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

scholarly journals Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohnʼs Disease

2016 ◽  
Vol 22 (3) ◽  
pp. 505-515 ◽  
Author(s):  
Isabelle Cleynen ◽  
Peter Konings ◽  
Caroline Robberecht ◽  
Debby Laukens ◽  
Leila Amininejad ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Susceptibility Gene ◽  
Complement Component ◽  
Genome Wide ◽  
Number Variation

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.

scholarly journals Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

2010 ◽  
Vol 20 (12) ◽  
pp. 1719-1729 ◽  
Author(s):  
M. D. Robinson ◽  
C. Stirzaker ◽  
A. L. Statham ◽  
M. W. Coolen ◽  
J. Z. Song ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number Variation ◽  
Copy Number ◽  
Methylation Data ◽  
Amplification Bias ◽  
Genome Wide ◽  
Number Variation

scholarly journals Genome-Wide Detection of Allele Specific Copy Number Variation Associated with Insulin Resistance in African Americans from the HyperGEN Study

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e24052 ◽  
Author(s):  
Marguerite R. Irvin ◽  
Nathan E. Wineinger ◽  
Treva K. Rice ◽  
Nicholas M. Pajewski ◽  
Edmond K. Kabagambe ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
African Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide ◽  
Number Variation ◽  
Allele Specific

Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen

2008 ◽  
Vol 7 (4) ◽  
pp. 319-326 ◽  
Author(s):  
Hylke M Blauw ◽  
Jan H Veldink ◽  
Michael A van Es ◽  
Paul W van Vught ◽  
Christiaan GJ Saris ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Copy Number Variation ◽  
Copy Number ◽  
Sporadic Amyotrophic Lateral Sclerosis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation ◽  
Lateral Sclerosis

scholarly journals A genome-wide analysis of copy number variation in Murciano-Granadina goats

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Dailu Guan ◽  
Amparo Martínez ◽  
Anna Castelló ◽  
Vincenzo Landi ◽  
María Gracia Luigi-Sierra ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation

scholarly journals Optimizing copy number variation analysis using genome-wide short sequence oligonucleotide arrays

2010 ◽  
Vol 38 (10) ◽  
pp. 3275-3286 ◽  
Author(s):  
Derek A. Oldridge ◽  
Samprit Banerjee ◽  
Sunita R. Setlur ◽  
Andrea Sboner ◽  
Francesca Demichelis
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Short Sequence ◽  
Variation Analysis ◽  
Oligonucleotide Arrays ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
Number Variation
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