scholarly journals A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation

2010 ◽  
Vol 4 (6) ◽  
pp. 421 ◽  
Author(s):  
Anis Karimpour-Fard ◽  
Laura Dumas ◽  
Tzulip Phang ◽  
James M Sikela ◽  
Lawrence E Hunter
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Comparative Genomic Hybridisation ◽  
Comparative Genomic ◽  
Analysis Software ◽  
Array Comparative Genomic Hybridisation ◽  
Number Variation

scholarly journals Copy Number Variation of Multiple Genes in SAPHO Syndrome

2019 ◽  
Vol 47 (9) ◽  
pp. 1323-1329
Author(s):  
Changlong Guo ◽  
Xin Tian ◽  
Feifei Han ◽  
Lihong Liu ◽  
Jianen Gao ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Candidate Genes ◽  
Copy Number ◽  
Nuclear Family ◽  
Sapho Syndrome ◽  
Unknown Etiology ◽  
Comparative Genomic ◽  
Number Variation ◽  
And Control ◽  
Control Samples

Objective.SAPHO (synovitis, acne, pustulosis, hyperostosis, osteitis) syndrome is a type of rare chronic aseptic inflammation of unknown etiology. To date, no research to our knowledge has reported copy number variation (CNV) of genes that could affect predisposition to SAPHO syndrome. We investigated the association between CNV profile and SAPHO syndrome.Methods.We used array comparative genomic hybridization (CGH) to screen for CNV in a nuclear family including 2 patients and a healthy control. We then validated the copy numbers of candidate genes found in the array CGH assay and other candidate genes by TaqMan real-time PCR in 360 case and control samples.Results.Ten regions from 8 chromosomes were found to have abnormal gene copies in the nuclear family, so the CNV of candidate genes (ADAM5, CSF2RA, IL3RA, and 9 other genes) were tested by TaqMan PCR. Significant copy number loss of CSF2RA (p = 0.000) and NOD2 (p = 0.005), and significant copy number gain of MEGF6 (p = 0.002) and ADAM5 (p = 0.000) were seen in patients with SAPHO compared with controls at the a = 0.05 level. There were no differences in the other 8 candidate genes between patient and control samples (p > 0.05).Conclusion.Our study established the first association between CNV in CSF2RA, NOD2, MEGF6, and ADAM5 and SAPHO syndrome. These findings may offer insight into the pathogenesis of SAPHO and provide the basis for improved diagnosis and treatment.

Array-based comparative genomic hybridization and copy number variation in cancer research

2006 ◽  
Vol 115 (3-4) ◽  
pp. 262-272 ◽  
Author(s):  
E.K. Cho ◽  
J. Tchinda ◽  
J.L. Freeman ◽  
Y.-J. Chung ◽  
W.W. Cai ◽  
...  
Keyword(s):  
Cancer Research ◽  
Copy Number Variation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Measurement of DNA sequence copy number variation using comparative genomic hybridization to microarrays

10.1038/14259 ◽  
1999 ◽  
Vol 23 (S3) ◽  
pp. 30-30
Author(s):  
D.G. Albertson ◽  
R. Segraves ◽  
B. Huey ◽  
X. Zhang ◽  
J. Palmer ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Dna Sequence ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Number Variation

scholarly journals Absence of AVPR2 copy number variation in eunatremic and dysnatremic subjects in non-Hispanic Caucasian populations

2010 ◽  
Vol 40 (3) ◽  
pp. 121-127 ◽  
Author(s):  
Yi Fu ◽  
Zhan Chen ◽  
Alexandra I. F. Blakemore ◽  
Eric Orwoll ◽  
David M. Cohen
Keyword(s):  
Water Balance ◽  
Copy Number Variation ◽  
Serum Sodium ◽  
Water Conservation ◽  
Copy Number ◽  
Osteoporotic Fractures ◽  
Sodium Concentration ◽  
Serum Sodium Concentration ◽  
Comparative Genomic ◽  
Number Variation

Copy number variation (CNV) is increasingly recognized as a source of phenotypic variation among humans. We hypothesized that a CNV in the human arginine vasopressin receptor-2 gene ( AVPR2) would be associated with serum sodium concentration based on the following lines of evidence: 1) the protein product of the AVPR2 gene is essential for renal water conservation; 2) mutations in the AVPR2 gene are associated with aberrant water balance in humans; 3) heritability of serum sodium concentration may be greater in females than in males; 4) the AVPR2 gene is X-linked; and 5) a common CNV spanning the AVPR2 gene was recently described in a non-Hispanic Caucasian population. We developed a highly reproducible assay for AVPR2 CNV. Among 279 subjects with measured serum sodium concentration in the Offspring Cohort of the Framingham Heart Study, no subjects exhibited CNV at the AVPR2 locus. Among 517 subjects in the Osteoporotic Fractures in Men Study (MrOS)—including 152 with hyponatremia and 183 with hypernatremia—no subjects with CNV at the AVPR2 locus were identified. CNV at the AVPR2 locus could not be independently confirmed, and CNV at the AVPR2 gene is unlikely to influence systemic water balance on a population-wide basis in non-Hispanic Caucasian subjects. A novel AVPR2 single nucleotide polymorphism affecting the reporter hybridization site gave rise to an artifactually low copy number signal (i.e., less than unity) in one male African American subject. Reanalysis of the original comparative genomic hybridization data revealed bona fide CNVs flanking—but not incorporating—the AVPR2 gene, consistent with our new genotyping data.

scholarly journals Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Yan Guo ◽  
Quanghu Sheng ◽  
David C. Samuels ◽  
Brian Lehmann ◽  
Joshua A. Bauer ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Exome Sequencing ◽  
Copy Number ◽  
Array Cgh ◽  
False Positive Rate ◽  
Comparative Genomic ◽  
Comparative Genome Hybridization ◽  
Sequencing Data ◽  
Number Variation ◽  
Low Sensitivity

Exome sequencing using next-generation sequencing technologies is a cost-efficient approach to selectively sequencing coding regions of the human genome for detection of disease variants. One of the lesser known yet important applications of exome sequencing data is to identify copy number variation (CNV). There have been many exome CNV tools developed over the last few years, but the performance and accuracy of these programs have not been thoroughly evaluated. In this study, we systematically compared four popular exome CNV tools (CoNIFER, cn.MOPS, exomeCopy, and ExomeDepth) and evaluated their effectiveness against array comparative genome hybridization (array CGH) platforms. We found that exome CNV tools are capable of identifying CNVs, but they can have problems such as high false positives, low sensitivity, and duplication bias when compared to array CGH platforms. While exome CNV tools do serve their purpose for data mining, careful evaluation and additional validation is highly recommended. Based on all these results, we recommend CoNIFER and cn.MOPs for nonpaired exome CNV detection over the other two tools due to a low false-positive rate, although none of the four exome CNV tools performed at an outstanding level when compared to array CGH.

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