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 log(2) 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.
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 log(2) 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.
Authors: Bixia Xiang; Hongbo Zhu; Yiping Shen; David T Miller; Kangmo Lu; Xiaofeng Hu; Hans C Andersson; Tarachandra M Narumanchi; Yueying Wang; Jose E Martinez; Bai-Lin Wu; Peining Li; Marilyn M Li; Tian-Jian Chen; Yao-Shan Fan Journal: J Mol Diagn Date: 2010-01-21 Impact factor: 5.568
Authors: D T Miller; Y Shen; L A Weiss; J Korn; I Anselm; C Bridgemohan; G F Cox; H Dickinson; J Gentile; D J Harris; V Hegde; R Hundley; O Khwaja; S Kothare; C Luedke; R Nasir; A Poduri; K Prasad; P Raffalli; A Reinhard; S E Smith; M M Sobeih; J S Soul; J Stoler; M Takeoka; W-H Tan; J Thakuria; R Wolff; R Yusupov; J F Gusella; M J Daly; B-L Wu Journal: J Med Genet Date: 2008-09-19 Impact factor: 6.318
Authors: N Wu; X Ming; J Xiao; Z Wu; X Chen; M Shinawi; Y Shen; G Yu; J Liu; H Xie; Z S Gucev; S Liu; N Yang; H Al-Kateb; J Chen; J Zhang; N Hauser; T Zhang; V Tasic; P Liu; X Su; X Pan; C Liu; L Wang; J Shen; J Shen; Y Chen; T Zhang; J Zhang; K W Choy; J Wang; Q Wang; S Li; W Zhou; J Guo; Y Wang; C Zhang; Hong Zhao; Yu An; Yu Zhao; J Wang; Z Liu; Y Zuo; Y Tian; X Weng; V R Sutton; H Wang; Y Ming; S Kulkarni; T P Zhong; P F Giampietro; S L Dunwoodie; S W Cheung; X Zhang; L Jin; J R Lupski; G Qiu; F Zhang Journal: N Engl J Med Date: 2015-01-07 Impact factor: 91.245
Authors: David T Miller; Margaret P Adam; Swaroop Aradhya; Leslie G Biesecker; Arthur R Brothman; Nigel P Carter; Deanna M Church; John A Crolla; Evan E Eichler; Charles J Epstein; W Andrew Faucett; Lars Feuk; Jan M Friedman; Ada Hamosh; Laird Jackson; Erin B Kaminsky; Klaas Kok; Ian D Krantz; Robert M Kuhn; Charles Lee; James M Ostell; Carla Rosenberg; Stephen W Scherer; Nancy B Spinner; Dimitri J Stavropoulos; James H Tepperberg; Erik C Thorland; Joris R Vermeesch; Darrel J Waggoner; Michael S Watson; Christa Lese Martin; David H Ledbetter Journal: Am J Hum Genet Date: 2010-05-14 Impact factor: 11.025
Authors: Okay Saydam; Yiping Shen; Thomas Würdinger; Ozlem Senol; Elvan Boke; Marianne F James; Bakhos A Tannous; Anat O Stemmer-Rachamimov; Ming Yi; Robert M Stephens; Cornel Fraefel; James F Gusella; Anna M Krichevsky; Xandra O Breakefield Journal: Mol Cell Biol Date: 2009-08-24 Impact factor: 4.272