Table 1.
Candidate genes and amplicons for VSMC bisulphite NGS: Genomic locations, primer sequences, annealing temperatures and CpG coverage are displayed for each amplicon targeting candidate genes
| Gene symbol | Chromosome and RefSeq ID | RefSeq ID coordinates | Primer sequence 5′-3’ | Annealing temp (°C) | CpG coverage |
|---|---|---|---|---|---|
| LRP1 | 3875–4240 | F: TAGAAGGGGGTAGTGATTAAAAGTA | 54 | 13 | |
| R: AAAACAAACCCTAATTTAAAAAAAA | |||||
| Chr: 12 | 4274–4640 | F: GGGTATTAAGGTGGGTTTTATTTT | 57 | 25 | |
| NG_016444.1 | R: TACTCTAAAATTTCAAACTCCCTCC | ||||
| 4680–5036 | F: GTATTAGGGAGGAGGGTTTAGTTAG | 54 | 24 | ||
| R: TCCTCAATACATAAACCTAAAACTC | |||||
| ERG | 282787–283319 | F:TTTTATTAGGTAGTGGTTAGATTTAGTTTT | 54 | 22 | |
| Chr: 21 | R: TACCCCCAATTAATAAATTCCAATATA | ||||
| NG_029732.1 | 283331–283680 | F: TTGGAATTTATTAATTGGGGGTATATAT | 57 | 6 | |
| R: ACACTATCTTTTACAAAATCAATCCAC | |||||
| 5162–5540 | F: AAAATTTTTGGAAGGGGTTTAGTT | 56 | 37 | ||
| R: ATAATATTTTTCCAACCTCATTAAAAAC | |||||
| MMP-9 | 3980–4579 | F: TTGGGTTTAAGTAATTTTTTTATTT | 52 | 7 | |
| Chr: 20 | R: TAACCCATCCTTAACCTTTTACAAC | ||||
| NG_011468.1 | 4640–5600 | F: GATGGGGGATTTTTTTAGTTTTATT | 57 | 8 | |
| R: TACCCATTTCTAACCATCACTACTC | |||||
| LDLR | 4376–4725 | F: TTTTTTAAGGGGAGAAATTAATATTTA | 54 | 5 | |
| R: CACAAAAAAATAACAACAACCTTTC | |||||
| 4776–5355 | F: GAAAGGTTGTTGTTATTTTTTTGTG | 57 | 28 | ||
| Chr: 19 | R: AAACTCCCTCTCAACCTATTCTAAC | ||||
| NG_009060.1 | 5464–5972 | F: TTTAAGTTTTTATAGGGTGAGGGAT | 56 | 31 | |
| R: ACACCCAACTCAAAATAACAATAAC | |||||
| 6054–6785 | F: AATTTTATTGGGTGTAGTTTAATAGGTTAT | 54 | 49 | ||
| R: CTCAAAATCATACACTAACCAACCTC | |||||
| IL6R | 2781–3061 | F: TTTTTGTTTAGGTTGGAGTGTAGTG | 52 | 8 | |
| Chr: 1 | R: CAAAATTTTAATATTATAATTCACATAAAA | ||||
| NG_012087.1 | 3095–3729 | F: GTTTGTTTTGGTGTAGAGATAGGTG | 58 | 7 | |
| R: ATAAAACTCCCAAATAAACAAAACC | |||||
| SORT1 | Chr: 1 | 4363–4804 | F: AGATTATTTTTTAGGTTTGTAGGAGTTA | 55 | 24 |
| NG_028280.1 | R: AACAAAAACTACTAAAATCAACCCC | ||||
| SMYD2 | 214280141–214280630 | F: TTTTATTTTGAAGTAGTGGTTTTTGTTAA | 55 | 13 | |
| R: TTTTCCAAAATTAAAAATTTTTAAACCT | |||||
| Chr: 1 | 214280631–214281330 | F: AAGGTTTAAAAATTTTTAATTTTGGAAA | 58 | 82 | |
| NC_000001.11 | R: AAATCCCCCACCTAAAAAAACTAC | ||||
| 214281331–214281733 | F: TTTTTTTAGGTGGGGGATTT | 55 | 46 | ||
| R: CCCACATTTAAAAACAAAAACCTAC | |||||
| SERPINB9 | 2891544–2892079 | F: GGTGTTGAAAATATTTTTGGAGGTA | 57 | 26 | |
| R: AAAATCTACCATTCATCAAACTAACAAA | |||||
| 2890564–2891263 | F: TTAGAGGGTGGGATTAGAGGTAGTT | 54 | 9 | ||
| Chr: 6 | R: TTTCCACCTAAAAAACCAAAATTAA | ||||
| NC_000006.12 | 2889934–2890423 | F: GTATTTGGGAATTGTTGATGTTTTT | 55 | 11 | |
| R: ACAACAAAAAATCATTATAATCTATTTTCT | |||||
| 2889425–2889933 | F: AGAATTTTATATGTAATTTATTTTGG | 54 | 31 | ||
| R: TATAATCCCAACACTTTAAAAAACC | |||||
| DAB2IP | 121689899–121690502 | F: TTGGAGTAGTTTGTTTGTTGTGTT | 57 | 10 | |
| R: TAAAAAATTAAATACCCAAAACCTC | |||||
| 121690573–121691062 | F: TTGTTATATTTTAAGTTGAGATTTTGGG | 57 | 6 | ||
| Chr: 9 | R: TAACCACATAAAAACATTCCAAACA | ||||
| NC_000009.12 | 121767430–121767872 | F: GGAGAGGAGATAGGAAAGTTTTTAG | 57 | 6 | |
| R: CTAACCTTATCCCTTACAACCACTAC | |||||
| 121768273–121768692 | F: AATGGAGTGGGAGTTTGTTATAGTG | 57 | 11 | ||
| R: TAATAACAACTTTTAACCCCACCTC |