Table 2.
Results of quantitative real-time PCR analysis of the 12 confirmed CNVRs
|
CNVR_No. |
Chr. |
Starta |
Enda |
Primer_ID |
Positive samples |
Negative samples |
validated |
Genes |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Frequency | Type | Number of samples | Confirmed samples | Confirmed rate | Number of sample | Confirmed samples | Confirmed rate | ||||||||
| 6 |
1 |
91513835 |
91584145 |
17-2 |
0.0148 |
gain |
7 |
7 |
1.0000 |
5 |
0 |
0.0000 |
Yes |
-- |
|
| |
|
|
|
17-8 |
|
|
7 |
0 |
-- |
5 |
0 |
-- |
No |
-- |
|
| 11 |
1 |
160653704 |
160713406 |
4-1 |
0.0675 |
loss |
32 |
32 |
1.0000 |
15 |
1 |
0.0667 |
Yes |
-- |
|
| |
|
|
|
4-4 |
|
|
32 |
32 |
1.0000 |
15 |
1 |
0.0667 |
Yes |
-- |
|
| 20 |
1 |
274307988 |
274570232 |
5-3 |
0.0274 |
loss |
13 |
0 |
-- |
11 |
0 |
-- |
No |
C5 |
|
| |
|
|
|
5-7 |
|
|
13 |
12 |
0.9200 |
11 |
2 |
0.18 |
Yes |
TRAF1 |
|
| 22 |
1 |
276291234 |
276800847 |
3-1 |
0.0738 |
both |
35 |
31 |
0.8857 |
11 |
1 |
0.0909 |
Yes |
ORs |
|
| |
|
|
|
3-5 |
|
|
35 |
35 |
1.0000 |
15 |
6 |
0.4000 |
Yes |
||
| 161 |
14 |
52620825 |
52720705 |
6-3 |
0.0211 |
loss |
10 |
10 |
1.0000 |
11 |
8 |
0.7273 |
Yes |
-- |
|
| |
|
|
|
6-6 |
|
|
10 |
10 |
1.0000 |
11 |
8 |
0.7273 |
Yes |
-- |
|
| 259 |
2 |
4834400 |
5424602 |
7-3 |
0.0759 |
both |
18 |
16 |
0.8889 |
12 |
6 |
0.5000 |
Yes |
EFEMP2 |
|
| |
|
|
|
7-5 |
|
|
36 |
31 |
0.8611 |
12 |
6 |
0.5000 |
Yes |
DPF2 |
|
| 276 |
2 |
137644872 |
137915976 |
15-4 |
0.0928 |
gain |
8 |
0 |
-- |
4 |
0 |
-- |
No |
ORs |
|
| |
|
|
|
15-5 |
|
|
38 |
26 |
0.6842 |
19 |
9 |
0.4737 |
Yes |
|
|
| |
|
|
|
15-6 |
|
|
8 |
7 |
0.8750 |
4 |
1 |
0.2500 |
yes |
|
|
| 285 |
3 |
87641425 |
87711895 |
16-2 |
0.0422 |
gain |
20 |
18 |
0.9000 |
12 |
8 |
0.6666 |
Yes |
-- |
|
| |
|
|
|
16-5 |
|
|
20 |
19 |
0.9500 |
18 |
10 |
0.5556 |
Yes |
-- |
|
| 314 |
5 |
59744851 |
60461526 |
13-1 |
0.0084 |
loss |
4 |
3 |
0.7500 |
12 |
0 |
0.0000 |
Yes |
CD4 |
|
| |
|
|
|
13-5 |
|
|
4 |
3 |
0.7500 |
8 |
0 |
0.0000 |
Yes |
GAPDH |
|
| 325 |
6 |
37641317 |
38387857 |
8-2 |
0.0211 |
loss |
10 |
10 |
1.0000 |
8 |
2 |
0.2500 |
Yes |
FTL |
|
| |
|
|
|
8-5 |
|
|
10 |
10 |
1.0000 |
8 |
2 |
0.2500 |
Yes |
IRF3 |
|
| 344 |
7 |
29445530 |
29634684 |
9-4 |
0.0105 |
loss |
5 |
0 |
-- |
7 |
0 |
-- |
No |
- |
|
| |
|
|
|
9-6 |
|
|
5 |
5 |
1.0000 |
16 |
10 |
0.6250 |
Yes |
- |
|
| 373 |
9 |
4203824 |
4364337 |
2-2 |
0.0928 |
loss |
28 |
28 |
1.0000 |
17 |
4 |
0.2353 |
Yes |
ORs |
|
| |
|
|
|
2-7 |
|
|
29 |
29 |
1.0000 |
17 |
2 |
0.1176 |
Yes |
|
|
| Mean | 0.9269 | 0.3182 | |||||||||||||
a The Sus scrofa assembly (9.0) (http://www.ensembl.org/Sus_scrofa/Info/Index) was used to indicate the position of the CNVRs.