Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions

The recent advance of single-cell copy number variation analysis plays an essential role in addressing intra-tumor heterogeneity, identifying tumor subgroups, and restoring tumor evolving trajectories at single-cell scale. Pleasant visualization of copy number analysis results boosts productive scientific exploration, validation, and sharing. Several single-cell analysis figures have the effectiveness of visualizations for understanding single-cell genomics in published articles and software packages. However, they almost lack real-time interaction, and it is hard to reproduce them. Moreover, existing tools are time-consuming and memory-intensive when they reach large-scale single-cell throughputs. We present an online visualization platform, scSVAS, for real-time interactive single-cell genomics data visualization. scSVAS is specifically designed for large-scale single-cell analysis. Compared with other tools, scSVAS manifests the most comprehensive functionalities. After uploading the specified input files, scSVAS deploys the online interactive visualization automatically. Users may make scientific discoveries, share interactive visualization, and download high-quality publication-ready figures. scSVAS provides versatile utilities for managing, investigating, sharing, and publishing single-cell copy number variation profiles. We envision this online platform will expedite the biological understanding of cancer clonal evolution in single-cell resolution. All visualizations are publicly hosted at https://sc.deepomics.org.

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Analysis of Copy Number Variation in Urine: c-Myc Evaluation Using a Real-Time PCR Approach

Urinary Biomarkers - Methods in Molecular Biology ◽

10.1007/978-1-0716-1354-2_5 ◽

2021 ◽

pp. 49-56

Author(s):

Valentina Casadio ◽

Filippo Martignano ◽

Roberta Gunelli ◽

Samanta Salvi

Keyword(s):

Copy Number Variation ◽

Real Time ◽

Real Time Pcr ◽

Copy Number ◽

Number Variation

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Diagnosing Smith–Magenis Syndrome and Duplication 17p11.2 Syndrome byRAI1Gene Copy Number Variation Using Quantitative Real-Time PCR

Genetic Testing ◽

10.1089/gte.2007.0058 ◽

2008 ◽

Vol 12 (1) ◽

pp. 67-73 ◽

Cited By ~ 11

Author(s):

Hoa T. Truong ◽

Sara Solaymani-Kohal ◽

Kevin R. Baker ◽

Santhosh Girirajan ◽

Stephen R. Williams ◽

...

Keyword(s):

Copy Number Variation ◽

Real Time ◽

Real Time Pcr ◽

Copy Number ◽

Quantitative Real Time Pcr ◽

Number Variation

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Amplification of theInsulin-Like Growth Factor 1 ReceptorGene Is a Rare Event in Adrenocortical Adenocarcinomas: Searching for Potential Mechanisms of Overexpression

BioMed Research International ◽

10.1155/2014/936031 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 6

Author(s):

Tamaya Castro Ribeiro ◽

Alexander Augusto Jorge ◽

Madson Q. Almeida ◽

Beatriz Marinho de Paula Mariani ◽

Mirian Yumi Nishi ◽

...

Keyword(s):

Copy Number Variation ◽

Real Time ◽

Real Time Pcr ◽

Adrenocortical Carcinoma ◽

Copy Number ◽

Molecular Mechanisms ◽

Prognostic Biomarker ◽

Rare Event ◽

Adrenocortical Tumors ◽

Number Variation

Context.IGF1Roverexpression appears to be a prognostic biomarker of metastatic pediatric adrenocortical tumors. However, the molecular mechanisms that are implicated in its upregulation remain unknown.Aim. To investigate the potential mechanisms involved inIGF1Roverexpression.Patients and Methods. We studied 64 adrenocortical tumors.IGF1Rcopy number variation was determined in all patients using MLPA and confirmed using real time PCR. In a subgroup of 32 patients, automatic sequencing was used to identifyIGF1Rallelic variants and the expression of microRNAs involved inIGF1Rregulation by real time PCR.Results.IGF1Ramplification was detected in an adrenocortical carcinoma that was diagnosed in a 46-year-old woman with Cushing’s syndrome and virilization.IGF1Roverexpression was demonstrated in this case. In addition, gene amplification of otherlociwas identified in this adrenocortical malignant tumor, but noIGF1Rcopy number variation was evidenced in the remaining cases. Automatic sequencing revealed three known polymorphisms but they did not correlate with its expression. Expression of miR-100, miR-145, miR-375, and miR-126 did not correlate withIGF1Rexpression.Conclusion. We demonstrated amplification and overexpression ofIGF1Rgene in only one adrenocortical carcinoma, suggesting that these combined events are uncommon. In addition,IGF1Rpolymorphisms and abnormal microRNA expression did not correlate withIGF1Rupregulation in adrenocortical tumors.

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