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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.

Jianan Wang1, Zhenyuan Sun2, Guohua Wang1

  • 1Faculty of Computing, Harbin Institute of Technology, No. 92 Xidazhi Street, Nangang District, Harbin 150001, China.

International Journal of Molecular Sciences
|June 26, 2025
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Summary

Haplotype phasing accurately determines inherited gene sequences using the novel HPTAS algorithm. This alignment-free method leverages transcriptome data for enhanced accuracy in allele-specific expression studies.

Keywords:
RNA-seqSNPallele-specific expressionhaplotype phasingtranscriptome

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Haplotype phasing is crucial for understanding genetic inheritance and downstream analyses.
  • Allele-specific (AS) expression and alternative splicing are vital biological processes.
  • Current methods often focus on exonic SNPs, requiring combined phased SNPs for robust inferences.

Purpose of the Study:

  • To introduce HPTAS, an alignment-free algorithm for haplotype phasing in allele-specific expression studies.
  • To utilize transcriptome data and a k-mer-based approach for deriving phasing counts.
  • To demonstrate the efficacy of HPTAS compared to existing advanced algorithms.

Main Methods:

  • Developed HPTAS, an alignment-free algorithm for haplotype phasing.
  • Constructed a mapping structure from transcriptome annotations and SNPs.
  • Employed a k-mer-based approach to derive phasing counts from RNA-seq data.

Main Results:

  • HPTAS achieved high phasing accuracy and performance on NA12878 RNA-seq data (NGS and TGS).
  • Demonstrated that transcriptome data significantly aids in phasing exonic SNPs.
  • Outperformed the most advanced existing algorithm in the field.

Conclusions:

  • HPTAS offers a novel and accurate approach to haplotype phasing, particularly for AS studies.
  • Transcriptome data integration enhances the phasing of exonic SNPs.
  • HPTAS provides a foundation for future advancements in haplotype phasing methodologies.