Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing

2008 ◽  
Vol 30 (3) ◽  
pp. 472-476 ◽  
Author(s):  
Dirk Goossens ◽  
Lotte N. Moens ◽  
Eva Nelis ◽  
An-Sofie Lenaerts ◽  
Wim Glassee ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Multiplex Pcr ◽  
Copy Number ◽  
Number Variation ◽  
Cnv Detection

scholarly journals CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome

2020 ◽  
Vol 36 (12) ◽  
pp. 3890-3891
Author(s):  
Linjie Wu ◽  
Han Wang ◽  
Yuchao Xia ◽  
Ruibin Xi
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Genome Structure ◽  
Real Data ◽  
Read Depth ◽  
Supplementary Information ◽  
Circular Genome ◽  
Number Variation ◽  
Copy Number Variation Detection ◽  
Cnv Detection

Abstract Motivation Whole-genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. Results We show that the replication bias is widespread using ∼200 bacterial WGS data. We develop CNV-BAC (CNV-Bacteria) that can properly normalize the replication bias and other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementation CNV-BAC is available at https://github.com/XiDsLab/CNV-BAC. Supplementary information Supplementary data are available at Bioinformatics online.

Identification of copy number variation of CAPN10 in Thais with type 2 diabetes by multiplex PCR and denaturing high performance liquid chromatography (DHPLC)

Gene ◽  
2012 ◽  
Vol 506 (2) ◽  
pp. 383-386 ◽  
Author(s):  
Nattachet Plengvidhya ◽  
Kanjana Chanprasert ◽  
Watip Tangjittipokin ◽  
Wanna Thongnoppakhun ◽  
Pa-thai Yenchitsomanus
Keyword(s):  
Type 2 Diabetes ◽  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
Copy Number Variation ◽  
Multiplex Pcr ◽  
Copy Number ◽  
High Performance ◽  
Number Variation

scholarly journals Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Joaquim Manoel da Silva ◽  
Poliana Fernanda Giachetto ◽  
Luiz Otávio da Silva ◽  
Leandro Carrijo Cintra ◽  
Samuel Rezende Paiva ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Production Traits ◽  
Genome Wide ◽  
Number Variation ◽  
Nelore Cattle ◽  
Cnv Detection

A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis

2018 ◽  
Vol 480 ◽  
pp. 173-179 ◽  
Author(s):  
Paola Concolino ◽  
Roberta Rizza ◽  
Flavio Mignone ◽  
Alessandra Costella ◽  
Donatella Guarino ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Copy Number Variation ◽  
Molecular Diagnosis ◽  
Copy Number ◽  
Breast And Ovarian Cancer ◽  
Number Variation ◽  
Cnv Detection

scholarly journals CNV-BAC: Copy Number Variation Detection in Bacterial Circular Genome

2019 ◽  
Author(s):  
Linjie Wu ◽  
Han Wang ◽  
Yuchao Xia ◽  
Ruibin Xi
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Genome Structure ◽  
Real Data ◽  
Read Depth ◽  
Replication Rate ◽  
Circular Genome ◽  
Number Variation ◽  
Copy Number Variation Detection ◽  
Cnv Detection

AbstractMotivationWhole genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias.ResultsWe show that the replication bias is widespread using ~200 bacterial WGS data. We develop CNV-BAC that can properly normalize the replication bias as well as other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms.Availability and implementationCNV-BAC is available at https://github.com/LinjieWu/[email protected]

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

2008 ◽  
Vol 29 (1) ◽  
pp. 182-189 ◽  
Author(s):  
Naoya Hosono ◽  
Michiaki Kubo ◽  
Yumiko Tsuchiya ◽  
Hiroko Sato ◽  
Takuya Kitamoto ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Multiplex Pcr ◽  
Real Time ◽  
Copy Number ◽  
Invader Assay ◽  
Number Variation ◽  
Novel Snp

Identification of Novel Germline and Tumor-Specific Nucleotide Variants and Copy Number Variation in Clival Chordomas by Exome Sequencing

2015 ◽  
Vol 76 (S 01) ◽  
Author(s):  
Georgios Zenonos ◽  
Peter Howard ◽  
Maureen Lyons-Weiler ◽  
Wang Eric ◽  
William LaFambroise ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Exome Sequencing ◽  
Copy Number ◽  
Number Variation ◽  
Specific Nucleotide

The impact of paralog genes: detection of copy number variation in spinal muscle atrophy patients

BIOCELL ◽  
2018 ◽  
Vol 42 (3) ◽  
pp. 87-91 ◽  
Author(s):  
Sergio LAURITO ◽  
Juan A. CUETO ◽  
Jimena PEREZ ◽  
Mar韆 ROQU�
Keyword(s):  
Copy Number Variation ◽  
Muscle Atrophy ◽  
Copy Number ◽  
Number Variation ◽  
The Impact
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