Table 2.

Prime Sequences and Cycling Conditions for Amplification and Direction of and HLADQα genes

Gene		Primer Name	Primer Sequences	PCR Cycling Conditions
		Positions		Temperature and Time	Cycles
TAg*	Outer PCR	T1; 2580 – 2602	5’-CCAGCTTTACTTAACAGTTGCAG-3’	94°C 2 min	1
		T3; 4368 – 4345	5’-GGGATGAAGACCTGGTTTGCCATG-3’	94°C 30 sec, 60°C 1 min 68°C 2 min	40
				68°C 7 min	1
	Nested PCR	JEP3; 3217 – 3233	5’-CCCTTGACTCTGCACCAGTGCC-3’	94°C 2 min	1
		JEP4; 3393 – 3274	5’-AGGGGCCAATAGACAGTGGC-3’	94°C 30 sec, 60°C 1 min 68°C 2 min	40
				68°C 7 min	1
VP1*	Outer PCR	JLP15; 1710 – 1724	5’-ACAGTGTGGCCAGAATTCCACTACC-3’	94°C 1 min	1
		JLP16; 1924 – 1902	5’-TAAAGCCTCCCCCCCAACAGAAA-3’	63°C 1 min, 94°C 1 min	50
				63°C 5 min
	Nested PCR	JLP1; 1769 – 1790	5’-CTCATGTGGGAGGCTGTKACCT-3’	94°C 2 min	40
		JLP4; 1897 – 1876	5’-ATGAAAGCTGGTGCCCTGCACT-3’	94°C 30 sec, 63°C 1 min	1
				65°C 5 min	1
	Probe	1851 – 1868	5’-CTCATGACAATGGTGCAG-3’
TCR*	Outer PCR	JRR27; 4990 – 5011	5’-CTCCCTATTCAGCACTTTGTCC-3’	94°C 2 min	1
		JRR28; 331 – 307	5’-TCCAGGTTTTACTAACTTTCACAGA-3’	94°C 45 sec, 58°C 30 sec 72°C 1 min	40
				72°C 5 min	1
	Nested PCR	JRR1; 5086 – 5110	5’-CCTCCACGCCCTTACTACTTCTGAG-3’	94°C 2 min	1
		JRR2; 298 – 274	5’-GTGACAGCTGGCGAAGAACCATGGC-3’	94°C 45 sec, 58°C 30 sec 72°C 1 min	40
				72°C 5 min	1
HLADQ-α*		HLA5; 34–51	5’-GGTGTAAACTTGTACCAG-3’	94°C 3 min	1
		HLA3; 255–237	5’-GGTAGCAGCGGTAGAGTTG-3’	94°C 30 sec, 55°C 30 sec 72°C 30 Sec	40
				72°C 5 min	1

^*Based on JCA sequences Genbank accession number NC_001699

⁺Based on HLA Genbank accession number L34091