ArticleGigaScience2018
Ximmer: a system for improving accuracy and consistency of CNV calling from exome data.
Article in GigaScience, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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Who cites it
27 citing papers in PubMed.
- Elucidating the Role of SET as a Key Contributor to Neurodevelopmental Disability Within the 9q34.11 Deletion Syndrome Interval.Clinical genetics · 2026Article
- Molecular analysis of individuals with suspected 46,XY differences of sex development in a homogenous and understudied population.Human molecular genetics · 2026Article
- <italic>WT1</italic> Deletion in 46,XY DSD: The Importance of Copy Number Variant Analysis.Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation · 2026Article
- Comprehensive Characterisation of the RFC1 Repeat in an Australian Cohort.Cerebellum (London, England) · 2025Article
- A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia.Genome research · 2025Article
- The genetic landscape and classification of infantile epileptic spasms syndrome requiring surgery due to suspected focal brain malformations.Brain communications · 2025Article
- Structural variant calling and clinical interpretation in 6224 unsolved rare disease exomes.European journal of human genetics : EJHG · 2024Article
- Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Article
- Diagnostic utility of exome sequencing followed by research reanalysis in human brain malformations.Brain communications · 2024Article
- Interstitial lung disease and pancreatic exocrine insufficiency in CADDS: Phenotypic expansion and literature review.JIMD reports · 2023Article
- PathogenicNeurology · 2023Article
- Integrated multi-omics for rapid rare disease diagnosis on a national scale.Nature medicine · 2023Article
- Genetic Basis of Early Onset Atrial Fibrillation in Patients without Risk Factors.Journal of cardiovascular development and disease · 2023Article
- Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma.International journal of molecular sciences · 2023Article
- The Australian Reproductive Genetic Carrier Screening Project (Mackenzie's Mission): Design and Implementation.Journal of personalized medicine · 2022Article
- Distinct diagnostic trajectories in NBAS-associated acute liver failure highlights the need for timely functional studies.JIMD reports · 2022Article
- A de novo ACTB gene pathogenic variant in identical twins with phenotypic variation for hydrops and jejunal atresia.American journal of medical genetics. Part A · 2022Article
- CNVind: an open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage.BMC bioinformatics · 2022Article
- Ethylmalonic encephalopathy masquerading as meningococcemia.Cold Spring Harbor molecular case studies · 2022Article
- Biallelic Variants inInternational journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Background: While exome and targeted next-generation DNA sequencing are primarily used for detecting single nucleotide changes and small indels, detection of copy number variants (CNVs) can provide highly valuable additional information from the data. Although there are dozens of exome CNV detection methods available, these are often difficult to use, and accuracy varies unpredictably between and within datasets. Findings: We present Ximmer, a tool that supports an end-to-end process for evaluating, tuning, and running analysis methods for detection of CNVs in germline samples. Ximmer includes a simulation framework, implementations of several commonly used CNV detection methods, and a visualization and curation tool that together enable interactive exploration and quality control of CNV results. Using Ximmer, we comprehensively evaluate CNV detection on four datasets using five different detection methods. We show that application of Ximmer can improve accuracy and aid in quality control of CNV detection results. In addition, Ximmer can be used to run analyses and explore CNV results in exome data. Conclusions: Ximmer offers a comprehensive tool and method for applying and improving accuracy of CNV detection methods for exome data.
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Registered trials
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