Cores

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Bioinformatics Core

The Bioinformatics Core provides the computational infrastructure to facilitate efficient and seamless informational cross-talk between the different Cores of the Genomics Program. Additionally, we offer individualized support and collaboration in the design of integrative genomics studies and data analysis-interpretation with study projects using any Genomics Core. Our scope of work includes:

  • Reviewing all relevant statistical and bioinformatical considerations prior to the implementation of multi-factorial genome-scale studies.
  • Maintaining a secure, web-accessible and MIAME-compliant database for molecular data (e.g., genotype, RNA expression profile) storage, curation and basic data analysis.
  • Implementing state-of-the-art data analyses and mathematical models of molecular data (genome, transcriptome, proteome, phenome) to optimally address the specific aims of respective study projects using the Genomics Cores.
  • Taking an integrative genomics approach to data analysis. For example, when and where relevant, external bio-data from the public domain (e.g., NIH-NCBI's Gene Expression Omnibus and EMBL-EBI's ArrayExpress) will be included in our analyses, serving both as rational means of in silico validation (via independent test datasets) and for prioritizing candidate molecules/pathways for further functional validation in the laboratory.
  • Scientific collaborations with study projects using the Genomics Cores.

Flow Cytometry Core

The Cell Sorter Core offers state-of-the-art sorting applications in a manner that is cost effective, carefully controlled, and a nidus for collaborations. This flow cytometry and sorting facility has been available to investigators of the MRRC since 1978 and reflects the exceptional benefit to this MRRC of our relationships with the Howard Hughes Medical Institute (HHMI), which has shared in the purchase and maintenance of our Vantage SE high speed sorter. Investigators use the cell sorter for a wide range of applications, including flow karyotyping, chromosome sorting, cell cycle analysis, stem cell isolation, green fluorescent protein (GFP) containing cell sorting, and immunocytochemistry.

Click here to go to the Flow Cytometry Core website.

Molecular Genetics Core

The Molecular Genetics Core Facility provides high quality DNA sequence data from cloned DNA fragments in various vectors and from PCR-generated fragments. We also offer a microsatellite and single nucleotide polymorphism (SNP) marker genotyping service that includes genome-wide screening of families or sib-pairs for linkage to inherited disorders.

Click here to go to the Molecular Genetics Core website.

Phenotyping Core

The Program in Genomics at Children's Hospital Boston provides the infrastructure for investigators to carry out projects aimed at genotyping and phenotyping individuals with a particular disease and their family members. The Phenotyping Core of the Program works with investigators to develop and coordinate these genotype-phenotype studies. The Core staff of geneticists and genetic counselors provides expertise on phenotyping, data collection, informatics including database management, and statistical support. Professional staff is also available to assist with grant writing.

Study Design

Potential investigators consult with the Phenotyping Core Director and the Supervisor of Genetic Research and Development to discuss the details of the project proposed. Topics to be covered by this interaction include the following:

  • Define and characterize the project
  • Identify patient population for study (inclusion and exclusion criteria)
  • Establish the criteria for a well-defined phenotype
  • Define environmental and lifestyle risk factors to be studied
  • Identify studies to be done and what studies are part of "routine clinical care" and which are research
  • Determine the most appropriate approach to the genetic analysis (eg. linkage analysis vs. sib-pair analysis, candidate gene approach vs. genome-wide scanning, etc.)
  • Create data collection forms
  • Assist the investigator in obtaining approval from the Children's Hospital Boston IRB

Project Implementation

The Phenotyping Core identifies and trains a genetic counselor who works with the investigator on patient recruitment, informed consent, collection of medical/family history and sample ascertainment. The Core provides space and facilities within the Clinical and Translational Study Unit (CTSU) at Children's Hospital Boston for patient evaluation, additional studies necessary for phenotyping and sample collection for genotyping and gene expression analysis.

The "flow" of any given study is generally as follows: Patients come to the CTSU for a visit with the genetic counselor who conducts the informed consent process, elicits the medical/family history, and addresses any participant questions. Additional phenotyping information is gathered at that time. The patient then has laboratory tests performed as indicated (for DNA/RNA and any other studies needed) and other specialized studies performed as needed (DXA scan, nutritional evaluation, etc.). Samples are processed in the Program in Genomics Core Laboratory for DNA and RNA extraction and storage. The Laboratory Director of the Molecular Genetics Core Facility works with investigators to direct the wet lab studies in the directions necessary to obtain short-term and long-term genotypic and gene expression data.

 

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