Core Personnel:

Mark Daly, PhD
Co-Director
mjdaly@chgr.mgh.harvard.edu
Curtis Huttenhower, PhD
Co-Director
chuttenh@hsph.harvard.edu
Aylwin Ng, PhD
Associate Director
Daniel MacArthur, PhD
Consultant
Elizabeth Andrews
Clinical Research Project Manager
eaandrews@mgh.harvard.edu
Christine Stevens
Project Manager
stevens@broadinstitute.org

 

Overview:

To most efficiently serve the CSIBD community, the former standalone Genetics, Genomics and Molecular Biology Core has been integrated with microbiome research activities (formerly centered in the Clinical/Tissue Core) to form the CSIBD Human Genetics and Microbiome Core. The Core continues to bring a variety of cutting-edge techniques in genetics/genomics and computational resources, while expanding its activities toward fully integrating cutting-edge microbiome research services. This core provides current and emerging technologies, pursues robust performance at the highest quality standards, and is committed to drive development toward future needs. The services are broadly divided between training and education, access to tools for molecular biology and ‘omics data generation, and computational resources for data analysis. In addition to building and supporting a vibrant community around a common interest, the leadership’s involvement in large-scale research projects worldwide also results in early access to emerging results.

The objectives of the Human Genetics and Microbiome Core are as follows:

  1. Facilitate the application of advanced experimental platforms for genetics, genomics and high-throughput data analysis to discovery efforts relevant to IBD
  2. Provide a centralized facility and personnel for performing state-of-the-art recombinant and PCR-based DNA procedures and RNA interference and provide cost-effective and high-quality molecular biology reagents and services including nucleic acid probes, expression plasmids, reporter gene constructs, viral vectors, real-time PCR, mutagenesis, expertise for differential mRNA display analysis, RNA purification for DNA microarray analysis, CRISPR reagents and facilitated access to bioinformatics support
  3. Provide a resource for disseminating a wide range of molecular biology, genetic and bioinformatics technologies
  4. Provide an end-to-end sampling and multi’omic profiling system for the host and microbiota in IBD and gastrointestinal disease
  5. Provide computational resources to analyze and interpret the microbiome in health and gastrointestinal disease
  6. Develop cutting-edge solutions in microbiome research that will drive therapeutic discovery

Available services:

  • Consultation and training. Central to all services are formal and informal end-to-end consultations on experimental design, data generation and bioinformatics analysis. A variety of training opportunities and workshops are also offered to aid investigators in study design and data analysis from genetics-, genomics- and microbiome-based projects. For experimental work, full access to protocols and reagents for sophisticated molecular biology approaches is provided.

  • Bioinformatics support. A team of bioinformaticists and software developers with in-depth expertise are available within the Core to provide collaborative capacity for data analysis. For data from human genetics assays, this includes handling RNA-Seq, data from the Landmark 1000 platform, metabolomics assays, EST profiling and pathway reconstruction tools. For microbiome data, this includes analysis of taxonomic and functional composition using tools available from the www.huttenhower.org/biobakery platform, other microbiome analysis platforms and novel tools such as profiling of individual strains present in metagenomics data.

  • Tools for molecular biology:

    • Routine molecular biology tools including PCR, DNA procedures, oligonucleotide synthesis, real-time qPCR, and microsatellite fragment analysis
    • Resource-intensive methodologies including cDNA library prep and siRNA/shRNA and CRISPR screens
    • Genotyping and DNA fragment analysis
    • Complete plasmid and RNA sequencing using next-generation sequencing
    • Repository of BACs, plasmids, libraries, RNA samples and probes
    • Access to the Landmark 1000 platform (L1000) that quantitates 1000 transcripts using a multiplexed Luminex bead assay and genomic run-on sequencing (GRO-Seq) to identify the genes that are being transcribed at a given time point
    • Gene profiling services by deep sequencing as an alternative to microarray analysis
  • Microbiome data generation:
    • Coordinated sample collection from patients, de-identified receipt and sample handling (portioning and long term storage)
    • Clinical sample receipt and handling for gut mucosal tissue and blood samples
    • High-throughput nucleotide extraction of microbiome samples
    • Metabolite profiling of microbiome samples
    • High-throughput 16S rRNA sequencing
    • DNA library construction and deep shotgun sequencing
    • RNA library construction, rRNA depletion and deep shotgun sequencing

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