Table 2. PCR primers, annealing temperature and RFLP pattern for genotyping of WDR36 SNPs.
SNP ID and location in the gene | Primer sequences | Annealing temperature | Restriction enzyme | RFLP pattern |
---|---|---|---|---|
rs1971050 (c.330+925 C>T) |
5′-GAGGTGAAGAGCAATTGGGTTTCTC-3′ |
60 °C |
AluI |
C: 203 bp, 35 bp
T: 238 bp |
|
5′-GCAGTGTCAGGAAAGACACTGTACC-3′ |
|
|
|
rs1993465 (c.459+183A>G) |
5′-TTCTTTACCCAGCACACTCTGGAA-3′ |
56 °C |
HinfI |
G: 147 bp, 25 bp
A: 172 bp |
|
5′-TTTTGAAGAAGGTCTCCAAGTGATT-3′ |
|
|
|
rs13153937 (c.460–112A>G) |
5′-GCAGATGAACATGCCTGGTCCCTTA-3′ |
58 °C |
BciVI |
G: 397 bp
A: 336 bp, 61 bp |
|
5′-ACAGGCAAAATCTCTGGCATAG-3′ |
|
|
|
rs10038177 (c.710+30C>T) |
5′-GCCTCTCATTTATTTTATTTCTCAAGG-3′ |
62 °C |
AluI |
C: 338 bp, 120 bp
T: 458 bp |
|
5′-CCTCTGATACAGGGGACCAACTG-3′ |
|
|
|
rs11241095
(c 772G>A, I264V) |
5′-GAGGATGGGATGTTGACTGGCAGA-3′ |
50 °C |
HpaI |
G: 268 bp, 23 bp
A: 293 bp |
|
5′-ATAACTTGACCTGACATAAGGTTAA-3′ |
|
|
|
rs10043631 (c.1494+90C>T) |
5′-TCCCTAGTGTCTGAAATATTGGATGC-3′ |
50 °C |
DdeI |
C: 328 bp, 25 bp T: 353 bp |
|
5′-TAAAATGTTAAACTACGTTTTCTCA-3′ |
|
|
|
rs10038058 (c.1494+143G>A) |
5′-TCTTGTTATACTCAAGGTTTCTCATCA-3′ |
50 °C |
ApoI |
G: 191 bp, 63 bp
A: 102 bp, 89 bp, 63 bp |
|
5′-AGAATAGTCTTTTGAACAAATAGTGCTG-3′ |
|
|
|
rs10491424 (c.1965–905C>T) |
5′-CTATCTCCTCTTAAGTGGTTAATGAATT-3′ |
58 °C |
EcoRI |
C: 147 bp, 24 bp
T: 171 bp |
|
5′-ATGTGGTGGATAAGGCAAGG-3′ |
|
|
|
rs17553936 (c.1965–30A>G) |
5′-TGGTGACTTTCTGATCAATGCTGGTG-3′ |
62 °C |
CvIQI |
G: 308 bp, 120 bp
A: 428 bp |
|
5′-TCAAGCAGATGTTGAATCACTCAGA-3′ |
|
|
|
rs13186912 (c.2181A>T; V727V) |
5′-GGTGTTTTGGGTCTAGTGATGG-3′ |
56 °C |
BstBI |
A: 234 bp
T: 210 bp, 24 bp |
5′ -CACTTGGTTCTACTGTTTCTTTCGA-3′ |
The dbSNP reference IDs for each SNP and their location in the genomic region are furnished. Ten SNPs (rs1971050, rs1993465, rs13153937, rs10038177, rs11241095, rs10043631, rs10038058, rs10491424, rs17553936, and rs13186912) were genotyped in 323 POAG patients (207 non-HTG, 116HTG) and 119 controls by RFLP analysis as mentioned in the Table.