Instruments of Progress
Pelotonia Funds Help Purchase Sophisticated Technology and Preserve Priceless Tissue Samples
Progress in cancer research – the process of moving from an observation made in the laboratory or clinic to discoveries that help patients – requires expensive technology and priceless biological samples such as tumor tissue and blood from patients. These samples must be stored under stringent conditions to preserve the fragile molecules their cells contain.
Pelotonia funds this past year were used in both areas. They supported the purchase of instruments that help decode cancer genomes, and a system that helps keep precious tissue samples viable for research. These examples of equipment purchased in 2013 with support from Pelotonia can benefit the more than 300 investigators at the OSUCCC – James.
Sciclone NGS Wokrstation
The Sciclone NGS (Next Generation Sequencing) Workstation fits on the laboratory bench and can robotically prepare batches of cancer samples for high-throughput genome sequencing. Genome sequencing reveals how cancer hijacks normal cell functions via mutations and other structural changes in DNA and RNA.
The device helps convert long lengths of DNA extracted from cancer cells into short pieces that are readable by high-throughput sequencers. The resulting collection of DNA fragments is called a sequencing library.
To generate a sequencing library, scientists first extract DNA from cancer cells, break it into fragments and attach the fragments to tiny metal beads. The goal is to duplicate, or amplify, the number of fragments in preparation for sequencing. Producing high-quality sequencing libraries is a tedious process that can involve more than a dozen steps, each of which must be done with precision.
Enter the robotic device. The instrument uses a magnet to gather the DNA-laden metal beads together, then uses multiple pipette tips to draw off the used solution and replace it with reagent needed for the next step.
The robotic system can prepare eight to 96 samples at a time while ensuring consistency and freeing lab personnel for other tasks.
OSUCCC – James researchers are working to develop protocols needed for particular components of the genome, such as RNA-seq libraries and exome libraries.
DNA sequencing can reveal gene mutations present in cancer cells that influence their growth and might determine the most effective therapy for that particular patient. In addition to gene mutations, other genomic alterations happen to DNA that contribute to cancer development.
Genome sequencing can detect these “epigenetic” changes in tumor and tissue samples by customizing how sequencing libraries are generated. Pelotonia funds were used to help purchase a Diagenode IP-Star Compact unit, a robotic device that automates the enrichment of genomic locations for these epigenetic analyses. This device, together with NGS whole-genome sequencing, provides genome-wide profiles of epigenetic modifications and sites on genes where proteins bind to activate them. It can also process up to 96 samples at a time.
Pelotonia funds also helped purchase the REES Enterprise Environmental Monitoring System to ensure that precious tumor tissue and other samples are safely stored, and that experimental conditions are properly maintained. The system warns users when critical equipment such as freezers, refrigerators, incubators, liquid-nitrogen tanks and cold rooms are at risk. Failure of such equipment can render large numbers of patient and animal samples unusable, and this can translate into years of lost work.
The system monitors critical parameters such as temperature, humidity, oxygen and carbon dioxide.