ArticleNucleic acids research2017
IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing.Nature communications · 2025Article
- HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data.International journal of molecular sciences · 2025Article
- Bayesian estimation of allele-specific expression in the presence of phasing uncertainty.Bioinformatics (Oxford, England) · 2025Article
- Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes.Cell genomics · 2024Article
- Characterizing the allele-specific gene expression landscape in high hyperdiploid acute lymphoblastic leukemia with BASE.Scientific reports · 2024Article
- Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer.Nature communications · 2024Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.bioRxiv : the preprint server for biology · 2023Article
- High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing.Nature communications · 2023Article
- LCAT: an isoform-sensitive error correction for transcriptome sequencing long reads.Frontiers in genetics · 2023Article
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (Life (Basel, Switzerland) · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.Plant communications · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Allele-specific expression (ASE) is a fundamental problem in studying gene regulation and diploid transcriptome profiles, with two key challenges: (i) haplotyping and (ii) estimation of ASE at the gene isoform level. Existing ASE analysis methods are limited by a dependence on haplotyping from laborious experiments or extra genome/family trio data. In addition, there is a lack of methods for gene isoform level ASE analysis. We developed a tool, IDP-ASE, for full ASE analysis. By innovative integration of Third Generation Sequencing (TGS) long reads with Second Generation Sequencing (SGS) short reads, the accuracy of haplotyping and ASE quantification at the gene and gene isoform level was greatly improved as demonstrated by the gold standard data GM12878 data and semi-simulation data. In addition to methodology development, applications of IDP-ASE to human embryonic stem cells and breast cancer cells indicate that the imbalance of ASE and non-uniformity of gene isoform ASE is widespread, including tumorigenesis relevant genes and pluripotency markers. These results show that gene isoform expression and allele-specific expression cooperate to provide high diversity and complexity of gene regulation and expression, highlighting the importance of studying ASE at the gene isoform level. Our study provides a robust bioinformatics solution to understand ASE using RNA sequencing data only.
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