ArticleJournal of human genetics2015
Detecting copy-number variations in whole-exome sequencing data using the eXome Hidden Markov Model: an 'exome-first' approach.
Article in Journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed, 63 citations in OpenAlex.
- Completely resolved structural variants by optical genome mapping with adaptive sampling from CNV discovery.NPJ genomic medicine · 2026Article
- AMolecular syndromology · 2025Article
- Molecular diagnosis of 405 individuals with autism spectrum disorder.European journal of human genetics : EJHG · 2024Article
- Review
- Long-read sequencing revealing intragenic deletions in exome-negative spastic paraplegias.Journal of human genetics · 2023Article
- Biallelic structural variations withinLife science alliance · 2023Article
- An integrated genetic analysis of epileptogenic brain malformed lesions.Acta neuropathologica communications · 2023Article
- Novel Intronic Mutations of theInternational journal of general medicine · 2023Article
- Multidimensional analyses of the pathomechanism caused by the non-catalytic GNE variant, c.620A>T, in patients with GNE myopathy.Scientific reports · 2022Article
- Monogenic causes of pigmentary mosaicism.Human genetics · 2022Article
- Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker.Bioinformatics (Oxford, England) · 2022Article
- Exome first approach to reduce diagnostic costs and time - retrospective analysis of 111 individuals with rare neurodevelopmental disorders.European journal of human genetics : EJHG · 2022Article
- Review
- Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases.Journal of clinical medicine · 2021Review
- Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder.Journal of human genetics · 2021Article
- Next Generation Sequencing Based Multiplex Long-Range PCR for Routine Genotyping of Autoinflammatory Disorders.Frontiers in immunology · 2021Article
- Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation.European journal of human genetics : EJHG · 2021Article
- Parallel detection of single nucleotide variants and copy number variants with exome analysis: Validation in a cohort of 700 undiagnosed patients.American journal of medical genetics. Part A · 2020Article
- Modeling epileptic spasms during infancy: Are we heading for the treatment yet?Pharmacology & therapeutics · 2020Review
- Novel compound heterozygous variant of BSCL2 identified by whole exome sequencing and multiplex ligation‑dependent probe amplification in an infant with congenital generalized lipodystrophy.Molecular medicine reports · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-exome sequencing (WES) is becoming a standard tool for detecting nucleotide changes, and determining whether WES data can be used for the detection of copy-number variations (CNVs) is of interest. To date, several algorithms have been developed for such analyses, although verification is needed to establish if they fit well for the appropriate purpose, depending on the characteristics of each algorithm. Here, we performed WES CNV analysis using the eXome Hidden Markov Model (XHMM). We validated its performance using 27 rare CNVs previously identified by microarray as positive controls, finding that the detection rate was 59%, or higher (89%) with three or more targets. XHMM can be effectively used, especially for the detection of >200 kb CNVs. XHMM may be useful for deletion breakpoint detection. Next, we applied XHMM to genetically unsolved patients, demonstrating successful identification of pathogenic CNVs: 1.5-1.9-Mb deletions involving NSD1 in patients with unknown overgrowth syndrome leading to the diagnosis of Sotos syndrome, and 6.4-Mb duplication involving MECP2 in affected brothers with late-onset spasm and progressive cerebral/cerebellar atrophy confirming the clinical suspect of MECP2 duplication syndrome. The possibility of an 'exome-first' approach for clinical genetic investigation may be considered to save the cost of multiple investigations.
Indexed as
Identifiers
What OpenQuestion holds
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.