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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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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Enhanced Detection of Splice-Altering Variants in Hematologic Malignancies Using Targeted RNA-Sequencing Data.

Muneeza Maqsood1, John Toubia2, Carol Wadham3

  • 1Department of Genetics and Molecular Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia; Data and Bioinformatics Innovation, Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.

The Journal of Molecular Diagnostics : JMD
|October 12, 2025
PubMed
Summary

New bioinformatics tools, SpliceChaser and BreakChaser, accurately detect splice-altering variants and gene deletions in cancer RNA sequencing data. These tools improve diagnostic precision for chronic myeloid leukemia and other malignancies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA-based sequencing detects variants in malignancies, but identifying splice-altering events is challenging due to transcriptome complexity and false positives.
  • Accurate detection of splice variants is crucial for understanding disease mechanisms and developing targeted therapies.

Purpose of the Study:

  • To develop and validate bioinformatics tools (SpliceChaser and BreakChaser) for enhanced detection and characterization of clinically relevant splice-altering variants and gene deletions.
  • To improve the accuracy and reliability of variant detection in RNA sequencing data for hematologic malignancies.

Main Methods:

  • SpliceChaser analyzes read length diversity around splice junctions to identify atypical splicing.
  • BreakChaser processes soft-clipped sequences and alignment anomalies to detect deletion breakpoints linked to atypical splice isoforms.
  • Tools were developed and validated on over 1400 RNA sequencing samples from chronic myeloid leukemia patients.

Main Results:

  • SpliceChaser and BreakChaser demonstrated high performance in detecting clinically relevant atypical splice-altering variants and gene deletions.
  • The tools achieved a 98% positive percentage agreement and a 91% positive predictive value.
  • Integration of splicing and breakpoint detection with filtering strategies enabled precise variant identification.

Conclusions:

  • SpliceChaser and BreakChaser significantly enhance the detection of clinically relevant splice-altering variants and gene deletions.
  • These tools offer improved diagnostic capabilities for chronic myeloid leukemia and other cancers.
  • Precise variant identification facilitates the development of advanced therapeutic strategies.