Molecular Phenotyping and Genotyping Core

The objective of the Molecular Phenotyping and Genotyping Core is to support Joslin and external investigators in the study of molecular mechanisms of disease by providing equipment, expertise, and services in molecular phenotyping, including nucleic acid sequence analyses, gene expression, and other "-omics" analyses, which would be too specialized or costly for individual laboratories to perform independently. Formerly known as the Advanced Genomics and Genetics Core, the Molecular Phenotyping Core is newly-named in recognition of the expansion of its analytical capacities to reflect not only genetic and genomic analyses but also metabolic phenotyping. 

The Core's current services include:

  1. DNA purification: Extraction of high quality DNA from human specimens, including blood samples.

  2. DNA repository: 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: The Core provides a single nucleotide polymorphism (SNP) typing service based on the Applied Biosystems TaqMan SNP Genotyping Assays. 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.

  1. 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.

  1. DNA shearing: The Covaris E220 Ultrasonicator provides high quality shearing of 1 to 96 gDNA samples in a single run.

  1. Next-generation sequencing: The Core offers full service library prep and capture for custom designed or whole exome NGS projects. Sequencing of prepared libraries is completed through a collaboration with the Harvard Biopolymers Facility ​(https://genome.med.harvard.edu/services/nextgen/ViewOverview.action).

  1. Expression analysis: The Core houses an Affymetrix platform for microarray analysis. Core personnel can provide sample prep from RNA as well as hybridization for multiple species. Additionally, the Core facilitates submission of microarray studies to papers and expression databases such as GEO.

  1. PCR expression analysis: The Core houses two ABI 7900's (386 well) and one ABI 7000 (96-well).

  1. Education and training: The Core assists Joslin investigators using DNA repository panels in accessing the corresponding clinical data and exporting them in formats compatible with genetic analysis programs. Additionally, core personnel provide extensive informal assistance with experimental design, choice of array type or sequencing approaches, and troubleshooting for both array and PCR analysis hardware and software issues.  

New Services  

  1. Bioenergetics and molecular phenotyping: The Core houses an XFe96. This instrument can be used to analyze cultured cells, tissue explants, and whole blood samples though quantification of oxygen consumption and extracellular acidification (a surrogate for glycemic flux and metabolic flexibility).

  2. Genetic characterization for clinical studies: A next-gen sequencing assay has been developed by the Core to simultaneously screen all known mongenic diabetes genes (e.g. MODY, neonatal diabetes) for mutations and to type all known SNPs associated with T1D, T2D, and complications. This assay will allow the standardized collection of genetic data to study the influence of genetic variation on the response to treatments and exposures in interventional and observational studies at a reasonable price.

Coming Soon

  1. Digital qPCR

  1. Plasma proteomics: The Core has partnered with the BIDMC Proteomics Core to provide access to the Somalogic platform, an aptamer-based method that can  quantify over 1200 plasma proteins. (http://www.bidmc.org/Research/Core-Facilities/Genomics-Proteomics-Core.aspx)

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