High-density oligonucleotide array with sub-kilobase resolution reveals breakpoint information of submicroscopic deletions in nevoid basal cell carcinoma syndrome

Abstract

Small submicroscopic genomic deletions and duplications constitute up to 15% of all mutations underlying human monogenic diseases. In this study, we used newly designed high-resolution oligonucleotide microarrays with a median distance between the probes of 776 bp (average probe interval 2,271 bp) to detect gene deletions in nevoid basal cell carcinoma syndrome (NBCCS) patients. NBCCS, also called Gorlin syndrome, is characterized by developmental defects and tumorigenesis such as medulloblastomas and basal cell carcinomas, caused by mutations of the human patched-1 (PTCH1) gene. Two out of three deletions could not be detected by a conventional chromosomal analysis. A submicroscopic deletion as small as 165 kb was detected affecting only PTCH1, whereas the other two deletions were much larger (5 and 11 Mb). We demonstrated not only the exact number of genes involved in the deletion but also rapidly determined the junction sequences after pinpointing the breakpoint regions in all individuals analyzed. This report of an array-based determination of junction sequences of long deletions circumvented a labor-intensive analysis such as Southern blotting or FISH. Alu-mediated recombination in one case and non-homologous end joining in the other two were probably implicated in the generation of deletions. This method will contribute to the understanding of molecular pathogenesis of gene deletions as well as rapid genetic testing.

Germline PTCH1 mutations in Japanese basal cell nevus syndrome patients

“…Recently, a SNPbased copy number array was applied successfully in several analyses to detect copy numbers of the whole genome. 27 Fujii et al 28 applied this method to BCNS cases with PTCH1 mutations that were not previously identified and found deletions with the PTCH1 gene. They also successfully determined their breakpoints.…”

Novel PTCH1 mutations in Japanese Nevoid basal cell carcinoma syndrome patients: two familial and three sporadic cases including the first Japanese patient with medulloblastoma

“…15,[17][18][19][20][21][22][23][24][25][26][27][28] Table 3 summarizes the spectrum of PTCH1 mutations and phenotypes of Japanese NBCCS patients. Overall 56 subjects who fulfilled the criteria for NBCCS were analyzed.…”

PTCH1 duplication in a family with microcephaly and mild developmental delay

“…To date, over 160 mutations (loss-of-function, mostly truncating), 5,6 and more than 20 constitutional deletions of entire PTCH1 have been reported in patients with BCNS. 7,8 Using an oligo array CGH, we have identified the first case of PTCH1 duplication, which segregates a family with microcephaly and mild developmental delay. We propose that patients with microcephaly or holoprosencephaly (HPE) of unknown origin should be screened also for PTCH1 duplication.…”