The Joslin Advanced Genomics and Genetics Core (AGGC) originates from the merging of the Joslin Genomics and Genetics Cores in response to the evolving scientific and technological landscape based on (1) the recognition that gene expression changes are mostly responsible for genetic predisposition to complex disorders and (2) the advent of new sequencing technologies providing a unified framework for DNA and RNA studies.
The new Core continues to provide services for genetic and genomic analysis, including DNA extraction from blood, access to DNA collections from the Core’s repository, SNP genotyping, and support for gene expression studies based on both high-density oligonucleotide arrays and real-time quantitative PCR.
However, its defining objective is to serve as an interface between Joslin investigators and next-generation sequencing by providing assistance with the complex protocols that must be accomplished in order to generate ready-to-sequence samples and which are often a barrier to sequencing approaches.
1. Extraction of high-quality DNA from human specimens. The Core extracts DNA from blood samples collected by Joslin investigators as part of their projects.
2. Distribution of DNA samples. The Core repository currently includes about 6,000 DNA samples organized in eight panels, some of which include special forms of diabetes not available in other collections.
3. SNP genotyping service. The Core provides a single nucleotide polymorphism (SNP) typing service for projects including up to 256 SNPs. Typically, these are SNPs that have been identified by genome-wide association studies (GWAS) or resequencing projects as being associated with diabetes or its complications, and for which replication is being sought in other studies.
4. Training, management and analysis of genetic data. The Core assists Joslin investigators using the DNA panels in accessing the corresponding clinical data and exporting them in formats compatible with genetic analysis programs. It also provides advice on the design of genetic studies and the analysis of genetic data through the Core Director Dr. Doria – a genetic epidemiologist.
5. Microarray expression analysis. The Core assists Joslin investigators wishing to perform expression analysis using the Affymetrix platform by cRNA preparation and experimental and test array hybridization. Arrays are processed in the fluidics instrument and scanned on the Gene Chip Scanner 3000, allowing analysis of all current Affymetrix platform arrays including exon and X3P arrays. Initial data analysis is facilitated by close interactions with the Bioinformatics Core.
6. PCR expression analysis. For PCR analysis of expression and/or allelic discrimination protocols, research staff within individual laboratories may utilize core equipment independently. Core staff provides training for new users, assistance with troubleshooting and methodological questions, and optimization and maintenance of equipment.
7. Education and training in genomics techniques. Genomics Core staff meet regularly with investigators and fellows to discuss experimental design, choice of microarrays best suited for the specific experiment planned, and sample number and quality and assists in analysis and interpretation of data.
8. Bioanalyzer quantification of DNA/RNA samples. The core provides sizing, quantitation, and quality control services of DNA and RNA samples using the Agilent 2100 Bioanalyzer system. This is often used in preparation for high-throughput sequencing, or other expression analysis.
9. DNA shearing. The Covaris E220 Ultrasonicator may be used to process 1 to 96 samples in a single run.
10. Next-generation sequencing. The Core’s goal is to assist Joslin investigators with all the tasks that must be accomplished in order to generate ready-to-sequence samples (i.e., samples that can be directly submitted to a next-gen sequencing platform without further processing). Specifically, the Core will provide assistance with 1) design of sequencing assays; 2) preparation of sequencing libraries from DNA and RNA samples provided by Joslin investigators; 3) in-house low-output next-gen sequencing; 4) access to high-output next-gen sequencing platforms at external cores.