Zoom-in comparative genomic hybridisation arrays for the characterisation of variable breakpoint contiguous gene syndromes

Abstract

Contiguous gene syndromes cause disorders via haploinsufficiency for adjacent genes. Some contiguous gene syndromes (CGS) have stereotypical breakpoints, but others have variable breakpoints. In CGS that have variable breakpoints, the extent of the deletions may be correlated with severity. The Greig cephalopolysyndactyly contiguous gene syndrome (GCPS-CGS) is a multiple malformation syndrome caused by haploinsufficiency of GLI3 and adjacent genes. In addition, non-CGS GCPS can be caused by deletions or duplications in GLI3. Although fluorescence in situ hybridisation (FISH) can identify large deletion mutations in patients with GCPS or GCPS-CGS, it is not practical for identification of small intragenic deletions or insertions, and it is difficult to accurately characterise the extent of the large deletions using this technique. We have designed a custom comparative genomic hybridisation (CGH) array that allows identification of deletions and duplications at kilobase resolution in the vicinity of GLI3. The array averages one probe every 730 bp for a total of about 14 000 probes over 10 Mb. We have analysed 16 individuals with known or suspected deletions or duplications. In 15 of 16 individuals (14 deletions and 1 duplication), the array confirmed the prior results. In the remaining patient, the normal CGH array result was correct, and the prior assessment was a false positive quantitative polymerase chain reaction result. We conclude that high-density CGH array analysis is more sensitive than FISH analysis for detecting deletions and provides clinically useful results on the extent of the deletion. We suggest that high-density CGH array analysis should replace FISH analysis for assessment of deletions and duplications in patients with contiguous gene syndromes caused by variable deletions. G enetic disorders can be caused by an enormously broad range of genomic aberrations. These range from singlenucleotide point mutations to duplications and deletions of millions of basepairs of DNA, up to entire chromosomes, as in Down's syndrome. An ongoing challenge for genetic diagnostics is to develop methods to sensitively and specifically diagnose this entire range of mutations. Although current methods reliably detect the largest and smallest mutations (microscopic cytogenetics and sequencing, respectively), the middle range of mutations is difficult to detect. We dealt with this challenge by applying the evolving technology of arraybased comparative genomic hybridisation (CGH) to a disorder that is caused by a wide range of mutations, including mutations in this intermediate range.Haploinsufficiency of the transcription factor gene GLI3, on chromosome 7p14.1, causes Greig cephalopolysyndactyly syndrome (GCPS).1 Many mutations have been identified, including translocations and large genomic deletions, as well as small intragenic deletions or duplications 2 and point mutations.2 3 This wide range of mutations complicates molecular diagnostics, requiring numerous tests to detect all possible mutations. In addition, when...

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Molecular analysis expands the spectrum of phenotypes associated with GLI3 mutations

“…Zoom-in comparative genomic hybridization (CGH) for chromosome 7p14 was performed as described previously (Johnston, et al, 2007) in a subset of individuals to identify large deletions and duplications on chromosome 7 including GLI3 (Tables 2, 3, 5, 6, 7, 8, 9 and 11). …”