Two BAC clones with known genes were significantly more often amplified, and 13 were more frequently deleted in WNY tumours.
Although these CN gain regions of PIOL were in common with those of IOCNSL, loss of 6q22.33 containing PTPRK and 9p21.3 containing CDKN2A were more frequently deleted in IOCNSL.
Interestingly, the flanking regions of recent L1 insertions contain a higher GC content than older inserts [ 19] suggesting that L1 preferentially inserts into areas of higher GC content or that they are more frequently deleted in areas of low GC content.
The main rearrangements were loss of 1p with a more frequently deleted region at 1pter, gains of 1q and of 8q, and losses of 11q and of 16q.
All features in Group ii are designed to capture the known fact that LoF genes have a tendency to be deleted, whereas Act genes are more frequently affected by amplifications (Davoli et al., 2013).
If the term is systematically over-represented in the upper part of the partitions (corresponding to the genes more frequently deleted) we will consider that this GO functionality is systematically deleted.
Calcification is more frequently seen in pseudogout.
Patients were more frequently women (88%).
In particular, NPAS3 and RUNX1 are known tumor suppressors and CELF4 is known to be frequently deleted in cancer.
