SQUID: transcriptomic structural variation detection from RNA-seq

• Main Authors: Cong Ma, Mingfu Shao, Carl Kingsford
• Format: Article
• Language: English
• Published: BMC 2018-04-01
• Series: Genome Biology
• Subjects: Transcriptomic structural variation; RNA-seq; TCGA
• Online Access: http://link.springer.com/article/10.1186/s13059-018-1421-5

Abstract Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem. We introduce SQUID, a novel algorithm to predict both fusion-gene and non-fusion-gene TSVs accurately from RNA-seq alignments. SQUID unifies both concordant and discordant read alignments into one model and doubles the precision on simulation data compared to other approaches. Using SQUID, we identify novel non-fusion-gene TSVs on TCGA samples.