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Genomics and Bioinformatics

The Genomics and Bioinformatics Shared Resource (GBSR) offers a central service that uses cutting-edge and high-throughput genomic technologies combined with expert data analysis. The principal goal for the GBSR is to provide timely, affordable, high quality genomic analyses and a wide range of bioinformatic services with a fast turnaround, as well as technical and scientific consultation, collaboration and initial data interpretation to all UHCC members at large, with a priority given to investigators with federal funding for cancer-related projects. The GBSR personnel has broad expertise in molecular biology, genetics, genomics and bioinformatics, and can provide project planning, advice, and troubleshooting during the execution of the project.

As a combined Genomics and Bioinformatics SR, led by two Co-Directors with complementing expertise, we now provide a convenient one stop service for a complete genomic analysis workflow; from the experimental design support, via biospecimen extraction and analysis, to the delivery of the analyzed data. The new bioinformatics component greatly enhances the capacity and depth of high-throughput omics data analysis services at the Center. The Genomics component is led by Dr. Maarit Tiirikainen who has over 20 years of experience in Cancer Genomics. The Bioinformatics component is led by Dr. Youping Deng, Professor of Bioinformatics at the John A. Burns School of Medicine (JABSOM), who has more than 16 years of experience in bioinformatic data analysis and management.

Services of the Genomics Laboratory include:

  1. DNA/RNA isolation, quantification and quality analysis
  2. DNA genotyping and copy number analysis
  3. Gene expression analysis (coding/non-coding)
  4. DNA methylation analysis
  5. Consultation for the services above

Nucleic acids are extracted from whole blood or different blood components, mouthwash, buccal cell/saliva, cell lines and fresh/frozen tissue as well as paraffin-embedded tissue samples. The genomic analyses are provided on various analytical platforms; by utilizing PCR, microarray or Next Generation Sequencing (NGS)-based approaches. The resource is equipped with qPCR instruments, Affymetrix and Illumina microarray systems, and the Illumina NextSeq 500.

The Bioinformatics component in GBSR provides expert and timely bioinformatics consulting, analysis, collaborative research, management, and training solutions for high-throughput data. The core provides a high-level expertise in bioinformatics, ensuring the support needed to design, conduct, analyze, interpret, and manage results requiring or facilitated by informatics applications. The bioinformatics services cover a wide range of molecular analyses of omics data (e.g. genomics, transcriptomics, epigenomics, metagenomics, proteomics, metabolomics) as well as systems biology. Data to be analyzed can originate in several of the UHCC resources such as the Genomics Laboratory of the GBSR, Metabolomics Shared Resource (MeSR), and the Microscopy and Imaging core.

The Bioinformatics Analytical Services include:

  1. Microarray data analysis including genotyping, gene expression and methylation arrays.
  2. NGS data analysis
  3. Gene pattern, function analysis, systems biology and gene network modeling
  4. Multivariate biomarker identification and classification
  5. Proteomics data and Protein array data analysis
  6. Metabolomics data analysis
  7. Image data analysis

Other bioinformatics services offered include Data Collection and Management; Database support for web based activities; Human-Computer Interface (HCI); Electronic medical record abstraction; and Programming Support.

Faculty Co-Directors:

Maarit Tiirikainen, PhD
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Youping Deng, PhD
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