ArticlePLoS computational biology2022
SavvyCNV: Genome-wide CNV calling from off-target reads.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 37 citations in OpenAlex.
- Effectiveness of Recombinant Human Growth Hormone Therapy in Small-for-Gestational-Age Children With Short Stature: A Stratified Analysis Based on Genetic Variant Status.Clinical endocrinology · 2026Article
- Dual phenotype in a patient with adult-onset hyperinsulinism and diabetes caused by an activatingJournal of the Endocrine Society · 2026Article
- Identification of the ACTB p.Ser348Leu de novo variant in individuals with syndromic neonatal diabetes.EBioMedicine · 2026Article
- Comprehensive genetic rescreening improves diagnostic yield in congenital hyperinsulinism.Journal of the Endocrine Society · 2026Article
- PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.Bioinformatics (Oxford, England) · 2026Article
- A new form of diabetes caused by INS mutations defined by zygosity, stem cell and population data.EMBO molecular medicine · 2026Article
- Neonatal diabetes mellitus is a significant feature of COXPD-24 caused by recessive NARS2 variants.Diabetic medicine : a journal of the British Diabetic Association · 2025Article
- Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity.Genome medicine · 2025Article
- Large copy number variants are an important cause of congenital hyperinsulinism that should be screened for during routine testing.Frontiers in endocrinology · 2025Article
- Characterization of congenital hyperinsulinism in Argentina: Clinical features, genetic findings, and treatment outcomes.PloS one · 2025Article
- Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the loss of FOXA2 or its regulatory elements.European journal of human genetics : EJHG · 2024Article
- Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor.The Journal of molecular diagnostics : JMD · 2024Article
- Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads.American journal of human genetics · 2024Article
- The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest.Molecular genetics and genomics : MGG · 2024Article
- Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.Briefings in bioinformatics · 2024Review
- Primate-specific ZNF808 is essential for pancreatic development in humans.Nature genetics · 2023Article
- SLC4A10 mutation causes a neurological disorder associated with impaired GABAergic transmission.Brain : a journal of neurology · 2023Article
- GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data.Nature genetics · 2023Article
- Infancy-onset diabetes caused by de-regulated AMPylation of the human endoplasmic reticulum chaperone BiP.EMBO molecular medicine · 2023Article
- Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Identifying copy number variants (CNVs) can provide diagnoses to patients and provide important biological insights into human health and disease. Current exome and targeted sequencing approaches cannot detect clinically and biologically-relevant CNVs outside their target area. We present SavvyCNV, a tool which uses off-target read data from exome and targeted sequencing data to call germline CNVs genome-wide. Up to 70% of sequencing reads from exome and targeted sequencing fall outside the targeted regions. We have developed a new tool, SavvyCNV, to exploit this 'free data' to call CNVs across the genome. We benchmarked SavvyCNV against five state-of-the-art CNV callers using truth sets generated from genome sequencing data and Multiplex Ligation-dependent Probe Amplification assays. SavvyCNV called CNVs with high precision and recall, outperforming the five other tools at calling CNVs genome-wide, using off-target or on-target reads from targeted panel and exome sequencing. We then applied SavvyCNV to clinical samples sequenced using a targeted panel and were able to call previously undetected clinically-relevant CNVs, highlighting the utility of this tool within the diagnostic setting. SavvyCNV outperforms existing tools for calling CNVs from off-target reads. It can call CNVs genome-wide from targeted panel and exome data, increasing the utility and diagnostic yield of these tests. SavvyCNV is freely available at https://github.com/rdemolgen/SavvySuite.
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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.