F7 and F11 were the only samples with loss of ABO allelic expression (lack of digestion with BstEII – Figure 1B; lanes 3 and 5) but with no detectable alterations in ABH antigens by flow cytometric analysis.
XIST, which is specifically expressed from the inactivated X chromosome, was not or hardly expressed in 9/10 samples with loss of X, indicating that they lost the inactivated copy of the X chromosome (Figure 5B).
When exploring mRNA expression levels of SH3KBP1 we did not find a difference between samples with loss and no loss, nor resistance.
Wilcoxon rank sum test was used to assess differences in expression between samples with loss and gains compared to samples without changes.
In previous studies, three out of 13 samples with loss of one 5q allele exhibited a disruption of the second GRAF allele by insertions (Borkhardt et al, 2000).
Furthermore, in two UM samples with loss of one copy of chromosome 3 and a BAP1 mutation, BAP1 protein could be detected by IHC (Koopmans et al, 2014).
A systematic analysis of loss-of-function gene fusions could identify additional cancer samples with loss of tumor suppressors that might be currently going unreported, and could help broaden our understanding of the role of gene fusions in cancer.
With respect to the three identified clusters, loss in 18q was more frequent in Cluster I than in Cluster III (P = 0.030), 11q loss occurred more often in Cluster II compared with Cluster III (P = 0.025), and Cluster II included more samples with loss on 16q compared with Clusters I and III (P = 0.007 and P = 0.022, respectively).
Also, the rate of follow-up in this study was 72%, and selective loss was observed in this sample, with greater loss among children who showed low height-for-age and were exposed to tobacco smoke.
In addition, for each miRNA DNA locus identified as altered in any of the samples, we performed separate non-parametric Wilcoxon rank sum tests to assess differences in expression between samples with losses and gains, compared to samples with no copy number alterations.
