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Treffer: HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.

Title:
HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.
Authors:
Wang J; Faculty of Computing, Harbin Institute of Technology, No. 92 Xidazhi Street, Nangang District, Harbin 150001, China., Sun Z; College of Computer and Control Engineering, Northeast Forestry University, No. 26 He Xing Road, Xiangfang District, Harbin 150040, China., Wang G; Faculty of Computing, Harbin Institute of Technology, No. 92 Xidazhi Street, Nangang District, Harbin 150001, China., Miao Y; College of Computer and Control Engineering, Northeast Forestry University, No. 26 He Xing Road, Xiangfang District, Harbin 150040, China.
Source:
International journal of molecular sciences [Int J Mol Sci] 2025 Jun 13; Vol. 26 (12). Date of Electronic Publication: 2025 Jun 13.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
Imprint Name(s):
Original Publication: Basel, Switzerland : MDPI, [2000-
MeSH Terms:
Haplotypes*/genetics , Transcriptome*/genetics , Algorithms*, High-Throughput Nucleotide Sequencing/methods ; Gene Expression Profiling/methods ; Polymorphism, Single Nucleotide ; Humans ; Alleles ; Alternative Splicing
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Grant Information:
2022YFF1202101 the National Key R&D Program of China; 62225109 the National Natural Science Foundation of China; 62172129 the National Natural Science Foundation of China
Contributed Indexing:
Keywords: RNA-seq; SNP; allele-specific expression; haplotype phasing; transcriptome
Entry Date(s):
Date Created: 20250626 Date Completed: 20250626 Latest Revision: 20250628
Update Code:
20260130
PubMed Central ID:
PMC12193515
DOI:
10.3390/ijms26125700
PMID:
40565162
Database:
MEDLINE

Weitere Informationen

Haplotype phasing refers to determining the haplotype sequences inherited from each parent in a diploid organism. It is a critical process for various downstream analyses, and numerous haplotype phasing methods for genomic single nucleotide polymorphisms (SNPs) have been developed. Allele-specific (AS) expression and alternative splicing play key roles in diverse biological processes. AS studies usually focus more on exonic SNPs, and multiple phased SNPs need to be combined to obtain better inferences. In this paper, we introduce an alignment-free algorithm HPTAS for haplotype phasing in AS studies. Instead of using sequence alignment to count the number of reads covering SNPs, HPTAS constructs a mapping structure from transcriptome annotations and SNPs and employs a k-mer-based approach to derive phasing counts from RNA-seq data. Using both next-generation sequencing (NGS) and the third-generation sequencing (TGS) NA12878 RNA-seq data and comparing with the most advanced algorithm in the field, we have demonstrated that HPTAS achieves high phasing accuracy and performance and that transcriptome data indeed facilitates the phasing of exonic SNPs. With the continued advancement of sequencing technology and the improvement in transcriptome annotations, HPTAS may serve as a foundation for future haplotype phasing methods.