scholarly journals aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

PLoS ONE ◽  
2017 ◽  
Vol 12 (12) ◽  
pp. e0189334 ◽  
Author(s):  
Victor Renault ◽  
Jörg Tost ◽  
Fabien Pichon ◽  
Shu-Fang Wang-Renault ◽  
Eric Letouzé ◽  
...  
Keyword(s):  
Copy Number ◽  
Absolute Copy Number ◽  
Genome Wide

scholarly journals Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Nayoung Han ◽  
Jung Mi Oh ◽  
In-Wha Kim
Keyword(s):  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Gain ◽  
Copy Number Variations ◽  
Gene Gain ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Control And Prevention

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

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 Genome-wide copy number variations as molecular diagnostic tool for cutaneous intermediate melanocytic lesions: a systematic review and individual patient data meta-analysis

2021 ◽  
Author(s):  
Chiel F. Ebbelaar ◽  
Anne M. L. Jansen ◽  
Lourens T. Bloem ◽  
Willeke A. M. Blokx
Keyword(s):  
Systematic Review ◽  
Sensitivity And Specificity ◽  
Copy Number ◽  
Individual Patient Data ◽  
Meta Analysis ◽  
Copy Number Variations ◽  
Patient Data ◽  
Melanocytic Lesions ◽  
Genome Wide ◽  
Malignant Lesions

AbstractCutaneous intermediate melanocytic neoplasms with ambiguous histopathological features are diagnostically challenging. Ancillary cytogenetic techniques to detect genome-wide copy number variations (CNVs) might provide a valuable tool to allow accurate classification as benign (nevus) or malignant (melanoma). However, the CNV cut-off value to distinguish intermediate lesions from melanoma is not well defined. We performed a systematic review and individual patient data meta-analysis to evaluate the use of CNVs to classify intermediate melanocytic lesions. A total of 31 studies and 431 individual lesions were included. The CNV number in intermediate lesions (median 1, interquartile range [IQR] 0–2) was significantly higher (p<0.001) compared to that in benign lesions (median 0, IQR 0–1) and lower (p<0.001) compared to that in malignant lesions (median 6, IQR 4–11). The CNV number displayed excellent ability to differentiate between intermediate and malignant lesions (0.90, 95% CI 0.86–0.94, p<0.001). Two CNV cut-off points demonstrated a sensitivity and specificity higher than 80%. A cut-off of ≥3 CNVs corresponded to 85% sensitivity and 84% specificity, and a cut-off of ≥4 CNVs corresponded to 81% sensitivity and 91% specificity, respectively. This individual patient data meta-analysis provides a comprehensive overview of CNVs in cutaneous intermediate melanocytic lesions, based on the largest pooled cohort of ambiguous melanocytic neoplasms to date. Our meta-analysis suggests that a cut-off of ≥3 CNVs might represent the optimal trade-off between sensitivity and specificity in clinical practice to differentiate intermediate lesions from melanoma.

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

Genome-Wide High-Resolution Screening in Dupuytren's Disease Reveals Common Regions of DNA Copy Number Alterations

2010 ◽  
Vol 35 (7) ◽  
pp. 1172-1183.e7 ◽  
Author(s):  
Barbara B. Shih ◽  
May Tassabehji ◽  
James S. Watson ◽  
Angus D. McGrouther ◽  
Ardeshir Bayat
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Dupuytren’S Disease ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Dupuytren's Disease ◽  
Genome Wide ◽  
Dna Copy Number Alterations

High-resolution genome-wide array-CGH reveals copy number variations associated with premature ovarian failure

Placenta ◽  
2011 ◽  
Vol 32 ◽  
pp. S282
Author(s):  
Paola Scaruffi ◽  
Sara Stigliani ◽  
Annamaria Jane Nicoletti ◽  
Pier Luigi Venturini ◽  
Gian Paolo Tonini ◽  
...  
Keyword(s):  
High Resolution ◽  
Premature Ovarian Failure ◽  
Copy Number ◽  
Array Cgh ◽  
Copy Number Variations ◽  
Ovarian Failure ◽  
Genome Wide

scholarly journals Genome-wide Association of Copy-Number Variation Reveals an Association between Short Stature and the Presence of Low-Frequency Genomic Deletions

2011 ◽  
Vol 89 (6) ◽  
pp. 751-759 ◽  
Author(s):  
Andrew Dauber ◽  
Yongguo Yu ◽  
Michael C. Turchin ◽  
Charleston W. Chiang ◽  
Yan A. Meng ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Short Stature ◽  
Copy Number ◽  
Low Frequency ◽  
Genome Wide Association ◽  
Genomic Deletions ◽  
Genome Wide ◽  
Number Variation
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