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High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results

Linda Siggberg1*, Ala-Mello Sirpa2, Linnankivi Tarja3, Avela Kristiina4, Scheinin Ilari157, Kristiansson Kati67, Lahermo Päivi7, Hietala Marja8, Metsähonkala Liisa3, Kuusinen Esa9, Laaksonen Maarit10, Saarela Janna7 and Knuutila Sakari1

Author Affiliations

1 Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland

2 Rinnekoti Foundation, Rehabilitation Home for Children, Espoo, Finland

3 Department of Pediatric Neurology, Helsinki University Central Hospital, Helsinki, Finland

4 Väestöliitto, The Family Federation of Finland, Department of Medical Genetics, Helsinki, Finland

5 Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands

6 Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland

7 Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland

8 Department of Clinical Genetics, Turku University Hospital and Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland

9 Department of Pediatrics, Satakunta Hospital District, Pori, Finland

10 Population Health Unit, Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 21 00014, Helsinki, Finland

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BMC Medical Genetics 2012, 13:84  doi:10.1186/1471-2350-13-84

Published: 17 September 2012



Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however.

Methods and Results

Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH) results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV) population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed.


In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

Developmental disorder; SNP array; Diagnostic yield