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Genomics

The purpose of the Genomics Shared Resource is to offer expertise in genomic analysis, with a focus on providing nucleic acid extraction, genotyping and expression profiling services in support of the peer-reviewed and Internal Review Board-approved research. A variety of assays are performed on samples collected in epidemiological, clinical, and basic science studies that take advantage of the genetic heterogeneity of Hawaii and California multiethnic populations. The goal is to translate information now available on the human genome into new knowledge about cancer etiology, prevention and treatment.

The resource is a central service that uses cutting-edge and high-throughput technologies. Personnel are knowledgeable in molecular biology and genetics, and can provide both novice and advanced users a level of technical support and consultation not found in Hawaii outside the resource. Personnel can also provide planning and consultation during project execution. Services offered include:

  1. DNA/RNA isolation and quality analysis
  2. Custom genotyping
  3. Gene expression analysis (including miRNAs)
  4. DNA copy number analysis
  5. Methylation analysis

Nucleic acids are extracted from whole blood, “buffy coat,” clot, mouthwash, buccal cell/saliva, cell lines and fresh tissue as well as paraffin-embedded tissue samples. The resource is also equipped with ultra low sample volume RNA/DNA quantification equipment (NanoDrop) and chip-based RNA quality measurement system (Bioanalyzer).

The TaqMan-based genotyping assays performed by the resource laboratory have included those for a large number of polymorphism in genes involved in DNA synthesis or repair, cell proliferation, or metabolism of xenobiotics, nutrients, or endogenous hormones. Tumor samples have also been tested for microsatellite instability and DNA mismatch repair gene mutations. A high-throughput genotyping platform, TaqMan OpenArray, utilizes the TaqMan chemistry in a 33nl reaction volume resulting in better cost-efficiency than the traditional TaqMan genotyping for studies of 960 samples and up. For whole genome SNP genotyping and DNA copy number analysis the resource offers services using the Affymetrix GeneChip and Illumina systems. Whole genome and individual gene expression profiling is offered on the Affymetrix and Illumina platforms or by real-time qPCR, respectively. The resource has recently expanded to epigenetic analyses of RNA and DNA.

The resource also develops protocols to facilitate the collection, long-term availability, and analysis of genetic material for molecular epidemiologic and translational research. A simple, non-invasive mouthwash method was developed to collect genomic DNA from buccal cells, a method now used worldwide. Other work focuses on isolating RNA and miRNAs for gene expression studies from whole blood, blood cell fractions, oral mucosa/saliva and archived fixed tissue.

Faculty Director:

Maarit Tiirikainen, PhD
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