Development of an Ultra-high Throughput Long Non-coding RNA Screening System

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SELECTBIO

Long non-coding RNAs (lncRNA) are an underexplored class of non-coding RNAs shown to be implicated in health and disease. They constitute a new class of biomarkers with disease associated lncRNA signatures yet to be discovered. In addition, they open up a new approach to understanding the function and organization of the genome. The lack of a sensitive high-throughput platform for lncRNA profiling has hampered their study so far. To address this, we are developing a new platform for ultra-high throughput RT-qPCR analysis of 10000 long non-coding RNAs. In the pilot phase, we designed qPCR assays for 1500 lncRNAs based on public sequence databases. All assays were designed using state-of-the-art in silico quality controls, followed by an extensive empirical validation according to MIQE guidelines. Validation of these 1500 lncRNAs in relevant biological systems demonstrated superior sensitivity and specificity of the technology. Data processing was done using qbasePLUS with an improved global mean normalization procedure to better remove technical variation. In conclusion, we have completed the first stage of the development of an ultra-high throughput and low-volume RT-qPCR platform for the quantitative detection of lncRNAs. The tool offers a unique way to investigate the expression patterns of lncRNAs in health and disease.