vaccine studies. More specifically the core will design and provide solutions for sample preparation for sequencing, run the 454/sequencer, offer comprehensive Laboratory Information Management System (LIMS) that will ensure sample tracking and data dissemination, and perform the primary analysis ofthe data.
The specific aims of this Genomics Core are: 1) Amplify and Sequence HLA Class I and II exons from patients. Sample preparation and novel exon amplification protocols that have been developed at the Stanford Genome Technology Center will be used to amplify selected HLA/MIC target sequences to determine sequence polymorphisms. Singleplex amplified exons from each patient will be pooled together and re-amplified with barcoded primer sequences design to be compatible with the 454/Sequencer. Up to 200 barcoded samples from individual participants in the vaccine studies will be pooled and sequenced in a single instrument run. 2) Analyze Exon sequences to determine the haplotype of exons. After the completion of each sequence run, the Genomics Core will compare each sequence to available reference sequences of HLA genes in the public database using our in-house tools that run on high-performance computational platforms, build the consensus sequence, and determine the haplotype for each HLA allele using the Assign SBT program. Both sequencing data and analysis results will be deposited into a central database and rendered through user-friendly web pages that will be available to the consortium. This web site can be made public when the steering committee decides to disseminate this information to the research community. 3) Analyze the sequences of VDJ recombination. An additional responsibility of the Genomics Core will be provide high-throughput sequencing support for rearranged immunoglobulin (Ig) and T cell receptor (TcR) loci, analyze those sequences for VDJ usage, and search for biologically significant patterns of VDJ sequences. A similar web site and database like these developed for HLA genotyping will be developed for both reviewing and sharing both sequence and sequence analysis results.
Accurate determination of the sequence of HLA/ MIC genes will provide the haplotype structure of each individual. This is the first critical step before the use of the data for association studies to determine the significance of each haplotype to vaccine response. In addition, analysis of the repertoire of (Ig and Ter) from individuals before and after vaccination will greatly improve our understanding of the immune response to vaccination.
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