Table 2 of Yip, Mol Vis 2011; 17:810-821.
Table 2. COL11A1, COL18A1, FBN1 and PLOD1 SNPs: PCR primers and conditions, primer extension (PE) primers, ddNTP added, and buffer B concentration ranges for DHPLC
ddNTP | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
SNP* |
Forward primer (5′>3′) |
Reverse primer (5′>3′) |
Primer (µM) |
Mg2+ (mM) |
Tm (°C) |
PE primer (5′>3′) |
G |
C |
A |
T |
DHPLC buffer B |
COL11A1 | |||||||||||
rs2061705 | GAAACCCTGCCTCTACTAAAAG | GGGCAAATCTTAGGAACTTACAAAA | 0.1 | 1.5 | 64 to 58 | CAACGTTTTCTGTGAAATTTTATAAAGAC | √ | √ | 27–33 | ||
rs2615987 | TAAGAGAAAAAAAACCAACAGCCTAT | AACACCAGAATTTGAACAGTAAGG | 0.1 | 1.5 | 64 to 58 | TACAGAATTAACCATAATTGAACAGC | √ | √ | ‡ | 27–33 | |
rs17127311 | CATAAGGAATAAAGGCATAAGAACATC | AGAGATTTAGAAGGGTCAAGATG | 0.1 | 1.5 | 64 to 58 | AGGAAAAAGCAAAGCAAAGTGATG | √ | √ | 23–29 | ||
rs12143740 | ATTAGGTGAGACAGATGAAAAATTATTG | TATTACCCACTTTATGTTACTGTCC | 0.1 | 1.5 | 64 to 58 | GATAACTGAAAGAGGATGGGGA | √ | √ | 22–28 | ||
rs4908273 | AAGCAGGTGTAGGCGTAAGT | TAATGAGTTGGGAAGGGAAAGTA | 0.3 | 2.5 | 62 to 56 | TATTATTGGTTTGGGAATTTCTTTTACA | √ | √ | 31–37 | ||
rs11164630 | CTCTTTGGGTGTATCTGTGTTTA | TATATGCCCTAACTCCACAACTA | 0.1 | 1.5 | 64 to 58 | CAAATATAATACACAGTTGATTAGATAGC | √ | √ | 28–34 | ||
rs9659030 | CTCCTTGTTTTCAGTGTGCTTC | CCTTAAAGTAAATACCTTAGTGGAAAAAA | 0.1 | 1.5 | 64 to 58 | CATATGGTGGACTGTTATTAAGAGT | √ | √ | 27–33 | ||
rs1241209 † | GTCCCCATCCAAATCTCATC | GCAAGGAGGAACAAGTCACAT | - | - | - | ATGATAGGGGCAAGTCATTCAAA | - | - | - | - | - |
COL18A1 | |||||||||||
rs11089001 | ATTCCCTCGTATGGTGCTGT | GCCTTAGACCCCAAACTCC | 0.1 | 1.5 | 64 to 58 | TTGGATAAGAGGAGCACCC | √ | √ | 21–27 | ||
rs2026885 | ACAGGGTCAAGTTTCAGCAG | ATGGAAGGAAGGTCTCTCTC | 0.1 | 1.5 | 64 to 58 | ATGCCAGACGGCGTGAAG | √ | √ | 19–25 | ||
rs1004133 | GTTTTGTGAGTCCCCATTGC | AAAGGCTGACCATAAACAATAAAAGTA | 0.1 | 1.5 | 64 to 58 | GTCGTGTTTCTCTGGGAAC | √ | √ | 22–28 | ||
rs2838907 | GCCCTTTCTGTATTGGATGC | CACAACATTCTCAGTCATTTTCACA | 0.1 | 1.5 | 64 to 58 | CAAAGGAATGGGCTCCAGT | √ | √ | 20–26 | ||
rs2838913 | TCCGTTGTTGTAGCCACTGT | CCTTTTCTCTCTTCCCTACG | 0.3 | 2.5 | 62 to 56 | CACCTCCTTCACCACTTCA | √ | √ | 26–32 | ||
rs2838916 | ATTTATCAGGCGTTTTGGGTGTA | AATGCTGAATAATGCTCCTGTTG | 0.3 | 2.5 | 62 to 56 | GCCACTTGGTTGCATTGTGAAAT | √ | √ | 26–32 | ||
rs2838917 | GTCCTGGTATTTATCTCAACTTCAT | GCTTACTGACTCCACATTACG | 0.3 | 2.5 | 62 to 56 | AAGCTGCTTTTTATTATTTGTGACC | √ | √ | 29–35 | ||
rs2838920 | TCAAAGGTTCTCTCCACTCG | AGTGTTGGGGGCTGTGTTG | 0.1 | 1.5 | 64 to 58 | CCTTGCACAGCCAGAAACG | √ | √ | 22–28 | ||
rs8131523 † | AGGACGGCGACTCACAGAT | AGGACAGAATAGATGGCAGAAG | 0.3 | 2.5 | 62 to 56 | CTGGCCTGACGCACCTCG | - | - | - | - | - |
rs2838922 | TCCCCACCTTTTCACAGTTG | AAACCCCATCTCTACTAAAAACACAA | 0.1 | 1.5 | 64 to 58 | GACAGCATTTAGTTTGAGTGACTTT | √ | √ | 28–34 | ||
rs2838923 | CTCTGTCTTTTCTCCTCTGTTGA | CAGAAAGCAAACGCACAGAC | 0.1 | 1.5 | 64 to 58 | AGACTCCTGAGGTGCAGAC | √ | √ | 23–29 | ||
rs11911327 | GTGTGCATCTTGAGTGCTGT | GGTCCTGGCTGCTACTGAA | 0.1 | 1.5 | 64 to 58 | GGCCTCGGGCCTCAAAGA | √ | √ | 21–27 | ||
rs8126757 | GTTTGAGGAGCGTGTGGTG | TCCAATCGTTTCCAGTCCTTC | 0.1 | 1.5 | 64 to 58 | CTGCTACTGAAGTCTCCTGA | √ | √ | 24–30 | ||
rs2838927 † | TTGAGGAGCGTGTGGTGAG | GAGTTGGGCAGTGGTGATG | - | - | - | GACCGAGGCCACCGGTTTC | - | - | - | - | - |
rs11702782 | ATCACCACTGCCCAACTCTA | AGAGGAGCCCGAAACAAAAG | 0.1 | 1.5 | 64 to 58 | CACTTTCCACCTCTGGATC | √ | √ | 24–30 | ||
rs2026887 | CCAAGATGAAAGGCCAGAGT | AAGAGGAGACAGGAAGTGGA | 0.1 | 1.5 | 64 to 58 | ACGGGGAGCTGTGGGTGA | √ | √ | 21–27 | ||
rs8129539 | CTAGAATAAGTATGAGAAACCCCAAAT | CTCACAAGGTCAGAAGGAATCAA | 0.1 | 1.5 | 64 to 58 | AGTGTACACAGATGTTAATCCTCTT | √ | √ | 28–34 | ||
rs8133622 | GACAGAATACTCCCTAAATCAACTA | GAACCAAAAGACCTCAATGTGC | 0.1 | 1.5 | 64 to 58 | TAAATTGAATTTCAAGGAACCCAGA | √ | √ | 28–34 | ||
rs7279077 | CACACAGGTTTCTGCATGGA | GCTCTGCAAAAAGAAAGACAGCT | 0.1 | 1.5 | 64 to 58 | CGTTTGGGAATGAGTGAACC | ? |
? |
√ | √ | 22–28 |
rs2236454 | TGGGTGAGTGAGTGAGATTG | TGGCTTTGCTTTCTTTGAACTTC | 0.3 | 2.5 | 62 to 56 | GAGATCCAGGAAACTCCCC | √ | √ | 22–28 | ||
rs2236457 | TGGGGTGAGTGACATCTGG | GAGGGTGGTTTCTGGTGTTTAT | 0.1 | 1.5 | 64 to 58 | AATGGTATCGCAGCTTCCCAGT | √ | √ | 26–32 | ||
rs2230687 | CAAACCAAGCAAGTCTCCAC | CACCACATCCAGAAAAGAGC | 0.1 | 1.5 | 64 to 58 | GCTCCCCGCGCCACCCCC | √ | √ | 20–26 | ||
rs9977482 † | ATGTGCATGTGTTTGAGTGTGTG | TGTGTATGCAAGTGTATCCACGT | 0.1 | 1.5 | 64 to 58 | TGTGCATGTGTGGTATGTGTAC | - | - | - | - | - |
rs3818661 † | AGGGAGTGTGGGGTTAGGT | GCAGGATGAGATGGCAGAG | 0.1 | 1.5 | 64 to 58 | CAACCCTACCGATGGGCGCTC | - | - | - | - | - |
rs2236475 | ACTGTCCTCCCCCAAGAAC | TGATGATTACCAGACACCTTCC | 0.1 | 1.5 | 64 to 58 | CCCACTGCCCTGTCTGCC | √ | √ | 21–27 | ||
rs7279445 | CTGTAAGTATGACGAGGGTAGA | CAAACCCACACCAGCCTCT | 0.3 | 1.5 | 62 to 56 | GGGAGCGTCTCTTGTAAGC | √ | √ | 23–29 | ||
rs3753019 | AGTAAGTCCCAGCCTGTGCA | GCAGAGACCTGACAACAGTG | 0.1 | 1.5 | 64 to 58 | CCATCAGTCCTGAAAGACTC | √ | √ | 22–28 | ||
rs2838951 | AAGTGGGCTTGGCTCCATC | CATACGCTGCCAGGTCAGA | 0.1 | 1.5 | 64 to 58 | GTTCCTCAAGGATGTGACAG | √ | √ | |||
rs7499 | GCTGCCATCACGCCTACAT | CTCTTTGGCTTCCTTTTATTTCTTG | 0.1 | 1.5 | 64 to 58 | TAGCCACCGCCTGGATGC | √ | √ | 22–28 | ||
rs1051296 | ATGGTCCTGTCTGTCCTTCT | GCACATACCAAGGCCAGCA | 0.3 | 1.5 | 62 to 56 | TCCCCTCCGGGCTGGCAC | √ | √ | 21–27 | ||
FBN1 | |||||||||||
rs6493334 | GCTCATAGTTCCCACAGTTTTTC | CTGGCTGCTGTAACTGGAG | 0.1 | 1.5 | 64 to 58 | TCAGCATGTCCATCATCACCAT | √ | √ | 24–30 | ||
rs6493333 | TAACTTGCCCAGGTCTCTCTA | GGCTGCTGTAACTGGAGAC | 0.3 | 1.5 | 62 to 56 | AGGTACCCTGGGAATGTATC | ? | √ | ? | √ | 22–28 |
rs6493331 | GCCACCTTTCAGAGACCATTTT | ACCCCATCTCTACTAAAAATACAAAAAA | 0.1 | 1.5 | 64 to 58 | TGAACTTTACTTACTTTTTATGTATCTTTAAT | √ | √ | 31–37 | ||
rs2247876 | TGGAAAGGGGGTCTGGTATT | CTTGTTGGACTAAATAATACTGTGTGA | 0.1 | 1.5 | 64 to 58 | ACCTCGGCTCTCACATCTG | √ | √ | 22–28 | ||
rs16961274 | CTGAGGAGATGTAGGCAAATG | CAGGCTCAAATAGGAAATAGTGT | 0.1 | 1.5 | 64 to 58 | GAGTTGAGGCCACTGACCT | √ | √ | 20–26 | ||
rs12438332 | ATCTGAGAATGAGCACACCAATA | CTAGCCCTCCCATCAAAACA | 0.1 | 1.5 | 64 to 58 | TGCATGCTTTTACCTAACTTCCT | √ | √ | 25–31 | ||
rs1807301 | GGGTGTCCTTTGTTGTGTGA | GTCAGGAGGCTCTTATTTCATATA | 0.1 | 1.5 | 64 to 58 | AGTTAATGGAGCAGGGTCAG | √ | √ | 22–28 | ||
rs16961220 † | AGAGCAGAGAGTGGTTTGTG | TCTGTGCAAGTTGTAAAGAGAAG | 0.1 | 1.5 | 64 to 58 | CAATGTAAAGGTCTATTATGCATTACA | - | - | - | - | - |
rs16961207 | GTTTTCTCTCATTTCTCCATCTG | GCATAACAGCCAACAGACTTTC | 0.1 | 1.5 | 64 to 58 | CTTGGGTAGGAATTTAACACAGAA | √ | √ | 25–31 | ||
rs12915677 | CTTTGCCATTCCTCTCTCCA | CTCCAGACCAGAAACAGTAAAAAA | 0.1 | 1.5 | 64 to 58 | TCAGTACTGGGGATTGTCTAAAA | √ | √ | 25–31 | ||
rs683282 | GAAGTTGGGGATAGAAGATAAGA | CTGTGGAGACTATTTGGCATTG | 0.1 | 1.5 | 64 to 58 | GTCAATGTACAGCAATACACCAT | √ | √ | 28–34 | ||
rs16961118 | TATTTATTCACTACCTCCTCCACAA | GATCACACCACTGCTCTCAA | 0.1 | 1.5 | 64 to 58 | GTGCTATTCACTGATACAGGGTT | √ | √ | 25–31 | ||
rs6493328 | CTGTCATTTTTTTCTCTTCTTCTGC | GACATCCTCTAATAAACATCCTGAA | 0.1 | 1.5 | 64 to 58 | GTGTGGGTCAGGCTATTGAAAA | √ | √ | 25–31 | ||
rs17361868 | CCGTGTGTGTGTTGGTAAGAAA | GCCTGGAGAAAACTGAAGAC | 0.1 | 1.5 | 64 to 58 | CAATAAAGCCCAATGGTAACAAAC | √ | √ | 23–29 | ||
rs11635140 | GCAGACACGCTCCAACAATA | CTGTTAGGTAAAATACTGC | 0.1 | 1.5 | 64 to 58 | TATTCTGAGAGATCCCACAGTG | √ | √ | 26–32 | ||
rs11070643 | CTATACAAGATATGAAAATAATGTGCATC | AATGTAAGTTTCCAGTCACTGCA | 0.3 | 2.5 | 62 to 56 | GACTTACTAAAAATACTAGCAAAAGAAAATAT | √ | √ | 28–34 | ||
rs3825963 | GAATAGGAAAATGAAGGTTGAGTG | AGAAACACAGGGGGCAGATT | 0.1 | 1.5 | 62 to 56 | GGTGATTTAGGGAGCTTCCA | √ | √ | 22–28 | ||
rs10519174 | TCTATATGATGAAAGAAAAAGCCTGTA | GAATTTTACAAGAACACTAAGACTCAT | 0.1 | 1.5 | 62 to 56 | AAAGATTAACCCACAAATCAGGAG | √ | √ | 24–30 | ||
rs1467953 | CTAGAGACAGGTTTTGCCATGT | CTTTAGTCGTGATTCTTCTTAGGAT | 0.1 | 1.5 | 64 to 58 | CAGTTTTATTAAAAGTGCCTTTAGCTATT | √ | √ | 28–34 | ||
PLOD1 | |||||||||||
rs1208984 | GGAAGGAAAGGGTGACAGC | ACGGGGATAATAGAAGGAAACAC | 0.3 | 1.5 | 62 to 56 | AAGGCTCAAATAATAATAGTTTTCATAATAATA | 30–36 | ||||
rs7529452 | TAAGGGGTGTTTCTCTCCAG | CACCTCCTCTTTATCTTTTCACC | 0.1 | 1.5 | 64 to 58 | AGGAGGATCTGGTCATTCTCTT | √ | √ | 24–30 | ||
rs7551175 | TAAGGGGTGTTTCTCTCCAG | ACCTCCTCTTTATCTTTTCACCA | 0.1 | 1.5 | 64 to 58 | TGACCCACCTACCTGTCTG | √ | √ | 22–28 | ||
rs11585018 | TGCTCTTGTGGTTGCTTGTC | GGTGGTGAAGAAACGGATTG | 0.1 | 1.5 | 64 to 58 | GCCAGGTTTCCCAGATAACT | √ | √ | 23–29 | ||
rs2273286 | GCTCTTGTGGTTGCTTGTCA | TGAGTTCCTAATGACCCCAAG | 0.1 | 1.5 | 64 to 58 | CAATCCGTTTCTTCACCACCTAT | √ | √ | 25–31 | ||
rs1130529 | ATCCCTGGTTAGTGCTGTCT | AGAAGCCAGATGAAGGTGTC | 0.1 | 1.5 | 64 to 58 | TCATCAGCGGGGCAATGAC | √ | √ | 21–27 | ||
rs2273291 | GACCAACATTTCAGGACCAG | ATATCAGAGACCAAGTGCAGTC | 0.1 | 1.5 | 64 to 58 | GAAGACTTCCCTGATCACATTCT | √ | √ | 24–30 | ||
rs3818157 | ACTCTTGACATAGGGGTGCT | CCTGCTGTCTGATGAACTTG | 0.1 | 1.5 | 64 to 58 | CTCCATCTCAGGTTTCTCAATC | √ | √ | 24–30 | ||
rs3753579 | GAGATTGTGGAGGAGGAAAC | ACACTGCCCTCTGAGTAGC | 0.1 | 1.5 | 64 to 58 | TGTCTGGGATGTAGCGTGC | √ | √ | 20–26 |