scholarly journals DIGITAL PCR ON A COMPACT STEP EMULSIFICATION DEVICE AND ITS APPLICATION IN DETECTION OF COPY NUMBER VARIATIONS OF CANCER

2017 ◽  
Author(s):  
Wenbin Du ◽  
Mengyue Nie
Keyword(s):  
Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations

scholarly journals A Simple, Universal, and Cost-Efficient Digital PCR Method for the Targeted Analysis of Copy Number Variations

2019 ◽  
Vol 65 (9) ◽  
pp. 1153-1160 ◽  
Author(s):  
Kévin Cassinari ◽  
Olivier Quenez ◽  
Géraldine Joly-Hélas ◽  
Ludivine Beaussire ◽  
Nathalie Le Meur ◽  
...  
Keyword(s):  
Copy Number ◽  
Segregation Analysis ◽  
Genetic Diseases ◽  
Genomic Medicine ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Locked Nucleic Acid ◽  
Targeted Analysis ◽  
Cost Efficient ◽  
High Flexibility

Abstract BACKGROUND Rare copy number variations (CNVs) are a major cause of genetic diseases. Simple targeted methods are required for their confirmation and segregation analysis. We developed a simple and universal CNV assay based on digital PCR (dPCR) and universal locked nucleic acid (LNA) hydrolysis probes. METHODS We analyzed the mapping of the 90 LNA hydrolysis probes from the Roche Universal ProbeLibrary (UPL). For each CNV, selection of the optimal primers and LNA probe was almost automated; probes were reused across assays and each dPCR assay included the CNV amplicon and a reference amplicon. We assessed the assay performance on 93 small and large CNVs and performed a comparative cost-efficiency analysis. RESULTS UPL-LNA probes presented nearly 20000000 occurrences on the human genome and were homogeneously distributed with a mean interval of 156 bp. The assay accurately detected all the 93 CNVs, except one (<200 bp), with coefficient of variation <10%. The assay was more cost-efficient than all the other methods. CONCLUSIONS The universal dPCR CNV assay is simple, robust, and cost-efficient because it combines a straightforward design allowed by universal probes and end point PCR, the advantages of a relative quantification of the target to the reference within the same reaction, and the high flexibility of the LNA hydrolysis probes. This method should be a useful tool for genomic medicine, which requires simple methods for the interpretation and segregation analysis of genomic variations.

Assessment Of Sfmbt1, Prkra, And Erlin1 Copy Number Variations In Patients With Carotid Atherosclerosis Using Droplet Digital Pcr

2019 ◽  
Vol 287 ◽  
pp. e165-e166
Author(s):  
A. Sleptcov ◽  
M. Nazarenko ◽  
A. Kazantsev ◽  
I. Lebedev ◽  
O. Barbarash ◽  
...  
Keyword(s):  
Copy Number ◽  
Carotid Atherosclerosis ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Droplet Digital Pcr

scholarly journals Digital PCR for determination of cytochrome P450 2D6 and sulfotransferase 1A1 gene copy number variations

2017 ◽  
Vol 11 (6) ◽  
pp. 336-341 ◽  
Author(s):  
Yutaro Motoi ◽  
Kazufumi Watanabe ◽  
Hiroyuki Honma ◽  
Yousuke Tadano ◽  
Hiroshi Hashimoto ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Copy Number ◽  
Gene Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Cytochrome P450 2D6 ◽  
Sulfotransferase 1A1 ◽  
P450 2D6

scholarly journals Droplet digital PCR for identifying copy number variations in patients with primary immunodeficiency disorders

2021 ◽  
Author(s):  
See-Tarn Woon ◽  
Julia Mayes ◽  
Alexander Quach ◽  
Hilary Longhurst ◽  
Antonio Ferrante ◽  
...  
Keyword(s):  
Primary Immunodeficiency ◽  
Copy Number ◽  
Sanger Sequencing ◽  
Cost Effective ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Droplet Digital Pcr ◽  
Inborn Errors ◽  
Primary Immunodeficiency Disorders ◽  
Large Deletions

Abstract Primary immunodeficiency disorders comprise a rare group of mostly monogenic disorders caused by inborn errors of immunity. The majority can be identified by either Sanger sequencing or Next Generation Sequencing. Some disorders result from large insertions or deletions leading to copy number variations (CNV). Sanger sequencing may not identify these mutations. Here we present droplet digital PCR as an alternative cost-effective diagnostic method to identify CNV in these genes. The data from patients with large deletions of NFKB1, SERPING1 and SH2D1A are presented.

scholarly journals Digital PCR for the Analysis of MYC Copy Number Variation in Lung Cancer

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Alexander Brik ◽  
Daniel G. Weber ◽  
Swaantje Casjens ◽  
Peter Rozynek ◽  
Swetlana Meier ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Clinical Diagnostics ◽  
Gene Copy ◽  
Clinicopathological Parameters ◽  
Lung Cancer Patients

Background. MYC (v-myc avian myelocytomatosis viral oncogene homolog) is one of the most frequently amplified genes in lung tumors. For the analysis of gene copy number variations, dPCR (digital PCR) is an appropriate tool. The aim of our study was the assessment of dPCR for the detection of MYC copy number variations (CNV) in lung tissue considering clinicopathological parameters. Material and Methods. MYC status was analyzed with dPCR as well as qPCR (quantitative PCR) using gDNA (genomic DNA) from tumor and adjacent nontumor tissue samples of lung cancer patients. The performance of MYC was estimated based on the AUC (area under curve). Results. The results of the MYC amplification correlated significantly between dPCR and qPCR (rS=0.81, P<0.0001). The MYC copy number revealed by dPCR showed statistically significant differences between tumor and adjacent nontumor tissues. For discrimination, a sensitivity of 43% and a specificity of 99% were calculated, representing 55 true-positive and one false-positive tests. No statistically significant differences could be observed for age, sex, and smoking status or the clinicopathological parameters (histological subtype, grade, and stage). Conclusion. The results of the study show that dPCR is an accurate and reliable method for the determination of MYC copy numbers. The application is characterized by high specificity and moderate sensitivity. MYC amplification is a common event in lung cancer patients, and it is indicated that the determination of the MYC status might be useful in clinical diagnostics.

Precise quantitation and sensitive detection of copy number within genetic variations using ligation-mediated droplet digital PCR in plasma

2019 ◽  
Vol 11 (45) ◽  
pp. 5761-5767
Author(s):  
Hui Tian ◽  
Mingyue Duan ◽  
Pingping Wei ◽  
Fei Hu ◽  
Shuhao Zhao ◽  
...  
Keyword(s):  
Copy Number ◽  
Digital Pcr ◽  
Copy Number Variations ◽  
Genetic Variations ◽  
Cancer Diagnostics ◽  
Droplet Digital Pcr ◽  
Sensitive Detection

The analysis of cancer-associated genetic copy number variations (CNVs) has been employed for cancer diagnostics, treatment, and prognostic assessments.

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