High resolution array in the clinical approach to chromosomal phenotypes |
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Authors: | Filges Isabel Suda Luzia Weber Peter Datta Alexandre N Fischer Dirk Dill Patricia Glanzmann Réné Benzing Jörg Hegi Lukas Wenzel Friedel Huber Andreas R Mori Andrea Capone Miny Peter Röthlisberger Benno |
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Institution: | 1. Division of Medical Genetics, University Children''s Hospital and Department of Biomedicine, Basel Switzerland;2. Division of Medical Genetics, Center of Laboratory Medicine, Cantonal Hospital Aarau, Switzerland;3. Division of Neuropediatrics and Developmental Medicine, University Children''s Hospital, Basel Switzerland;4. Division of Neonatology, University Children''s Hospital, Basel Switzerland;5. Division of Neuropediatrics, Cantonal Hospital Aarau, Switzerland |
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Abstract: | Array genomic hybridization (AGH) has recently been implemented as a diagnostic tool for the detection of submicroscopic copy number variants (CNVs) in patients with developmental disorders. However, there is no consensus regarding the choice of the platform, the minimal resolution needed and systematic interpretation of CNVs. We report our experience in the clinical diagnostic use of high resolution AGH up to 100 kb on 131 patients with chromosomal phenotypes but previously normal karyotype. We evaluated the usefulness in our clinics and laboratories by the detection rate of causal CNVs and CNVs of unknown clinical significance and to what extent their interpretation would challenge the systematic use of high-resolution arrays in clinical application. Prioritizing phenotype-genotype correlation in our interpretation strategy to criteria previously described, we identified 33 (25.2%) potentially pathogenic aberrations. 16 aberrations were confirmed pathogenic (16.4% syndromic, 8.5% non-syndromic patients); 9 were new and individual aberrations, 3 of them were pathogenic although inherited and one is as small as approx 200 kb. 13 of 16 further CNVs of unknown significance were classified likely benign, for 3 the significance remained unclear. High resolution array allows the detection of up to 12.2% of pathogenic aberrations in a diagnostic clinical setting. Although the majority of aberrations are larger, the detection of small causal aberrations may be relevant for family counseling. The number of remaining unclear CNVs is limited. Careful phenotype-genotype correlations of the individual CNVs and clinical features are challenging but remain a hallmark for CNV interpretation. |
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Keywords: | AGH array genomic hybridization CNV copy number variation MCA multiple congenital anomalies MA minor anomalies DD developmental delay ID intellectual disability ASD autism spectrum disorders FISH fluorescence in situ hybridization |
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