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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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RNA Structure01:23

RNA Structure

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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ScanNeo: identifying indel-derived neoantigens using RNA-Seq data.

Ting-You Wang1, Li Wang1, Sk Kayum Alam1

  • 1The Hormel Institute, University of Minnesota, Austin, MN, USA.

Bioinformatics (Oxford, England)
|March 20, 2019
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Summary

This study introduces ScanNeo, a computational pipeline that uses RNA sequencing to identify tumor neoantigens from insertions and deletions (indels). These indel neoantigens show potential for predicting patient response to cancer immunotherapy.

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Area of Science:

  • Computational Biology
  • Cancer Genomics
  • Immunogenomics

Background:

  • Insertion and deletion (indels) are key sources of tumor-specific neoantigens.
  • Current neoantigen identification primarily uses DNA sequencing, with RNA sequencing underutilized.
  • Developing efficient methods for indel-derived neoantigen prediction from RNA sequencing is crucial.

Purpose of the Study:

  • To present ScanNeo, a computational pipeline for predicting neoepitopes from indels using RNA-seq data.
  • To validate the efficacy of ScanNeo in a prostate cancer cell line.
  • To assess the association of RNA-seq-derived indel neoantigens with immunotherapy response.

Main Methods:

  • Development of ScanNeo, a fast and streamlined computational pipeline for RNA-seq analysis.
  • Application of ScanNeo to a prostate cancer cell line.
  • Validation of predicted neoantigens using matched mass spectrometry data.
  • Analysis of indel neoantigens in a melanoma patient cohort for association with checkpoint inhibitor response.

Main Results:

  • ScanNeo successfully predicts neoepitopes derived from small to large indels from RNA-seq data.
  • Predictions made by ScanNeo were validated using mass spectrometry data.
  • Indel neoantigens identified via RNA-seq were significantly associated with checkpoint inhibitor response in melanoma patients.

Conclusions:

  • ScanNeo provides an effective computational approach for identifying indel-derived neoantigens from RNA-seq.
  • RNA-seq is a viable and valuable data source for neoantigen discovery, complementing DNA sequencing.
  • Indel neoantigens identified by ScanNeo may serve as predictive biomarkers for immunotherapy response.