Characterization of chromosome abnormalities

Abstract: Inborn chromosome abnormalities are a frequent cause of mental retardation and birth defects. Apart from aberrations that are visible in the microscope, a number of submicroscopic alterations have recently been discovered, and all of these chromosome changes are in fact the result of DNA alterations at the molecular level. In order to fully understand the mechanisms and consequences behind chromosome changes it is therefore important to characterize the breakpoints in detail. Moreover, the breakpoints are not evenly distributed in the genome. The recurrent genomic disorders illustrate how genomic architectural features make specific chromosomal regions susceptible to non-allelic homologous recombination. Recent technological advances have enabled high resolution, genome-wide analysis and the structure of several non-recurrent aberrations has been clarified. In addition, an unexpectedly high number of complex rearrangements have been detected. We have used molecular cytogenetic methods to characterize the breakpoints of chromosome abnormalities. FISH and array-CGH were used to map the breakpoints and for the detection of genomic imbalances. By customizing arrays it was possible to increase the resolution in a targeted genomic region of interest and determine the structure of the breakpoints with high accuracy, as well as to detect very small imbalances. We were able to identify and narrow down minimal chromosomal regions of overlap in patients with partial deletions and duplications of the same chromosomal region. In two of the these, we actually narrowed down the deletion/duplication region to include only one candidate gene. Hence, deletion of ITSN1 on chromosome 21 seems to be involved in severe mental retardation and duplication of YWHAE, on chromosome 17, was associated with autism. Two extremely complex, intrachromosomal rearrangements of chromosome 1 and 21 were found to include 14 and 16 breakpoints, respectively. These are the most complex chromosome rearrangements involving only a single chromosome that have been reported. We also used targeted custom oligonucleotide arrays to fine map the breakpoints from both balanced and unbalanced rearrangements, and demonstrated that it is possible to characterize unbalanced breakpoints within 17 to 20 000 base pairs, depending on the structure of the genome. The deletion and duplication breakpoints were further refined, and did not seem to be associated with low copy repeats, thus diverse molecular mechanisms are probably responsible for these rearrangements. Contrary to previous reports, we were unable to detect any clinically significant imbalances within the breakpoint regions in patients with apparently balanced reciprocal translocations. The results of this thesis emphasizes the importance of different molecular cytogenetic techniques in the investigation of chromosome aberrations. Our results illustrate that array-CGH is a convenient method to detect and map genomic deletions and duplications with high resolution. However, FISH-analysis remains an important tool to map and characterize both balanced and unbalanced rearrangements and to unravel the complexity of the genomic imbalances detected by array. By combining the two approaches, we have been able to characterize the breakpoints of deletions, duplications, reciprocal translocations and complex rearrangements in detail.