Identity of polymorphisms and details of PCR and ASO hybridization
| Polymorphisms . | PCR . | ASO probes . | |||
|---|---|---|---|---|---|
| Identity . | dbSNP . | DNA fragment . | Size, bp . | Primers . | |
| G−2011A | 1650693 | 7 | 211 | R7: cccactgctattggtgttct, F7: aaaaagcggggagagtagat | gcaaattagtataGaat, gcaaattagtataAaat |
| G−1725C | 1677667 | 6 | 382 | R6: agagggcagaagagcgtatt, F6: aatttttgagcttatgactatgcac | agagctaCaattctg, agagctaGaattctg |
| C−1610G (T) | 1650694 | 5 | 401 | R5: gttcacccatagggttttcc, F5: gcccccgccgacaaaagggacctttctcca | gaagagcGtattag, gaagagcC/Atattag |
| A−1574G | 1643639 | 5 | — | — | ataccagAgccatga, ataccagTgccatga |
| G−1349C | 1382540* | 5 | — | — | attgCttcacatacg, attgGttcacatacg |
| C−1338T | 1382539* | 5 | — | — | cagttgtaaGgttt, cagttgtaaAgttt |
| T−1218C | 380691* | 4 | 422 | R4: ttaaagggtagctggtgaagg, F4: ctacttttagctctggaaaaccc | agtctgaCagtcagg, agtctgaTagtcagg |
| T−993C | 453544 | 4 | — | — | gacatgttcaTtgca, gacatgttcaCtgca |
| G−929A | — | 4 | — | — | gtgacaagattatGaat, gtgacaagattatAaat |
| C−680A | 442767 | 3 | 387 | R3: atactgccacaggaaaagcc, F3:cccccgccgttcattgcaatttaagtgtttcc | ccttccacagCctc, ccttccacagActc |
| A−675G | 1643641 | 3 | — | — | ctcaAtctgaaaaatac, ctcaGtctgaaaaatac |
| T−566C | 1650695 | 2 | 400 | R2: cgggacgcgcgtcttttaacctccatcc, F2: aaatactgtgcaggtgaccc | tgaaggaTggcaaca, tgaaggaCggcaaca |
| A−464T | 1650696 | 2 | — | — | acaaaaagAgttcactg, acaaaaagTgttcactg |
| A−317G | 408626 | 1 | 400 | R1: gtaggttctgtctgggactgg, F1: gcagctttcttctagtcaccc | gaagagtTttactga, gaagagtCttactga |
| T−216C | 6151599* | 1 | — | — | agacaggAactcagg, agacaggGactcagg |
| Indel 19 bp (intron 1 +57) | — | NA | 118/137 | R: aaaaggggaatccagtcgg, F: atgggacccaaacgggcgca | NA |
| Polymorphisms . | PCR . | ASO probes . | |||
|---|---|---|---|---|---|
| Identity . | dbSNP . | DNA fragment . | Size, bp . | Primers . | |
| G−2011A | 1650693 | 7 | 211 | R7: cccactgctattggtgttct, F7: aaaaagcggggagagtagat | gcaaattagtataGaat, gcaaattagtataAaat |
| G−1725C | 1677667 | 6 | 382 | R6: agagggcagaagagcgtatt, F6: aatttttgagcttatgactatgcac | agagctaCaattctg, agagctaGaattctg |
| C−1610G (T) | 1650694 | 5 | 401 | R5: gttcacccatagggttttcc, F5: gcccccgccgacaaaagggacctttctcca | gaagagcGtattag, gaagagcC/Atattag |
| A−1574G | 1643639 | 5 | — | — | ataccagAgccatga, ataccagTgccatga |
| G−1349C | 1382540* | 5 | — | — | attgCttcacatacg, attgGttcacatacg |
| C−1338T | 1382539* | 5 | — | — | cagttgtaaGgttt, cagttgtaaAgttt |
| T−1218C | 380691* | 4 | 422 | R4: ttaaagggtagctggtgaagg, F4: ctacttttagctctggaaaaccc | agtctgaCagtcagg, agtctgaTagtcagg |
| T−993C | 453544 | 4 | — | — | gacatgttcaTtgca, gacatgttcaCtgca |
| G−929A | — | 4 | — | — | gtgacaagattatGaat, gtgacaagattatAaat |
| C−680A | 442767 | 3 | 387 | R3: atactgccacaggaaaagcc, F3:cccccgccgttcattgcaatttaagtgtttcc | ccttccacagCctc, ccttccacagActc |
| A−675G | 1643641 | 3 | — | — | ctcaAtctgaaaaatac, ctcaGtctgaaaaatac |
| T−566C | 1650695 | 2 | 400 | R2: cgggacgcgcgtcttttaacctccatcc, F2: aaatactgtgcaggtgaccc | tgaaggaTggcaaca, tgaaggaCggcaaca |
| A−464T | 1650696 | 2 | — | — | acaaaaagAgttcactg, acaaaaagTgttcactg |
| A−317G | 408626 | 1 | 400 | R1: gtaggttctgtctgggactgg, F1: gcagctttcttctagtcaccc | gaagagtTttactga, gaagagtCttactga |
| T−216C | 6151599* | 1 | — | — | agacaggAactcagg, agacaggGactcagg |
| Indel 19 bp (intron 1 +57) | — | NA | 118/137 | R: aaaaggggaatccagtcgg, F: atgggacccaaacgggcgca | NA |
The base substitution that distinguishes the 2 variants of each polymorphism is given as capital letter in corresponding ASO probes. PCR primers and ASO probes were taken from human chromosome 5 clone sequence (GenBank accession no. AC008434) on which the minor transcript initiation site12 is positioned according to DHFR mRNA sequence information (GenBank accession no. NM_000791). When available, the respective number from SNP database (dbSNP13 ) at the National Center for Biotechnology Information is provided.
R indicates reverse; F, forward; —, as above; and NA, not applicable.
SNPs analyzed in HapMap samples (HapMapData Rel 21a/dbSNP b125, www.hapmap.org) are marked. Allele frequency and pairwise r2 values for these four SNPs in CEU HapMap samples (CEPH, Utah residents with ancestry from northern and western Europe) are compatible with the data obtained in this study.