Campomelic Dysplasia Translocation Breakpoints Are Scattered over 1 Mb Proximal to SOX9: Evidence for an Extended Control Region

Abstract

Campomelic dysplasia (CD), a skeletal malformation syndrome with or without XY sex reversal, is usually caused by mutations within the SOX9 gene on distal 17q. Several CD translocation and inversion cases have been described with breakpoints outside the coding region, mapping to locations >130 kb proximal to SOX9. Such cases are generally less severely affected than cases with SOX9 coding-region mutations, as is borne out by three new translocation cases that we present. We have cloned the region extending 1.2 Mb upstream of the SOX9 gene in overlapping bacterial-artificial-chromosome and P1-artificial-chromosome clones and have established a restriction map with rare-cutter enzymes. With sequence-tagged-site-content mapping in somatic-cell hybrids, as well as with FISH, we have precisely mapped the breakpoints of the three new and of three previously described CD cases. The six CD breakpoints map to an interval that is 140-950 kb proximal to the SOX9 gene. With exon trapping, we could isolate five potential exons from the YAC 946E12 that spans the region, four of which could be placed in the contig in the vicinity of the breakpoints. They show the same transcriptional orientation, but only two have an open reading frame (ORF). We failed to detect expression of these fragments in several human and mouse cDNA libraries, as well as on northern blots. Genomic sequence totaling 1,063 kb from the SOX9 5'-flanking region was determined and was analyzed by the gene-prediction program GENSCAN and by a search of dbEST and other databases. No genes or transcripts could be identified. Together, these data suggest that the chromosomal rearrangements most likely remove one or more cis-regulatory elements from an extended SOX9 control region.

Impact of BRCA1 and BRCA2 variants on splicing: clues from an allelic imbalance study

“…Although highly speculative, it might be hypothesized that disruption of regulatory elements could lead to a less severe phenotype compared with classical deleterious mutations. 38 Haplotype and co-segregation analyses need to be performed in the relevant families to confirm the transmission of an altered cis-regulatory element. It could also be of interest to search for BRCA1/2 mutations in the tumor and, in the case of loss of heterozygosity, determine whether the retained allele is the one with low expression.…”

Position effect leading to haploinsufficiency in a mosaic ring chromosome 14 in a boy with autism

“…Chromosomal breakpoints altering the expression of adjacent genes, referred to as position effects, has been repeatedly demonstrated as a mechanism causing human genetic disease, with breakpoints up to a distance of 1 Mb, for example in campomelic dysplasia (SOX9 gene 23 ). In the present case, the breakpoint where ring fusion occurred is located at 300 kb from the 5 0 end of both copies of amisyn.…”

Identification of novel autism candidate regions through analysis of reported cytogenetic abnormalities associated with autism

“…Positional effects due to rearrangements up to 1.3 Mb away from the breakpoints have been reported. [77][78][79] New high-resolution methods of detection of copy number changes across the genome, such as array based comparative genomic hybridization (array-CGH), [80][81][82] representational oligonucleotide microarray analysis (ROMA) 83 and SNP-based arrays, 84 are increasingly applied in clinical and research studies. In the data collected for the current review, a small number of array-CGH findings is included, for instance, at 1p36.33 85 and at 6q21.…”