Analytical and clinical validity of whole-genome oligonucleotide array comparative genomic hybridization for pediatric patients with mental retardation and developmental delay

2008 ◽  
Vol 146A (15) ◽  
pp. 1942-1954 ◽  
Author(s):  
Bixia Xiang ◽  
Ao Li ◽  
Dinu Valentin ◽  
Norma J. Nowak ◽  
Hongyu Zhao ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Developmental Delay ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Pediatric Patients ◽  
Oligonucleotide Array ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Clinical Validity ◽  
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.

scholarly journals A novel de novo paracentric inversion [inv(20)(q13.1q13.3)] accompanied by an 11q14.3-q21 microdeletion in a pediatric patient with an intellectual disability

2018 ◽  
Vol 21 (2) ◽  
pp. 63-67
Author(s):  
S Zachaki ◽  
E Kouvidi ◽  
A Mitrakos ◽  
L Lazaros ◽  
A Pantou ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
De Novo ◽  
Chromosomal Abnormalities ◽  
Mendelian Inheritance ◽  
Paracentric Inversion ◽  
Comparative Genomic ◽  
Published Data ◽  
Genomic Hybridization

Abstract A novel de novo paracentric inversion of the long arm of chromosome 20 [inv(20)(q13.1q13.3)], detected by conventional karyotyping in a 14-year-old boy with mental retardation is described. Further investigation by array comparative genomic hybridization (aCGH) revealed that the 20q inversion was not accompanied by microdeletions/microduplications containing disease-associated genes near or at the breakpoints. Two deletions at chromosomal regions 11q14.3q21 and 20q12 of 4.5 and 1.97 Mb size, respectively, containing important online Mendelian inheritance in man (OMIM) genes, were detected. The 4.5Mb 11q14.3q21 microdeletion was contained within a region that is involved, in most of the reported cases, with the interstitial 11q deletion and may be related to the mental retardation and developmental delay present in the patient. On the other hand, the published data about the 20q12 microdeletion are very few and it is not possible to correlate this finding with our patient’s phenotype. This case report contributes to the description of a new chromosomal entity, not previously reported, and is therefore important, especially in prenatal diagnosis and management of patients. Array comparative genomic hybridization has proven a useful technique for detecting submicroscopic rearrangements and should be offered prenatally, especially in cases of de novo karyotypically balanced chromosomal inversions or translocations in order to unveil other unbalanced chromosomal abnormalities such as deletions and amplifications.

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