ArticleBriefings in bioinformatics2022
Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 33 citations in OpenAlex.
- Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data.Quantitative biology (Beijing, China) · 2026Article
- Nanopore sequencing combined with adaptive sampling and NanoExpansion enables accurate characterization of repeat expansion disorders.NAR genomics and bioinformatics · 2026Article
- Small variant calling in the era of long-read sequencing.Nature reviews. Genetics · 2026Review
- Amplicon-based long-read sequencing for accurate CYP2D6 gene deletion and duplication detection using CYP2D7 as a reference gene.The pharmacogenomics journal · 2026Article
- Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian.Nature ecology & evolution · 2026Article
- AI in variant analysis: fast track to genetic diagnoses.Human genetics · 2026Review
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- Patient-derived organoid xenografts reveal the multifaceted role of the lncRNAbioRxiv : the preprint server for biology · 2026Article
- Clair3-RNA: a deep learning-based small variant caller for long-read RNA sequencing data.Nature communications · 2025Article
- Targeted Sequencing Identifies SNPs Associated with Antimalarial Drug Resistance and the CSP Vaccine Antigen inInternational journal of molecular sciences · 2025Article
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain.Genome research · 2025Article
- Splice-modulating antisense oligonucleotides targeting a pathogenic intronic variant in adult polyglucosan body disease correct mis-splicing and restore enzyme activity in patient cells.Nucleic acids research · 2025Article
- Indel calling from ONT sequencing data of family trios via sparse attention and 3D convolution.Briefings in bioinformatics · 2025Article
- Feasibility of long-read sequencing to identify molecular alterations in an Indonesian cohort of locally advanced to advanced nasopharyngeal cancer.Scientific reports · 2025Article
- Development and validation of a carnitine cycle and transport disorders (CCD) panel: an ONT-compatible multi-gene diagnostic kit for newborn and selective screening.Orphanet journal of rare diseases · 2025Article
- Benchmarking Nanopore Sequencing for CLN2 (TPP1) Mutation Detection: Integrating Rapid Genomics and Orthogonal Validation for Precision Diagnostics.International journal of molecular sciences · 2025Article
- Investigating the Performance of Oxford Nanopore Long-Read Sequencing with Respect to Illumina Microarrays and Short-Read Sequencing.International journal of molecular sciences · 2025Article
- Bidirectional disruption ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Long-read whole-genome sequencing-based concurrent haplotyping and aneuploidy profiling of single cells.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio's predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods. We also demonstrated that our Trio-to-Trio model is more accurate than competing architectures. Clair3-Trio is accessible as a free, open-source project at https://github.com/HKU-BAL/Clair3-Trio.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.