Entire PTCH1 deletion is a common event in point mutation‐negative cases with nevoid basal cell carcinoma syndrome in Japan

To the Editor : Nevoid basal cell carcinoma syndrome [NBCCS (OMIM 109400)], also called Gorlin syndrome, is an autosomal dominant neurocutaneous disorder characterized by large body size, developmental and skeletal abnormalities, sensitivity to radiation, and an increased incidence of cancers such as basal cell carcinoma (BCC) and medulloblastoma (1). NBCCS is caused by inactivating mutations in the Patched-1 (PTCH1 ) gene (2, 3). Heterozygous loss of PTCH1 found in certain sporadic and familial cases of BCC indicates that PTCH1 is also a tumor suppressor gene (4, 5). Despite extensive efforts to detect mutations, they are still unidentified in 25–60% of patients (6–8). To date, we have analyzed 38 patients with NBCCS from 32 families. Eight of the families did not harbor any PTCH1 mutations detectable by polymerase chain reaction (PCR)based direct sequencing of the exons. To investigate the possibility of large deletions involving the PTCH1 gene, we employed a high-resolution array-based comparative genomic hybridization technology. Consequently, we identified genomic deletions involving PTCH1 in seven individuals from five of the eight point mutation-negative families (Fig. S1). These patients are listed in Table 1. Some of them have been reported previously by us (9) and one patient reported by others (NS6) (10) is also included in the table, all of which are of Japanese origin. To our knowledge, this table includes all the patients with PTCH1 deletions in which the breakpoints have been identified at the nucleotide level. A schematic representation of each deletion’s size together with the deleted genes is shown in Fig. 1a. Unlike in cases of Sotos syndrome and neurofibromatosis type 1, no recurrent breakpoints were observed in these patients (11, 12). Whereas deletions larger than 2.4 Mb were generated by non-homologous end joining, smaller ones (less than 1.2 Mb) were produced by Alu-mediated nonallelic homologous recombination (Fig. S2). G19 and G36 inherited the deletion from their mothers (G27 and G43, respectively), whereas the deletion in NS6 is of paternal origin. The breakpoint sequences in these cases were completely conserved through generations. Other patients (G35, G10 and G5) did not have a family history of NBCCS and, therefore, the deletions seemed to be de novo. Patients harboring deletions of less than 2.4 Mb did not exhibit any phenotypes atypical for NBCCS despite that up to 22 RefSeq genes (four disease genes) were included in the deleted region. This implies that hemizygous loss of these genes, except for PTCH1, might not have an influence on any observable phenotypes. In contrast, deletions larger than 5.3 Mb led to phenotypes unusual for NBCCS including severe mental and motor retardation, epilepsy, and hypotonia (Table 1). Interestingly, each Alu-mediated deletion was mediated by a distinct path of rearrangement (Fig. 1b). G36/43 had a crossing over point within the Alu elements generating a hybrid Alu element. In G19/27, however, the crossing over occurred near the poly-A tail of the proximal Alu element (9). Therefore, the proximal Alu remained intact while the distal Alu was deleted. In the third case, NS6, crossing over occurred at the 5′ end of the Alu elements and removed both Alu sequences leaving two short direct repeats flanking an Alu element on both sides called target-site duplications (10). To date, we have analyzed 32 NBCCS families and identified entire deletions of PTCH1 in 5 families. This implies that 16% of NBCCS families (five of the eight point mutation-negative families) can be explained by the entire loss of PTCH1. Mutations are not observed in the PTCH1 -coding sequences in considerable numbers of NBCCS cases not only in Japanese but also in other ethnicities and, apart from PTCH1, only one PTCH2 and one SUFU mutation in NBCCS have been