SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data

Chen, Yong; Zhao, Li; Wang, Yi; Cao, Ming; Gelowani, Violet; Xu, Min; Agrawal, Smriti A.; Li, Yumei; Daiger, Stephen P.; Gibbs, Richard A.; Wang, Fei; Chen, Rui

doi:10.1186/s12859-017-1566-3

Cited by 55 publications

(36 citation statements)

References 49 publications

(46 reference statements)

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“…The axon protection conferred by NMNAT1 seems to be closely related to mitochondria, which is a critical organelle for the maintenance of redox state (59,60). In addition, NMNAT1 also has other functional implications (50,59,(61)(62)(63)(64)(65)(66)(67)(68)(69)(70)(71)(72)(73)(74)(75)(76)(77)(78).…”

Section: Discussionmentioning

confidence: 99%

Targeted deletion of Nmnat1 in mouse retina leads to early severe retinal dystrophy

Wang

Fang

Liao

et al. 2017

Preprint

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Mutations in NMNAT1 can lead to a very severe type of retinal dystrophy, Leber congenital amaurosis, in human patients, characterized by infantile-onset or congenital retinal dystrophy and childhood blindness. The loss-of-function mouse models of Nmnat1 have not been well-established, since the complete knock-out (KO) of Nmnat1 in mice results in embryonic lethality. Here, we generated retina-specific KO by using the Crxpromotor-driving Cre combined with the flox allele. By a panel of histological and functional analyses, we found that Nmnat1 conditional KO (cKO) mice have early severe retinal dystrophy. Specifically, the photoreceptors of Nmnat1 cKO mice are almost diminished and the retinal functions also become completely abolished. Our results established a loss-of-function model for Nmnat1 in mice, which will be useful for studying the detailed functions of NMNAT1 in the retina.peer-reviewed)

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Section: Discussionmentioning

confidence: 99%

Targeted deletion of Nmnat1 in mouse retina leads to early severe retinal dystrophy

Wang

Fang

Liao

et al. 2017

Preprint

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“…Copy number variation analysis methods based on Next-Generation Sequencing (NGS) are evolving [12], but the precision and reliability of aCGH remains to be matched by computer algorithms.…”

Section: Introductionmentioning

confidence: 99%

An Extended Targeted Copy Number Variation Detection Array Including 187 Genes for the Diagnostics of Neuromuscular Disorders

Sagath

Lehtokari

Välipakka

et al. 2018

JND

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Background:Our previous array, the Comparative Genomic Hybridisation design (CGH-array) for nemaline myopathy (NM), named the NM-CGH array, revealed pathogenic copy number variation (CNV) in the genes for nebulin (NEB) and tropomyosin 3 (TPM3), as well as recurrent CNVs in the segmental duplication (SD), i.e. triplicate, region of NEB (TRI, exons 82–89, 90–97, 98–105). In the light of this knowledge, we have designed and validated an extended CGH array, which includes a selection of 187 genes known to cause neuromuscular disorders (NMDs).Objective:Our aim was to develop a reliable method for CNV detection in genes related to neuromuscular disorders for routine mutation detection and analysis, as a much-needed complement to sequencing methods.Methods:We have developed a novel custom-made 4×180 k CGH array for the diagnostics of NMDs. It includes the same tiled ultra-high density coverage of the 12 known or putative NM genes as our 8×60 k NM-CGH-array but also comprises a selection of 175 additional genes associated with NMDs, including titin (TTN), at a high to very high coverage. The genes were divided into three coverage groups according to known and potential pathogenicity in neuromuscular disorders.Results:The array detected known and putative CNVs in all three gene coverage groups, including the repetitive regions of NEB and TTN.Conclusions:The targeted neuromuscular disorder 4×180 k array-CGH (NMD-CGH-array v1.0) design allows CNV detection for a broader spectrum of neuromuscular disorders at a high resolution.

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“…Furthermore, copy number loss of PRPF31 was also reported to cause RP. 19 Therefore, we here cannot exclude this possibility in explaining our results. We will investigate the copy number variations of PRPF3 in our further studies.…”

Section: Discussionmentioning

confidence: 70%

Novel Mutations in PRPF31 Causing Retinitis Pigmentosa Identified Using Whole-Exome Sequencing

Xiao

Cao

Zhang

et al. 2017

Invest. Ophthalmol. Vis. Sci.

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SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data

Cited by 55 publications

References 49 publications

Targeted deletion of Nmnat1 in mouse retina leads to early severe retinal dystrophy

Targeted deletion of Nmnat1 in mouse retina leads to early severe retinal dystrophy

An Extended Targeted Copy Number Variation Detection Array Including 187 Genes for the Diagnostics of Neuromuscular Disorders

Novel Mutations in PRPF31 Causing Retinitis Pigmentosa Identified Using Whole-Exome Sequencing

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