NOTCH2 is neither rearranged nor mutated in t(1;19) positive oligodendrogliomas.

The combined deletion of 1p and 19q chromosomal arms is frequent in oligodendrogliomas (OD) and has recently been shown to be mediated by an unbalanced t(1;19) translocation. Recent studies of 1p/19q co-deleted OD suggest that the NOTCH2 gene is implicated in oligodendrocyte differentiation and may be involved in this rearrangement. The objective of the present study was to analyze the NOTCH2 locus either as a chromosomal translocation locus that may be altered by the 1p/19q recurrent rearrangement or as a gene that may be inactivated by a two hit process. We performed an array-CGH analysis of 15 ODs presenting 1p/19q co-deletion using a high-density oligonucleotide microarray spanning 1p and 19q pericentromeric regions with 377 bp average probe spacing. We showed that the 1p deletion extends to the centromere of chromosome 1 and includes the entire NOTCH2 gene. No internal rearrangement of this gene was observed. This strongly suggests that the t(1;19) translocation does not lead to an abnormal NOTCH2 structure. The analysis of the entire NOTCH2 coding sequence was performed in four cases and did not reveal any mutation therefore indicating that NOTCH2 does not harbor genetic characteristics of a tumor suppressor gene. Finally, the detailed analysis of chromosome 19 pericentromeric region led to the identification of two breakpoint clusters at 19p12 and 19q11-12. Interestingly, these two regions share a large stretch of homology. Together with previous observations of similarities between chromosome 1 and 19 alphoid sequences, this suggests that the t(1;19) translocation arises from complex intra and interchromosomal rearrangements.This is the first comprehensive deletion mapping by high density oligo-array of the 1p/19q co-deletion in oligodendroglioma tumors using a methodological approach superior to others previously applied. As such this paper provides clear evidence that the NOTCH2 gene is not physically rearranged by t(1;19) translocation of oligodendroglioma tumors.

Innovative integrated system for real-time measurement of hybridization and melting on standard format microarrays.

Despite the great popularity and potential of microarrays, their use for research and clinical applications is still hampered by lengthy and costly design and optimization processes, mainly because the technology relies on the end point measurement of hybridization. Thus, the ability to monitor many hybridization events on a standard microarray slide in real time would greatly expand the use and benefit of this technology, as it would give access to better prediction of probe performance and improved optimization of hybridization parameters. Although real-time hybridization and thermal denaturation measurements have been reported, a complete walk-away system compatible with the standard format of microarrays is still unavailable. To address this issue, we have designed a biochip tool that combines a hybridization station with active mixing capability and temperature control together with a fluorescence reader in a single compact benchtop instrument. This integrated live hybridization machine (LHM) allows measuring in real time the hybridization of target DNA to thousands of probes simultaneously and provides excellent levels of detection and superior sequence discrimination. Here we show on an environmental single nucleotide polymorphism (SNP) model system that the LHM enables a variety of experiments unachievable with conventional biochip tools.

Deletion of the parkin and PACRG gene promoter in early-onset parkinsonism.

Autosomal recessive mutations in the parkin gene (PARK2) have been identified as a common cause of familial and also sporadic, early-onset parkinsonism (EOPD): point mutations, exonic deletions, and duplications or triplications have been described. Here we report a novel mutation, consisting of a deletion of the promoter and exon 1 of parkin (c.1-?_7+?del), in a family compatible with autosomal recessive EOPD and an isolated case. The former was compound heterozygous for the parkin c.1-?_7+?del mutation and an exon 3 deletion (c.172-?_412+?del). The latter was homozygous for the parkin c.1-?_7+?del mutation. The promoter region is shared by parkin and the neighboring parkin coregulated gene (PACRG), which are oriented head-to-head and are transcribed on opposite DNA strands. There were no parkin transcripts in lymphoblasts from the patients carrying the parkin c.1-?_7+?del mutation. The phenotypes of patients with promoter deletions and consequently absence of parkin and possibly PACRG expression, were similar to and no more severe than those of other EOPD patients with parkin mutations.

BAP1 and breast cancer risk.

BAP1 whose protein interacts with BRCA1 was analysed in a series of 47 French familial breast cancer cases negatively tested for BRCA1/2 mutations. The lack of detection of deleterious mutations suggests that BAP1 is not a high risk breast cancer predisposing gene. However, a common identified variant, rs123602, may be tested in sporadic cases as candidate for moderate risk.