Table 2.
Validation of 11 ASEs in vitro (qRT-PCR) and in silico (TCGA).
| Discovery |
Validation |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| RNA-seq JHU cohort (nT = 47, nN = 25) |
PCR (in vitro) JHU cohort (nT = 31, nN = 22) |
RNA-Seq (in silico) TCGA cohort (nT = 44, nN = 16) |
||||||||
| nT (%) | nN (%) | FDR | nT (%) | nN (%) | FDR | nT (%) | nN (%) | FDR | ||
| Associated gene | GIT2 | 19 (41.4) | 1 [4] | 6.92E-04 | 14 (45.2) | 1 (4.6) | 1.70E-04 | 5 (11.4) | 0 (0) | 3.11E-01 |
| CTNNB1 | 18 (39.2) | 1 [4] | 1.50E-03 | 6 (19.4) | 1 (4.6) | 1.04E-01 | 25 (56.9) | 0 (0) | 4.56E-05 | |
| MKNK2 | 29 (63.1) | 1 [4] | 6.19E-07 | 24 (77.5) | 1 (4.6) | 1.12E-09 | 7 (16) | 0 (0) | 1.73E-01 | |
| MRPL33 | 26 (56.6) | 1 [4] | 6.59E-06 | 28 (90.4) | 1 (4.6) | 2.29E-13 | 31 (70.5) | 0 (0) | 4.54E-07 | |
| SIPA1L3 | 15 (31.9) | 0 (0) | 6.52E-04 | 16 (51.7) | 0 (0) | 2.46E-06 | 22 (29) | 0 (0) | 1.78E-04 | |
| SNHG6 | 24 (52.2) | 0 (0) | 2.39E-06 | 19 (61.3) | 0 (0) | 4.26E-09 | 28 (63.7) | 0 (0) | 4.22E-06 | |
| SYCP2 | 18 (39.2) | 0 (0) | 1.16E-04 | 7 (22.6) | 1 (4.6) | 5.29E-02 | 35 (79.6) | 0 (0) | 1.37E-08 | |
| TPRG1 | 29 (63.1) | 0 (0) | 2.74E-08 | 29 (93.6) | 1 (4.6) | 6.41E-14 | 12 (27.3) | 0 (0) | 2.53E-02 | |
| ZHX2 | 20 (43.5) | 1 [4] | 3.30E-04 | 22 (71) | 1 (4.6) | 2.12E-08 | 31 (70.5) | 0 (0) | 4.54E-07 | |
| ZNF331 | 21 (45.7) | 0 (0) | 1.81E-05 | 17 (54.9) | 0 (0) | 6.19E-07 | 0 (0) | 0 (0) | 1.00E+00 | |
| ELOVL1a | 33 (71.8) | 1 [4] | 1.28E-08 | 8 (25.9) | 1 (4.6) | 2.26E-02 | 40 (91) | 0 (0) | 3.24E-11 | |
nN is the number of normal samples.
nT is the number of tumour samples.
aASE underexpressed in tumours.
Bold indicates significant (FDR < 0.05).
RNA-Seq analysis of ASE prevalence was originally performed on the discovery ‘JHU cohort’ (left-most column) with 25 non-cancer controls (nN) and n = 47 HPV+ HNSCC (nT). In vitro validation by qRT-PCR using custom assays (Table S1) was performed on a partial JHU cohort with available tissue for analysis (nT = 31 and nN = 22), and in silico RNA-seq validation was performed on an independent TCGA cohort (nT = 44 and nN = 16). All p-values are adjusted comparing ASE outlier prevalence between the normal and tumour groups. All ASEs except ELOVL1 exhibited outlier over-expression in the tumour group relative to normal tissues.