Detection of pathogenic gene copy number variations in patients with mental retardation by genomewide oligonucleotide array comparative genomic hybridization

2007 ◽  
Vol 28 (11) ◽  
pp. 1124-1132 ◽  
Author(s):  
Yao-Shan Fan ◽  
Parul Jayakar ◽  
Hongbo Zhu ◽  
Deborah Barbouth ◽  
Stephanie Sacharow ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Array Comparative Genomic Hybridization ◽  
Gene Copy Number ◽  
Copy Number Variations ◽  
Oligonucleotide Array ◽  
Gene Copy ◽  
Comparative Genomic ◽  
Pathogenic Gene

A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

2017 ◽  
Vol 114 (8) ◽  
pp. 1903-1908 ◽  
Author(s):  
Nandita Vishwanathan ◽  
Arpan Bandyopadhyay ◽  
Hsu-Yuan Fu ◽  
Kathryn C. Johnson ◽  
Nathan M. Springer ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Cell Lines ◽  
Copy Number ◽  
Chinese Hamster ◽  
Gene Copy Number ◽  
Chinese Hamster Cell ◽  
Copy Number Variations ◽  
Gene Copy ◽  
Comparative Genomic ◽  
Genomic Hybridization

Gene Copy Number Analysis by Fluorescencein SituHybridization and Comparative Genomic Hybridization

Methods ◽  
1996 ◽  
Vol 9 (1) ◽  
pp. 113-121 ◽  
Author(s):  
Anne Kallioniemi ◽  
Tapio Visakorpi ◽  
Ritva Karhu ◽  
Dan Pinkel ◽  
Olli-P. Kallioniemi
Keyword(s):  
Comparative Genomic Hybridization ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Comparative Genomic ◽  
Copy Number Analysis ◽  
Genomic Hybridization

scholarly journals Development of a Focused Oligonucleotide-Array Comparative Genomic Hybridization Chip for Clinical Diagnosis of Genomic Imbalance

2007 ◽  
Vol 53 (12) ◽  
pp. 2051-2059 ◽  
Author(s):  
Yiping Shen ◽  
David T Miller ◽  
Sau Wai Cheung ◽  
Va Lip ◽  
Xiaoming Sheng ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Developmental Disorders ◽  
Array Cgh ◽  
Clinical Laboratory ◽  
Oligonucleotide Array ◽  
Comparative Genomic ◽  
Genomic Hybridization ◽  
Genomic Imbalance

Abstract Background: Submicroscopic genomic imbalance underlies well-defined microdeletion and microduplication syndromes and contributes to general developmental disorders such as mental retardation and autism. Array comparative genomic hybridization (CGH) complements routine cytogenetic methods such as karyotyping and fluorescence in situ hybridization (FISH) for the detection of genomic imbalance. Oligonucleotide arrays in particular offer advantages in ease of manufacturing, but standard arrays for single-nucleotide polymorphism genotyping or linkage analysis offer variable coverage in clinically relevant regions. We report the design and validation of a focused oligonucleotide-array CGH assay for clinical laboratory diagnosis of genomic imbalance. Methods: We selected >10 000 60-mer oligonucleotide features from Agilent’s eArray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci. Sensitivity and specificity were measured for 105 patient samples, including 51 with known genomic-imbalance events, as detected by bacterial artificial chromosome–based array CGH, FISH, or multiplex ligation-dependent probe amplification. Results: Focused array CGH detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signal-to-noise ratio. The mean SD among log2 ratios of all noncontrol features without copy number alteration was 0.062 (median, 0.055). Clinical testing of another 211 samples from individuals with developmental delay, unexplained mental retardation, dysmorphic features, or multiple congenital anomalies revealed genomic imbalance in 25 samples (11.9%). Conclusions: This focused oligonucleotide-array CGH assay, a flexible, robust method for clinically diagnosing genetic disorders associated with genomic imbalance, offers appreciable advantages over currently available platforms.

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