Abstract 2285: Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer

Abstract

The interpretation of variants in cancer is frequently focused on direct protein coding alterations. However, most somatic mutations are in noncoding regions of the genome, and even exonic mutations may have unidentified noncoding consequences. Here we present Regtools, a software package designed to efficiently identify variants that may cause aberrant splicing in tumors. Our tool integrates variant calls from genomic data with junctions extracted from transcriptomic data in order to examine potential cis alterations to splicing near a somatic variant. Based on user-defined parameters and position relative to known exons, variants are first annotated as splicing relevant or not. Splicing junctions are inferred from transcriptomic sequencing data, and comparison of junctions to a reference transcriptome allows for identification and annotation of novel junctions and nearby regulatory or splicing motifs. From there, mutations are associated with junctions that overlap with a flanking region. In order to evaluate Regtools, we used it to analyze the transcriptional output of tumor-sequencing data from two cohorts of cancer patients, one of hepatocellular carcinoma and one of small cell lung cancer with 28 and 21 samples, respectively. We performed whole-exome and RNA sequencing on each sample. Somatic variants were called on whole-exome alignment data. For each cohort, we compared the junctional profiles between tumors and identified numerous examples of variants for which there are elevated levels of proximal novel or known junctions. Moreover, out of 754 (153 in HCC; 601 in SCLC) variants identified as splicing relevant by our approach, only 165 (20 in HCC; 145 in SCLC) were annotated as splicing relevant by Ensembl's Variant Effect Predictor, using the recommended “per_gene” option. This preliminary analysis illustrates the importance of an efficient, user-friendly computational tool for identifying important noncoding variants that would otherwise be undervalued or perhaps even completely ignored by traditional methods and annotators. Regtools is freely available and open source (https://github.com/griffithlab/regtools). Citation Format: Yang-Yang Feng, Avinash Ramu, Zachary L. Skidmore, Jason Kunisaki, Kelsy C. Cotto, Obi L. Griffith, Malachi Griffith. Regtools: Integrated analysis of genomic and transcriptomic data for discovery of mutations associated with aberrant splicing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2285.

A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome

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Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation

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iFLAS: positive‐unlabeled learning facilitates full‐length transcriptome‐based identification and functional exploration of alternatively spliced isoforms in maize

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