CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications

Rapti, Melivoia; Zouaghi, Yassine; Meylan, J; Ranza, Emmanuelle; Antonarakis, Stylianos E.; Santoni, Federico

doi:10.1093/bib/bbac049

Cited by 9 publications

(5 citation statements)

References 30 publications

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“…This is achievable with tools such as CoNIFER ( Krumm et al, 2012 ), exomeCopy ( Love et al, 2011 ), CNVkit ( Talevich et al, 2016 ), cn. MOPS ( Klambauer et al, 2012 ), CNest ( Fitzgerald and Birney, 2022 ), CNVind ( Kusmirek and Nowak, 2022 ), CoverageMaster ( Rapti et al, 2022 ) and EXCAVATOR2 ( D’Aurizio et al, 2016 ; D’Aurizio et al, 2018 ). More recently, Olfe et al have demonstrated CTLA-4 insufficiency due to a novel CTLA-4 deletion using ClinCNV ( German and Stephan, 2019 ; Olfe et al, 2023 ), further highlighting the synergy of CNV calling with WES analysis.…”

Section: Discussionmentioning

confidence: 99%

Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus

Yeo,

Lim,

Yaung

et al. 2024

Front. Genet.

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Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.

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Section: Discussionmentioning

confidence: 99%

Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus

Yeo,

Lim,

Yaung

et al. 2024

Front. Genet.

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“…Despite a lot of algorithms have been developed to detect CNVs from sequencing data, high resolution version of aCGH is still an appropriate methodology for the analysis of chromosome aberrations in a cohort (Corallo et al, 2021; Retterer et al, 2015). The application of whole‐exome sequencing (WES) surely reduced related costs of sequencing while there is also deficiency considering the restricted detection in exomic space and the data processing itself (Rapti et al, 2022). Chromosome aberrations in MRKH patients has been only analyzed using WES data in the Chinese population (Chen, Zhao, et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Recurrent human 16p11.2 microdeletions in type I Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome patients in Chinese Han population

Su,

Liu,

et al. 2023

Molec Gen & Gen Med

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BackgroundsMayer‐Rokitansky‐Küster‐Hauser (MRKH) syndrome, a severe congenital malformation of the female genital tract, is a highly heterogeneous disease which has no clear etiology. Previous studies have suggested that copy number variations (CNVs) and single‐gene mutations might contribute to the development of MRKH syndrome. In particular, deletions in 16p11.2, which are suggested to be involved in several congenital diseases, have been reported in Chinese type II MRKH patients and European MRKH patients. However, few CNVs including 16p11.2 microdeletions were identified in Chinese type I MRKH cases although it accounted for the majority of MRKH patients in China. Thus, we conducted a retrospective study to identify whether CNVs at human chromosome 16p11.2 are risk factors of type I MRKH syndrome in the Chinese Han population.MethodsWe recruited 143 patients diagnosed with type I MRKH between 2012 and 2014. Five hundred unrelated Chinese without congenital malformation were enrolled in control group, consisting of 197 from the 1000 Genomes Project and 303 from Fudan University. Quantitative PCR, array comparative genomic hybridization, and sanger sequencing were conducted to screen and verify candidate variant.ResultsOur study identified recurrent 16p11.2 microdeletions of approximately 600 kb in two out of the 143 type I MRKH syndrome patients using high‐density array‐based comparative genomic hybridization (aCGH), while no 16p11.2 deletion was found in the control group. We did not find any mutations in TBX6 gene in our samples.ConclusionsThe results of the study identify 16p11.2 deletion in Chinese MRKH I patients for the first time, as well as support the contention that 16p11.2 microdeletions are associated with MRKH syndrome in both types across populations. It is suggested that 16p11.2 microdeletions should be included in molecular diagnosis and genetic counseling of female reproductive tract disorders.

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“…It has been established that mNGS exhibits limited ability for structural rearrangement and CNV detection. However, numerous techniques and algorithms have been put forward, such as Sat-BSA (SVs associated with traits), CoverageMaster, and KNNCNV (K-Nearest Neighbor-based CNV detection) (37)(38)(39). Besides, the sensitivity and specificity of mNGS require further improvement, and combining mNGS with other assays is a promising strategy.…”

Section: Discussionmentioning

confidence: 99%

Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis

Chen²,

Ouyang³

et al. 2022

Front. Neurol.

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ObjectiveIt is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis.MethodsFollowing the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation.ResultsA total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70–82%, I2 = 39.69%) and specificity was 96% (95% CI: 93–98%, I2 = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88–0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p > 0.05).ConclusionOverall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application.Study registration numberINPLASY202120002

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CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications

Cited by 9 publications

References 30 publications

Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus

Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus

Recurrent human 16p11.2 microdeletions in type I Mayer–Rokitansky–Küster–Hauser (MRKH) syndrome patients in Chinese Han population

Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis

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