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| Abstract Title:
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| Novel Lab-on-a-Chip and Bead Polony Technologies for High Throughput RNA (cDNA) Exontyping of Human Leukemia Cells
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| Graduate Student Presenter:
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Nick Carroll
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| Name of the Author(s) and Affiliation(s):
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Nick Carroll, University of New Mexico: UNM IGERT Program on Integrating Nanotechnology with Cell Biology and Neuroscience; Dimiter N. Petsev, University of New Mexico; Jeremy Edwards, University of New Mexico.
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An important technological development is the ability to quantitatively measure the relative abundance of all splice variants of a specific gene in a cancer sample. In other words, the ability to measure the exon expression of all exons in the context of the complete structure of the spliced mRNA. Currently there are approaches to measure exon expression levels (e.g. QPCR or exon junction microarrays), however these approaches fail to identify the complete transcript context, or which exons are expressed together in an individual mRNA. Since a major effect of alternative splicing is to produce different forms of an encoded protein, it is critical to understand which exons are combined in alternatively spliced mRNAs. However, predicting which versions of a protein type will be expressed in particular cells or tumors and whether those proteins will be normal or activated requires contextual and quantitative information about the different exons incorporated in the transcripts, and points to the need for new and improved methods of exontyping.
Our work has centered on development a complete droplet-based microfluidic device or “Lab-on-a-Chip” system for the high-throughput analysis of splice variant patterns in hundreds of samples per day. The Lab-on-a-Chip system will automate the measurements so that quantitative and contextual information about alternative RNA splicing can be obtained from large numbers of patient samples. In parallel, we have worked on the development of a high throughput, bead based polony assay capable of simultaneous exontyping of many RNA (cDNA) samples.
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