High-resolution karyotyping by oligonucleotide microarrays : the next revolution in cytogenetics

Abstract

Conventional karyotyping has been used as the standard cytogenetic technique since the 1970s. With conventional karyotyping one can detect aberrations larger than 5 __ 10 Mb and it can detect chromosomal aberrations in approximately 5% of patients with mental retardation (MR). To identify smaller copy number variants (CNVs) new molecular cytogenetic techniques have been developed. One of these techniques is the Single Nucleotide Polymorphism (SNP) array. This method allows the detection of SNP-genotype as well as the presence of small deletions and amplifications. In this thesis we have studied patients with MR and/or congenital malformations. The question we have tried to answer by studying the genome of the patient is whether we can find a cause for the signs and symptoms observed in the patient. The SNP array was successfully used for the detection of novel CNVs and has replaced the conventional karyotyping in the routine diagnostic flow in MR patients in our diagnostic setting. We are therefore able to make a diagnosis in a higher number of MR patients, thus improving medical care and genetic counselling. However, a major complexity is the finding of potentially pathogenic CNVs for which the clinical significance is not immediately clear.