Variability in interpreting and reporting copy number changes detected by array-based technology in clinical laboratories.

PURPOSE: : The purpose of this study was to assess the variability in interpretation and reporting of copy number changes that are detected by array-based technology in the clinical laboratory. METHODS: : Thirteen different copy number changes, detected by array comparative genomic hybridization, that have not been associated with an abnormal phenotype in the literature were evaluated by directors from 11 different clinical laboratories to determine how they would interpret and report the findings. RESULTS: : For none of the thirteen copy number changes was there complete agreement in the interpretation of the clinical significance of the deletion or duplication. For some cases, the interpretations ranged from normal to abnormal. CONCLUSION: : There is a need for more specific guidelines for interpreting and reporting copy number changes detected by array-based technology to clearly and more consistently communicate the clinical significance of these findings to ordering providers.

Small deletions of SATB2 cause some of the clinical features of the 2q33.1 microdeletion syndrome.

Recurrent deletions of 2q32q33 have recently been reported as a new microdeletion syndrome. Clinical features of this syndrome include severe mental retardation, growth retardation, dysmorphic features, thin and sparse hair, feeding difficulties and cleft or high palate. The commonly deleted region contains at least seven genes. Haploinsufficiency of one of these genes, SATB2, a DNA-binding protein that regulates gene expression, has been implicated as causative in the cleft or high palate of individuals with 2q32q33 microdeletion syndrome. In this study we describe three individuals with smaller microdeletions of this region, within 2q33.1. The deletions ranged in size from 173.1 kb to 185.2 kb and spanned part of SATB2. Review of clinical records showed similar clinical features among these individuals, including severe developmental delay and tooth abnormalities. Two of the individuals had behavioral problems. Only one of the subjects presented here had a cleft palate, suggesting reduced penetrance for this feature. Our results suggest that deletion of SATB2 is responsible for several of the clinical features associated with 2q32q33 microdeletion syndrome.

aCGH detects partial tetrasomy of 12p in blood from Pallister-Killian syndrome cases without invasive skin biopsy.

Pallister-Killian syndrome (PKS) is a genetic disorder characterized by mental retardation, seizures, streaks of hypo- or hyperpigmentation and dysmorphic features. PKS is associated with tissue-limited mosaic partial tetrasomy of 12p, usually caused by an isochromosome 12p. The mosaicism is usually detected in cultured skin fibroblasts or amniotic cells and rarely in phytohemagluttinin-stimulated lymphocytes, which suggests stimulation of T-lymphocytes may distort the percentage of abnormal cells. We recently reported on the identification by microarray-based comparative genomic hybridization (aCGH) of a previously unsuspected case of partial tetrasomy of 12p caused by an isochromosome 12p. Here we report on seven additional individuals with partial tetrasomy of 12p characterized by our laboratory. All individuals were referred for mental retardation/developmental delay and/or dysmorphic features. In each case, aCGH using genomic DNA extracted from whole peripheral blood detected copy-number gain for all clones for the short arm of chromosome 12. In all but one case, FISH on metaphases from cultured lymphocytes did not detect the copy-number gain; in the remaining case, metaphase FISH on cultured lymphocytes showed an isochromosome in 10% of cells. However, interphase FISH using probes to 12p on peripheral blood smears showed additional hybridization signals in 18-70% of cells. Microarray and FISH analysis on cultured skin biopsies from four individuals confirmed the presence of an isochromosome 12p. Our results demonstrate the usefulness of aCGH with genomic DNA from whole peripheral blood to detect chromosome abnormalities that are not present in stimulated blood cultures and would otherwise require invasive skin biopsies for identification.

Identification of a rare de novo three-way complex t(5;20;8)(q31;p11.2;p21) with microdeletions on 5q31.2, 5q31.3, and 8p23.2 in a patient with hearing loss and global developmental delay: case report.

BACKGROUND: Complex chromosome rearrangements (CCRs), which involve more than two breakpoints on two or more chromosomes, are uncommon occurrences. Although most CCRs appear balanced at the level of the light microscope, many demonstrate cryptic, submicroscopic imbalances at the translocation breakpoints. RESULTS: We report a female with hearing loss and global developmental delay with a complex three-way unbalanced translocation (5;20;8)(q31;p11.2;p21) resulting in microdeletions on 5q31.2, 5q31.3, and 8p23.2 identified by karyotyping, microarray analysis and fluorescence in situ hybridization. DISCUSSION: The microdeletion of bands 8p23.2 may be associated with the hearing impairment. Furthermore, the characterization of this patient's chromosomal abnormalities demonstrates the importance of integrated technologies within contemporary cytogenetics laboratories.

Comparison of microarray-based detection rates for cytogenetic abnormalities in prenatal and neonatal specimens.

OBJECTIVE: To compare the detection rate by microarray analysis for chromosome abnormalities in a prenatal population to that of a neonatal population referred for diagnostic testing. METHODS: Array comparative genomic hybridization (aCGH) analysis was performed for 151 prenatal cases and compared with the results from 1375 postnatal cases less than 3 months of age. RESULTS: Two of 151 prenatal cases (1.3%) showed a clinically significant cytogenetic abnormality. In contrast, of the 1375 postnatal cases studied, 11.4% showed a cytogenetic abnormality by aCGH. Many of these (40%) were referred for aCGH because of dysmorphic features, a clinical indication unlikely to be identified in the prenatal population. CONCLUSIONS: The chance of detecting a chromosome abnormality in a prenatal population that has already been screened by routine cytogenetics is approximately 1.3%. However, given that many of the abnormal array results in the neonatal population were among those with dysmorphic features as the primary indication for testing, which are not easily identifiable by ultrasound, offering prenatal testing by aCGH to a wider population would likely result in a higher detection rate.

Unexpected structural complexity of supernumerary marker chromosomes characterized by microarray comparative genomic hybridization.

BACKGROUND: Supernumerary marker chromosomes (SMCs) are structurally abnormal extra chromosomes that cannot be unambiguously identified by conventional banding techniques. In the past, SMCs have been characterized using a variety of different molecular cytogenetic techniques. Although these techniques can sometimes identify the chromosome of origin of SMCs, they are cumbersome to perform and are not available in many clinical cytogenetic laboratories. Furthermore, they cannot precisely determine the region or breakpoints of the chromosome(s) involved. In this study, we describe four patients who possess one or more SMCs (a total of eight SMCs in all four patients) that were characterized by microarray comparative genomic hybridization (array CGH). RESULTS: In at least one SMC from all four patients, array CGH uncovered unexpected complexity, in the form of complex rearrangements, that could have gone undetected using other molecular cytogenetic techniques. Although array CGH accurately defined the chromosome content of all but two minute SMCs, fluorescence in situ hybridization was necessary to determine the structure of the markers. CONCLUSION: The increasing use of array CGH in clinical cytogenetic laboratories will provide an efficient method for more comprehensive characterization of SMCs. Improved SMC characterization, facilitated by array CGH, will allow for more accurate SMC/phenotype correlation.

In the middle of it all: a centered approach to chromosome analysis.

BACKGROUND: The pericentromeric areas immediately flanking the centromeres are prone to instability owing to their high levels of repetitive sequences. This genomic instability makes the pericentromeric regions ideal candidates for the investigation of chromosomal abnormalities resulting in genetic disease. However, it is this instability that confounds attempts to analyze these regions of the genome. The sequencing of the human genome, while illuminating the complexity of the pericentromeric regions, has enabled the development of high-resolution microarrays for the characterization of chromosomal abnormalities. OBJECTIVE: The MarkerChip(™) was developed specifically to target the pericentromeres for the identification and characterization of pericentromeric chromosomal abnormalities. METHODS: The authors' experience with this microarray is reviewed in their clinical diagnostic laboratory. RESULTS/DISCUSSION: The MarkerChip demonstrates the utility of constructing a microarray for the analysis of chromosome abnormalities with coverage concentrated on areas of the genome particularly susceptible to rearrangement.