ArticleAmerican journal of human genetics2020
Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data.
Article in American journal of human genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation.Science advances · 2026Article
- Self-organizing maps for allele specific expression data reconstruction and identification of anomalous genomic regions.Frontiers in bioinformatics · 2026Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data.Nature protocols · 2024Review
- Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.Briefings in bioinformatics · 2023Review
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Allele-specific expression analysis for complex genetic phenotypes applied to a unique dilated cardiomyopathy cohort.Scientific reports · 2023Article
- Severe choline deficiency induces alternative splicing aberrance in optimized duck primary hepatocyte cultures.Animal bioscience · 2022Article
- Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders.NPJ genomic medicine · 2022Article
- Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome.Comprehensive Physiology · 2021Article
- Rett syndrome linked to defects in forming the MeCP2/Rbfox/LASR complex in mouse models.Nature communications · 2021Article
- Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes.Genome biology · 2021Article
- Breeding for Climate Change Resilience: A Case Study of Loblolly Pine (Frontiers in plant science · 2021Review
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Authors and funding
9 authors.
Funding
Abstract
RNA sequencing (RNA-seq) is a powerful technology for studying human transcriptome variation. We introduce PAIRADISE (Paired Replicate Analysis of Allelic Differential Splicing Events), a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, we formulate ASAS detection using PAIRADISE as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates. PAIRADISE outperforms alternative statistical models in simulation studies. Applying PAIRADISE to replicate RNA-seq data of a single individual and to population-scale RNA-seq data across many individuals, we detect ASAS events associated with genome-wide association study (GWAS) signals of complex traits or diseases. Additionally, PAIRADISE ASAS analysis detects the effects of rare variants on alternative splicing. PAIRADISE provides a useful computational tool for elucidating the genetic variation and phenotypic association of alternative splicing in populations.
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