Clinical OMICS

JUL-AUG 2019

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com 28 Clinical OMICs July/August 2019 The rise of long-read transcriptome sequencing Nearly 95% of the genes in humans undergo alternative splicing, the process through which exons are differentially included in the mature transcripts, leading to the production of many different protein isoforms from a single gene. For the past decade, researchers have relied on existing annotations and short-read sequencing to reconstruct alternatively spliced transcripts and quantify their expression across individuals, development, tissues, and single cells. This approach has led to fundamental novel biological insights on the prevalence and importance of splicing. While short-read sequencing power stems from large read output and high accuracy in base calling enabling exon and splice junction quantification, end-to-end transcript reconstruction remains a significant challenge. 1 Because of the short read size and often complex gene models, most existing algorithms predicting transcripts have high false positive rates. The rise of long-read technologies now opens the possibility to fully capture a full-length transcript within a single read and thereby accurately annotate and quantify transcripts. The need for such technologies is exemplified by a single fruit fly gene: Dscam. This gene is predicted to have nearly 36,000 isoforms due to the presence of blocks of mutually exclusive exons. 2 The application of long-read sequencing and long-range PCR allowed validation of nearly 18,000 of these transcripts in an organism predicted to have almost 14,000 protein coding genes. In the past few years, similar studies for disease-relevant genes revealed significantly underappreciated transcript diversity, even in organisms such as humans – considered to have gold standard annotations. For single genes, hundreds of novel transcripts, either including previously unannotated exons, novel splice junctions, and/or splice sites have been added to a single gene, while only a fraction of previously annotated transcripts could be confirmed. 3,4 Review written by Wilfried Haerty – Earlham Institute, from London Calling 2019 Find out more about transcriptome analysis with nanopore sequencing at www.nanoporetech.com/transcriptome London Calling is an annual conference hosted by Oxford Nanopore Technologies, dedicated to sharing the latest nanopore sequencing research from scientists around the world. Oxford Nanopore offers scalable DNA/RNA sequencing devices from portable to benchtop. Our goal is to enable the analysis of any living thing, by any person, in any environment. 28 Clinical OMICs July/August 2019 www.clinicalomics.com SPONSORED CONTENT

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