Table 2.
Primer and probe sequences used in htSNP detection
| htSNP* | ref SNP I1D#) | IIPGA# | Major allele | Minor allele | Location | Sequence**(5′ to 3′) |
|---|---|---|---|---|---|---|
| Forward primer | ||||||
| Reverse primer | ||||||
| Probe (wild-type) | ||||||
| Probe (variant) | ||||||
| 1 | 10759932 | 2856 | T | C | Promoter | GCAAGCTTCTGCTATGATTAAAAGTGA |
| CACAAATGGTGTACAGGAGTTCTCA | ||||||
| FAM-TTCACCAACACTTATT-MGB | ||||||
| VIC-CTTCACCAACGCTTATT–MGB | ||||||
|
| ||||||
| 2 | 1927911 | 7764 | C | T | Intron 1 | Applied Biosystems Assay on Demand-proprietary |
| N/A*** | ||||||
| N/A | ||||||
| N/A | ||||||
|
| ||||||
| 3 | 11536878 | 9263 | C | A | Intron 2 | CTGGAAACTGATATAAAGATAGCGACATATAACA |
| CTTGACTACCCACCACAGAGAAG | ||||||
| FAM- AAACTAAAGGTAACTAATTG-MGB | ||||||
| VIC- TTTAAACTAAAGGTAAATAATTG–MGB | ||||||
|
| ||||||
| 4 | 2149356 | 1191 | G | T | Intron 2 | GCTGTCATGTAAGCACTTTTCATAAACA |
| 2 | GTTGGTAGCCAAGATAAATGACTGGTA | |||||
| VIC-ACTTATGTGTAATGTTTCG-MGB | ||||||
| FAM-TTATGTGTAATTTTTCG –MGB | ||||||
|
| ||||||
| 5 | 5030728 | 1199 | G | A | Intron 2 | CCAGTCATTTATCTTGGCTACCAACT |
| 5 | CAAGTTTAGCCATTTTCTGTCACACA | |||||
| FAM- CTGTACCAATCAGATGTAT-MGB | ||||||
| VIC- CTGTACCAATCAAATGTAT–MGB | ||||||
|
| ||||||
| 6 | 11536889 | 1584 | C | G | 3′UTR | GTTGGGCAATGCTCCTTGAC |
| 4 | ACCCCATTAATTCCAGACACATTGT | |||||
| FAM-ATAACATCCACTCTTCCCA-MGB | ||||||
| VIC-ATAACATCCACTGTTCCCA–MGB | ||||||
htSNP, Haplotype tagging SNP
II
PGA# Innate Immunity PGA number
MGB, minor groove binder
*
For ease of discussion, each SNP was assigned a number from 1 to 6.
**
Polymorphic nucleotide is underlined.
***
Not available