from Genetic engineering News by Kathy Liszewski

NGS is already capable of producing billions of short reads, and it can do so quickly and economically. And NGS is reaching well beyond genomics. For example, it is revolutionizing transcriptomics through advances in RNA sequencing (RNA-Seq). Yet, despite this dazzling progress, a number of significant challenges remain.

Removing Toxic Transcripts

Creating high-specificity RNA-Seq libraries remains an ongoing challenge. “It is critical to minimize the population of undesirable transcripts (often greater than 80% of a library) such as rRNA, globin, and other housekeeping species, while at the same time maintaining desirable transcripts from the original total RNA population,” advises Luke Sherlin, Ph.D., director of technical services, NuGEN Technologies. (read more…)

Alternative Splicing and RNA-Seq Data

RNA-Seq technology also provides an invaluable tool for deciphering the extensive alternative splicing of the transcriptome. Using this shuffling process, genes can code for multiple forms of the same protein. Alternative splicing creates two to potentially thousands of variants and occurs in more than 90% of human genes. This RNA processing mechanism, however, also plays a major role in multiple genetic disorders.

“The Human Genome Project created an initial map of splice variations more than 10 years ago,” notes Liliana Florea, Ph.D.,  assistant professor, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine. “But the map remains largely incomplete. There is still no repository for all alternative splicing events.” (read more…)