Array-Based Comparative Genomic Hybridization for the Genomewide Detection of Submicroscopic Chromosomal Abnormalities

Abstract

Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using approximately 3,500 flourescent in situ hybridization-verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome.

The 2q23.1 microdeletion syndrome: clinical and behavioural phenotype

“…10,11 In recent years, six submicroscopic deletions comprising chromosome band 2q23.1 have been reported. [12][13][14][15][16][17] Unlike deletions mediated by a nonallelic homologous recombination, these deletions did not have common break points. Nevertheless, except for one case, all deletions did show a common region of overlap in the 2q23.1 region, including two candidate genes, EPC2 and MBD5.…”

Recurrent copy number changes in mentally retarded children harbour genes involved in cellular localization and the glutamate receptor complex

“…These labelled DNAs were co-hybridized to the array-slides using a GeneTAC Hybstation (Genomic Solutions, Ann Arbor, MI, USA). 5 The array has been created by spotting in triplicate DOP-PCR products of 3783 BAC DNA probes that cover the entire human genome with an average spacing of B0.7 Mb. 5 Only BACs with a unique chromosomal location, as ascertained by FISH, have been included.…”

“…5 The array has been created by spotting in triplicate DOP-PCR products of 3783 BAC DNA probes that cover the entire human genome with an average spacing of B0.7 Mb. 5 Only BACs with a unique chromosomal location, as ascertained by FISH, have been included. 36 After hybridization and washing, the slides were scanned and imaged on a ScanArray Express HT (Perkin Elmer, Wellesley, MA, USA) using ScanArray Express software (version 2.1).…”

“…3 Although the very genetic heterogeneity of mental retardation renders genetic linkage and association studies difficult, chromosomal aberrations, occurring with an incidence of 1 per 120 newborns, 4 frequently provide a clue regarding the genetic locus underlying the phenotype of the affected child. Techniques allowing the detection of submicroscopic segmental aneuploidy have enabled us to pinpoint novel microdeletion and microduplication syndromes, such as CHARGE (coloboma, heart anomalies, chonal atresia, retardation, genital and ear anomalies), 5 Peters Plus, 6 recurrent 17q12 rearrangements, 7 del(17)(q21), 8,9 and the 22q13.3 deletion, 10 Pitt-Hopkins 11 and thrombocytopenia-absentradius syndromes 12 (for reviews see Lee and Lupski 3 and Slavotinek 13 ). In addition, clinically inconsequential segmental deletions [14][15][16] and segmental duplications in healthy individuals 17 have been reported.…”

A novel microdeletion in 1(p34.2p34.3), involving the SLC2A1 (GLUT1) gene, and severe delayed development

“…* Pilot studies with a 1-megabase (Mb) to 300-kilobase resolution bacterial artificial chromosome (BAC) array in selected cohorts of individuals with delayed development were able to detect submicroscopic, interstitial abnormalities in about 10% of cases. [3][4][5][6][7] Array CGH is not only useful in detecting submicroscopic gains and losses involved in delayed development but also allows the identification of genes that contribute to the phenotype by precisely mapping genomic alterations onto the human genome sequence. 8 We report a case with a 4.1Mb deletion in 1p34.2p34.…”