The most significant were two probes for each of CIDEA, ADHFE1, and GLOX1 (Table 1; Table S4).
However, the fragments containing GA/CT repeats were found most using three probes separately.
For most of the sequences, two probes twice-spotted were designed into different regions, while in the case of non-oriented sequences, two probes were designed into each direction with the suffix 'RC' added to the name of the probe corresponding to the Reverse Complement strand.
This was chosen based on an assessment that the two probes most likely to be found in a resource limited setting were a linear probe (for superficial assessments and procedures) and a phased-array probe (for cardiac, intra-abdominal, and obstetric assessment).
Putative cross-hybridizations were therefore defined when a non-targeted sequence harbours at most two mismatches with a probe.
Similarly, these two probes were the most negatively correlated with MGMT gene expression in the E-GBM and the TCGA-GBM dataset for which expression data were available (Supplementary Fig. S3).
When comparing performance of the three HER2 probes, the third probe showed most frequently a discordance with the other two probes, possibly due to its lower ratio values.
At most, three rounds of probe hybridization were conducted.
Out of the 22,690 probe sets on the microarray, the two probes corresponding to p21 occupied the 14th-most and 17th-most stabilized positions.
In most cases, the new probe set contains at least two probes, in one case even nine probes.
