ArticleProceedings of the National Academy of Sciences of the United States of America2013
Rare variant detection using family-based sequencing analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed, 59 citations in OpenAlex.
- Using dried blood spot samples from a trio for linked-read whole-exome sequencing.European journal of human genetics : EJHG · 2019Trial
- Clinical and genetic spectrum of dual rare genetic diseases revealed by whole-exome sequencing in 14 pediatric patients.Orphanet journal of rare diseases · 2026Article
- Haplotyping-Assisted Diploid Assembly and Variant Detection with Linked Reads.Methods in molecular biology (Clifton, N.J.) · 2023Review
- A complete pedigree-based graph workflow for rare candidate variant analysis.Genome research · 2022Article
- Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder.Frontiers in genetics · 2022Article
- Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.Nature communications · 2021Article
- Linkage of Alzheimer disease families with Puerto Rican ancestry identifies a chromosome 9 locus.Neurobiology of aging · 2021Article
- CRISPR-mediated gene correction links the ATP7A M1311V mutations with amyotrophic lateral sclerosis pathogenesis in one individual.Communications biology · 2020Article
- The genetic etiology of eosinophilic esophagitis.The Journal of allergy and clinical immunology · 2020Review
- Rare and common variant discovery in complex disease: the IBD case study.Human molecular genetics · 2019Review
- 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
- geck: trio-based comparative benchmarking of variant calls.Bioinformatics (Oxford, England) · 2018Article
- HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.BMC genomics · 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
- Possible role of rare variants in Trace amine associated receptor 1 in schizophrenia.Schizophrenia research · 2017Article
- Molecular genetic findings and clinical correlations in 100 patients with Joubert syndrome and related disorders prospectively evaluated at a single center.Genetics in medicine : official journal of the American College of Medical Genetics · 2017Article
- Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions.Bioinformatics (Oxford, England) · 2017Article
- VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data.Nucleic acids research · 2017Article
- Joint detection of copy number variations in parent-offspring trios.Bioinformatics (Oxford, England) · 2016Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
Next-generation sequencing is revolutionizing genomic analysis, but this analysis can be compromised by high rates of missing true variants. To develop a robust statistical method capable of identifying variants that would otherwise not be called, we conducted sequence data simulations and both whole-genome and targeted sequencing data analysis of 28 families. Our method (Family-Based Sequencing Program, FamSeq) integrates Mendelian transmission information and raw sequencing reads. Sequence analysis using FamSeq reduced the number of false negative variants by 14-33% as assessed by HapMap sample genotype confirmation. In a large family affected with Wilms tumor, 84% of variants uniquely identified by FamSeq were confirmed by Sanger sequencing. In children with early-onset neurodevelopmental disorders from 26 families, de novo variant calls in disease candidate genes were corrected by FamSeq as mendelian variants, and the number of uniquely identified variants in affected individuals increased proportionally as additional family members were included in the analysis. To gain insight into maximizing variant detection, we studied factors impacting actual improvements of family-based calling, including pedigree structure, allele frequency (common vs. rare variants), prior settings of minor allele frequency, sequence signal-to-noise ratio, and coverage depth (∼20× to >200×). These data will help guide the design, analysis, and interpretation of family-based sequencing studies to improve the ability to identify new disease-associated genes.
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Registered trials
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.