ArticleNature communications2016
Rare variant phasing and haplotypic expression from RNA sequencing with phASER.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 papers.
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Who cites it
101 citing papers in PubMed.
- The landscape of allele-specific expression in human kidneys.Science advances · 2026Article
- Allele-specific expression in the brain links genetic risk and cortical thinning in psychiatric disorders.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026Article
- Defining Haplosufficiency in Autosomal Recessive Limb-Girdle Muscular Dystrophy Using Molecular Markers in Disease Carriers.Neurology. Genetics · 2026Article
- Integrative Multi-Omics Analysis Reveals the Genetic Architecture Landscape of the Blood Metabolome in Jersey Cattle.Animals : an open access journal from MDPI · 2026Article
- Protocol for haplotype-resolved genome comparison and allele-specific expression analysis across multiple tissues and individuals.STAR protocols · 2026Article
- Atlas of glomerular disease-specific genetic effects on blood transcriptome.medRxiv : the preprint server for health sciences · 2026Article
- Molecular Evolution of a Sex-Linked Inversion Polymorphism in Zebra Finches.Genome biology and evolution · 2026Article
- Mapping the landscape of allele-specific expression in porcine genomes.Genome biology · 2026Article
- BCL2 promoter region mutations are an independent marker of BCL2 level in lymphoid malignancies.NPJ genomic medicine · 2026Article
- Dynamics of Gene and Allelic Expression During Modern Hybrid Maize Breeding.Plant biotechnology journal · 2026Article
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Monoallelic expression characterizes a distinct molecular and clinical group of breast tumors.Research square · 2026Article
- Advances in haplotype phasing and genotype imputation.Nature reviews. Genetics · 2026Review
- Construction of a Multitissue Cell Atlas Reveals Cell-Type-Specific Regulation of Molecular and Complex Phenotypes in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune related GWAS loci in CD4+ T cells.medRxiv : the preprint server for health sciences · 2026Article
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications.Research square · 2026Article
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications.medRxiv : the preprint server for health sciences · 2026Article
- Improved Identification of Large-effect Rare Genetic Variants using Haplotype Aggregated Allele-specific Expression Data.medRxiv : the preprint server for health sciences · 2025Article
- Integrative and accurate annotations enhance current nonsense-mediated mRNA decay rules.Nucleic acids research · 2025Article
41 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Haplotype phasing of genetic variants is important for clinical interpretation of the genome, population genetic analysis and functional genomic analysis of allelic activity. Here we present phASER, an accurate approach for phasing variants that are overlapped by sequencing reads, including those from RNA sequencing (RNA-seq), which often span multiple exons due to splicing. Using diverse RNA-seq data we demonstrate that this provides more accurate phasing of rare variants compared with population-based phasing and allows phasing of variants in the same gene up to hundreds of kilobases away that cannot be obtained from DNA sequencing (DNA-seq) reads. We show that in the context of medical genetic studies this improves the resolution of compound heterozygotes. Additionally, phASER provides measures of haplotypic expression that increase power and accuracy in studies of allelic expression. In summary, phasing using RNA-seq and phASER is accurate and improves studies where rare variant haplotypes or allelic expression is needed.
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