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New Technologies Unique to Kuakini Medical Center

Kuakini Medical Center continues to remain at the forefront of biomedical research with the recent addition of two new machines for its Genetics Laboratory.

Kuakini Genetics Laboratory is now the first research department in the state of Hawaii to own the QuantStudio 12K Flex, which is instrumental for deciphering the huge number of single nucleotide variations that can be associated with diseases and personal characteristics.

Kuakini Genetics Laboratory is also the second research department in Hawaii to own an Ion Torrent Personal Genome Machine (PGM), which is used for next-generation DNA sequencing and can process these sequencing results in a fraction of the time compared to previous methods.

Already receiving local, national and international recognition for its genetic research, Kuakini can extend its lead in the research of aging, longevity, and the study of age-related diseases with the addition of these two new pieces of equipment. The Kuakini Honolulu Heart Program (Kuakini HHP) and the Kuakini Honolulu-Asia Aging Study have been continuously collecting data from its research participants since 1965. More than 8,000 American men of Japanese ancestry were the original participants in the Kuakini HHP, and the two new pieces of equipment will enhance the research on data supplied by these participants.

Dr. Timothy Donlon, Director of the Kuakini Genetics Laboratory, provided these instrument details:

QuantStudio 12K Flex

The QuantStudio 12K Flex System sets a new standard for automated analysis for large genotyping and gene expression studies. The streamlined OpenArray®* workflow helps save time and resources compared to running experiments in multiple plates on multiple systems. The QuantStudio 12K Flex system can produce up to 110,000 data points or more within an 8-hour day with minimal training, no third-party robotics and in as little as 20 minutes of hands-on time per run.

This system will perform the following types of genetic analyses:

• Gene expression analysis. TaqMan®** Gene Expression Assays are the most comprehensive set of quantitative gene expression assays available, providing more than 1.3 million primer/probe sets for 23 species. Custom assays are available for studying the expression of any gene or splice variant in any organism.

• SNP genotyping. The precision of TaqMan® chemistry makes SNP genotyping studies easy. There are over 4.5 million predesigned human and mouse TaqMan® SNP Genotyping Assays and 2,700 TaqMan® DME (Drug Metabolizing Enzymes) Genotyping Assays, or Custom TaqMan® SNP Genotyping Assays, in various sizes.

• Copy number analysis. TaqMan® Copy Number Assays*** are a collection of over 1.6 million predesigned assays with coverage of the entire human genome (DNA in the cell), over 180,000 assays targeting exons for mouse, and Custom Plus and standard Custom TaqMan® Copy Number Assays when a predesigned assay is not readily available.

• Digital PCR technology. Ideal for sensitive detection of rare targets such as in cancer mutations, viruses, and GMO (Genetically Modified Organisms) detection. In digital PCR, reactions are split into hundreds to thousands of mini-reactions to provide a digital readout of real-time PCR results.

• castPCRTM technology. TaqMan® Mutation Detection Assays are designed to detect and measure DNA mutations with extremely high specificity against a background of wild- type genomic DNA (gDNA, i.e. genomic DNA). These assays are powered by competitive allele-specific TaqMan® PCR technology, known as castPCRTM technology, for detection of mutations present at less than 0.1% in gDNA (genomic (nuclear) DNA).

• MicroRNA**** and other noncoding RNA analysis. Innovative TaqMan® Assays and tools are available for long noncoding RNA quantification, miRNA profiling, pri-miRNA quantification, small RNA quantification, and targeted miRNA quantification.

Ion Torrent Personal Genome Machine: for “Next Generation DNA Sequencing”

The sequencing of DNA has become a mainstay of genetic epidemiologic study to find the causes of disease, both rare and common, and to provide therapies that are targeted to the individual patient. Strategies for sequencing someone’s DNA can involve either all of the “protein coding” regions of their genome, referred to as “whole exome sequencing,” or it can involve a targeted approach, in which a select number of genes are scanned from a patient’s genome.

The Personal Genome Machine provides rapid (less than 3 hours) results for the sequencing of gene panels that are found in specific diseases. For example, familial breast cancer is now known to include more than several dozen genes. This instrument will deliver up to 10 Gb (10,000,000,000 base pairs) of DNA sequencing results. Since the data are overlapping, it generally includes about 1,000,000 bp, or the equivalent of about 40 genes. This information can be gained from as little as 10 ng (0.000,000,010 gram) of DNA.

DNA sequencing is accomplished using a chip that detects specific changes in pH as the DNA sequence is “read.” Improvements in chip technology, similar to that evolving in the computer industry, will lead to improvements in the amount and quality of DNA sequence data, without having to develop a whole new instrument. These new improved chips can be used in the existing instrument.

* OpenArray is a system that can examine as few as 16 and as many as 256 genetic changes (i.e. genotypes) at once on a single array.

** TaqMan® is a method of measuring genetic differences in a single tube (reaction) using the system of PCR (polymerase chain reaction) which is a method of amplifying DNA from a small amount so that the precious DNA is not consumed all at once.

*** Some genes are known to be involved in changes in copy number, such as deletions and duplications. This is particularly prevalent in cancer.

**** microRNAs are now known to modify the expression of some genes, such as those involved in cancer progression.