ArticleNature communications2018
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
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- Population-scale genomic medicine with the Hong Kong Genome Project.Nature medicine · 2026Article
- The potential of whole genome sequencing in pharmacogenetics: a retrospective health record study in rare disease patients.European journal of human genetics : EJHG · 2026Article
- Analytical Validation of an Annotation Tool for WGS-Based Pharmacogenomics: Preparing for Clinical Implementation in Pediatric Oncology.Clinical and translational science · 2026Article
- Pharmacogenomics-guided personalized medicine in a clinical setting: real-world data.Pharmacogenetics and genomics · 2026Article
- MTAP-Null Tumors: A Comprehensive Review on Synthetic Vulnerabilities and Therapeutic Strategies.Cells · 2025Review
- Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.Nature genetics · 2025Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
- Enhancing CYP2D6 genotyping with nanopore sequencing to address allele diversity P. vivax malaria elimination.Scientific reports · 2025Article
- Genotyping of selected germline adaptive immune system loci using short-read sequencing data.Genome research · 2025Article
- Analysis ofIranian journal of medical sciences · 2025Article
- Return of Clinically Actionable Pharmacogenetic Results From Molecular Tumor Board DNA Sequencing Data: Workflow and Estimated Costs.Clinical pharmacology and therapeutics · 2025Article
- Translating pharmacogenomic sequencing data into drug response predictions-How to interpret variants of unknown significance.British journal of clinical pharmacology · 2025Review
- StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data.bioRxiv : the preprint server for biology · 2024Article
- Complete genomic profiles of 1496 Taiwanese reveal curated medical insights.Journal of advanced research · 2024Article
- Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool.Bioinformatics (Oxford, England) · 2024Article
- Development of a Multifaceted Program for Pharmacogenetics Adoption at an Academic Medical Center: Practical Considerations and Lessons Learned.Clinical pharmacology and therapeutics · 2024Article
- Pharmacogenetic analysis of structural variation in the 1000 genomes project using whole genome sequences.Scientific reports · 2024Article
- Biologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool.bioRxiv : the preprint server for biology · 2024Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
11 authors.
Funding
Abstract
High-throughput sequencing provides the means to determine the allelic decomposition for any gene of interest-the number of copies and the exact sequence content of each copy of a gene. Although many clinically and functionally important genes are highly polymorphic and have undergone structural alterations, no high-throughput sequencing data analysis tool has yet been designed to effectively solve the full allelic decomposition problem. Here we introduce a combinatorial optimization framework that successfully resolves this challenging problem, including for genes with structural alterations. We provide an associated computational tool Aldy that performs allelic decomposition of highly polymorphic, multi-copy genes through using whole or targeted genome sequencing data. For a large diverse sequencing data set, Aldy identifies multiple rare and novel alleles for several important pharmacogenes, significantly improving upon the accuracy and utility of current genotyping assays. As more data sets become available, we expect Aldy to become an essential component of genotyping toolkits.
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