ArticleEuropean journal of human genetics : EJHG2017
A framework for the detection of de novo mutations in family-based sequencing data.
Article in European journal of human genetics : EJHG, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 33 citations in OpenAlex.
- Evaluating concordance of preimplantation genetic testing-whole-genome sequencing with genetic findings in live-born children.F&S reports · 2026Article
- Improved discovery of de novo mutations using TrioDNM and VRFS.GigaScience · 2026Article
- Systematic evaluation of de novo mutation calling tools using whole genome sequencing data.Briefings in bioinformatics · 2025Article
- Detection of Genetic Variants in Thai Population by Trio-Based Whole-Genome Sequencing Study.Biology · 2025Article
- Characterization and distribution of de novo mutations in the zebra finch.Communications biology · 2024Article
- Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks.Briefings in bioinformatics · 2022Article
- No evidence of increased mutations in the germline of a group of British nuclear test veterans.Scientific reports · 2022Article
- De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.American journal of human genetics · 2021Article
- Distinct error rates for reference and nonreference genotypes estimated by pedigree analysis.Genetics · 2021Article
- Filtering de novo indels in parent-offspring trios.BMC bioinformatics · 2020Article
- Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes.Nature communications · 2020Article
- Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review.Frontiers in genetics · 2020Review
- Exome sequencing in genetic disease: recent advances and considerations.F1000Research · 2020Review
- Article
- novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data.Bioinformatics (Oxford, England) · 2019Article
- Comparative Analysis for the Performance of Variant Calling Pipelines on Detecting theFrontiers in pharmacology · 2019Article
- Comparing complex variants in family trios.Bioinformatics (Oxford, England) · 2018Article
- Precise detection of de novo single nucleotide variants in human genomes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy.NPJ genomic medicine · 2018Article
- Mapping and phasing of structural variation in patient genomes using nanopore sequencing.Nature communications · 2017Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Germline mutation detection from human DNA sequence data is challenging due to the rarity of such events relative to the intrinsic error rates of sequencing technologies and the uneven coverage across the genome. We developed PhaseByTransmission (PBT) to identify de novo single nucleotide variants and short insertions and deletions (indels) from sequence data collected in parent-offspring trios. We compute the joint probability of the data given the genotype likelihoods in the individual family members, the known familial relationships and a prior probability for the mutation rate. Candidate de novo mutations (DNMs) are reported along with their posterior probability, providing a systematic way to prioritize them for validation. Our tool is integrated in the Genome Analysis Toolkit and can be used together with the ReadBackedPhasing module to infer the parental origin of DNMs based on phase-informative reads. Using simulated data, we show that PBT outperforms existing tools, especially in low coverage data and on the X chromosome. We further show that PBT displays high validation rates on empirical parent-offspring sequencing data for whole-exome data from 104 trios and X-chromosome data from 249 parent-offspring families. Finally, we demonstrate an association between father's age at conception and the number of DNMs in female offspring's X chromosome, consistent with previous literature reports.
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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.