Cytochrome P450 2D6 profiles and their relationship with outcomes of primaquine anti-relapse therapy in Australian Defence Force personnel deployed to Papua New Guinea and East Timor

Chen, Nanhua; Dowd, Simone; Gatton, Michelle L.; Auliff, Alyson; Edstein, Michael D.; Cheng, Qin

doi:10.1186/s12936-019-2774-2

Table 1 Primers used for PCR and sequencing CYP2D6

From: Cytochrome P450 2D6 profiles and their relationship with outcomes of primaquine anti-relapse therapy in Australian Defence Force personnel deployed to Papua New Guinea and East Timor

Purpose	Primer (position, bp)	SNPs/indels to detect	Primer sequence (5′–3′)	PCR condition	Ref
Nested PCR Round 1	2D6-DPKup (− 352 to − 320)	Full length	GTT ATC CCA GAA GGC TTT GCA GGC TTC A	95 °C 1 min; 95 °C 20 s, 65 °C 20 s, 72 °C 2 min 30 s, 50 cycles	[34]
Nested PCR Round 1	2D6-DPKlow (4763 to 4743)	Full length	GCC GAC TGA GCC CTG GGA GGT AGG TA		[34]
Nested PCR Round 2	2D6gene sense (− 270 to − 239)	Full length	GGC GGC CTA CCC TGG GTA AGG GCC TGG AGC AGG A	95 °C 1 min; 95 °C 20 s, 72 °C 2 min 30 s, 40 cycles	[35]
Nested PCR Round 2	2D6gene antisense (4413 to 4382)	Full length	CTC AGC CTC AAC GTA CCC CTG TCT CAA ATG CG	95 °C 1 min; 95 °C 20 s, 72 °C 2 min 30 s, 40 cycles	[35]
Sanger sequencing	2D6Ex1FH (− 126 to − 103)	31G>A, 77G>A, 100C>T, 124G>A, 137_138insT	CAG CTC CCT TTA TAA GGG AAG GGT	96 °C 2 min; 96 °C 10 s, 50 °C 5 s, 60 °C 4 min, 30 cycles	[34]
	2D6-SF4 (695 to 717)	883G>C, 1023C>T, 1039C>T	CCA AAC TGA GTT CCT CCA TCA CA
	2D6-SF6 (1417 to 1436)	1584delG, 1659G>A, 1661G>C, 1707delT, 1716G>A, 1758G>T	AGA GAC GAG GTG GGG CAA AG
	2D6Ex4F1s (1780 to 1797)	1846G>A, 1863_1864insTTTCGCCC, 1973_1974insG, 1978C>T, 1979T>C, 2291G>A	ACA AAG CGG GAA CTG GGA
	2D6Ex5F2s (2318 to 2339)	2539_2542delAACT, 2549delA, 2573_2574insC, 2587_2590delGACT, 2615_2617delAAG	TTG GTG AGG TCA GTG GTA AGG A
	2D6-SF11 (2735 to 2756)	2850C>T, 2935A>C, 2950G>C, 2988G>A, 3183G>A, 3201C>T, 3259_3260insGT	TGA CAG GTG CAG AAT TGG AGG T
	2D6-Ex9F2s (3920 to 3938)	4125_4133insGTGCCCACT, 4180G>C	CCT TCC TGC CTT TCT CAG C
2D6 duplication detection	2D6dup sense	Gene duplication	CCT GGG AAG GCC CCA TGG AAG	95 °C 2 min; 95 °C 20 s, 68 °C 20 s, 72 °C 2 min, 40 cycles	[33]
2D6 duplication detection	2D6dup antisense	Gene duplication	CAG TTA CGG CAG TGG TCA GCT	95 °C 2 min; 95 °C 20 s, 68 °C 20 s, 72 °C 2 min, 40 cycles	[33]
2D6 deletion detection Round 1	2D6del01 sense	Gene deletion	GTT GGA GCT CCT GAC CTC TTC	95 °C 2 min; 95 °C 20 s, 60 °C 20 s, 72 °C 2 min, 50 cycles	This study
2D6 deletion detection Round 1	2D6del antisense	Gene deletion	TAT ATG CCA GGG CTA CCT CCC	95 °C 2 min; 95 °C 20 s, 60 °C 20 s, 72 °C 2 min, 50 cycles	This study
2D6 deletion detection Round 2	2D6del sense	Gene deletion	ACC GGG CAC CTG TAC TCC TCA	95 °C 2 min; 95 °C 20 s, 68 °C 20 s, 72 °C 2 min, 40 cycles	[33]
2D6 deletion detection Round 2	2D6del antisense	Gene deletion	GCA TGA GCT AAG GCA CCC AGA C	95 °C 2 min; 95 °C 20 s, 68 °C 20 s, 72 °C 2 min, 40 cycles	[33]

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