Molecular Vision: Yip, Mol Vis 2011; 17:810-821. Table 2

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

*SNPs are arranged down the column in the order of 5′>3′ along the sense strand of the respective gene. †These six SNPs failed to be analyzed by the DNA pooling approach because of failure in PCR (rs1241209 in COL11A1, and rs2838927 in COL18A1) or PE reaction (rs8131523, rs9977482 and rs3818661 in COL18A1, and rs16961220 in FBN1) even after repeated optimization. This is the reason why specific conditions for PCR and/or PE are left blank (indicated as “-”). ‡In addition to ddGTP and ddATP, dTTP was also used in the primer extension reaction for rs2615987 (COL11A1) for an optimal discrimination of the extended products.