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RESEARCH Oliogopaints - A high-resolution, low-cost method for visualizing chromosome position
Oligopaints are bioninformatically-designed FISH probes derived from single stranded oligonucleotide libraries. We believe that this technology can improve the dynamic range of the existing FISH technology, while substantially lowering its cost.
Although FISH probes derived from BAC and cosmid inserts have been used successfully for decades, there are several limitations to these probes that we think we can improve upon. These inserts typically range in size from 50 – 150 kb. While targeting regions up to a few megabases in size is possible by using multiple probes, this approach is often technically difficult. A gap exists in the dynamic range of euchromatic FISH, as chromosome paints can be used to visualize entire chromosomes (tens to hundreds of megabases), but currently no assay exists to easily probe a portion of a chromosome that is on the order of several megabases to tens of megabases. Furthermore, the ability to produce complex hybridization patterns such as multicolor banding is limited and very expensive with commercially produced probes. Our method seeks to allow researchers to probe regions ranging from tens of kilobases to hundreds of megabases with little to no variation in the probe production and hybridization protocols, and our design and production pipelines are anticipated to easily support a broad range of band sizes and patterns.
The development of FISH in 384-well plates enabled the first FISH-based whole-genome RNAi screen (Wu lab, unpublished data). Currently these screens are limited to assaying highly repetitive sequences that can be targeted with a single oligonucleotide, as the cost of BAC/cosmid and chromosome paint probes would be on the order of hundreds of thousands to millions of dollars for a whole-genome screen. Our goal is to dramatically reduce the cost of FISH against unique genomic regions, in order to enable a broader range of targets to be screened on the genome-wide level. These screens would enable researchers to assay for changes in chromosome positioning, intra/inter-chromosomal interactions, and gene expression patterns on a cell-by-cell basis. The combination of high-throughput FISH and efficient, inexpensive probes also has great potential to improve the sensitivity and resolution of clinical cytogenetic assays, where the use of FISH is hindered by its low throughput and high cost.
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