Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designs

Paul, Sinu; Piontkivska, Helen

doi:10.1186/1471-2180-10-212

Table 3 Description of the 44 epitopes used in association rule mining.

From: Frequent associations between CTL and T-Helper epitopes in HIV-1 genomes and implications for multi-epitope vaccine designs

Gene	Protein	Non-overlapping genomic regions	Epitope sequence	amino acid coordin ates^@		Type of epitope	Epitopes involved in 2T-3G^	Non-overlapping genomic regions of 2T-3G epitopes	Number of "unique" association rules each epitope is involved	HLA allele/MAb^$	Class-I HLA allele supertype association	Alternate HLA allele in case of promiscuous HLA alleles (if known)*	+ if cumulative frequencies of HLA supertype alleles over 10% in the population
				Start	End								European	North American	Sub-Saharan African
Gag	p17	1	WASRELERF^#	36	44	CTL			0	B3501, B5801, B53	B07, B58		+	+	+
	p24	2	SPRTLNAWV	16	24	CTL	✓	1	712	B*0702, B42	B07	B42, B39, B81	+	+	+
		3	FSPEVIPMF	32	40	CTL			8	B*57	B58		-	-	-
			EVIPMFSAL	35	43	CTL			1	A2601, A6901, B1501, B4001	A01, A02, B62, B44		+	+	+
			SEGATPQDL	44	52	CTL			257	A2601, B4001	B44, A01	B44	+	+	+
		4	GHQAAMQML	61	69	CTL	✓	2	2752	A0201, A3, B1510, B38, B*3901	B27, A03, B07, A02	A03, B38	+	+	+
		5	EPRGSDIAGT	98	107	TH			17	DQ7			+	-	+
		6	IYKRWIILGLNKIVR	129	143	TH			1167				-	-	-
			KRWIILGLNK	131	140	CTL			1541	B2703, B2705, B35, DRB1*0101	B27, B07		+	+	+
			KRWIILGLNKIVRMY	131	145	TH			1541	DR1, DRB10101, DRB10301, DRB10405, DRB10701, DRB10802, DRB10901, DRB11101, DRB11201, DRB11302, DRB11501, DRB40101, DRB50101			+	+	+
			WIILGLNKIVRMYSP	133	147	TH	✓	3	1885				-	-	-
			GLNKIVRMY	137	145	CTL	✓		2868	B*1501	B62		-	-	+
			LNKIVRMYSPVSILD	138	152	TH			15				-	-	-
			VRMYSPVSI	142	150	CTL			46	Cw*18			-	-	-
		7	PKEPFRDYV	157	165	TH	✓	4	1866	DQ5			+	-	+
	p2p7p1p6	8	CRAPRKKGC	42	50	CTL			9	B*14	B27		-	+	-
		9	TERQANFL	64	71	CTL			29	B1801, B4002, B4001, B4402, B*4403	B44		+	+	+
Pol	PR	10	LVGPTPVNI	76	84	CTL			1	A0201, A0202, A0203, A6802	A02		+	+	+
	RT	11	IETVPVKL	5	12	CTL			17	B*4001	B44		+	+	+
		12	GPKVKQWPL	18	26	CTL			6	B*0801, B8	B08		+	-	-
		13	KLVDFRELNK	73	82	CTL	✓	5	1554	A*0301	A03		+	+	+
		14	GIPHPAGLK	93	101	CTL	✓	6	971	A*0301, A11	A03		+	+	+
		15	TVLDVGDAY	107	115	CTL	✓	7	783	A1101, B1501, B*3501	B07, A03, B62	B07	+	+	+
		16	NETPGIRYQY	137	146	CTL			30	B1801, B4001, B4002, B4402, B*4403	B44		+	+	+
			IRYQYNVL	142	149	CTL			31	B*1401	B27		-	+	-
		17	LVGKLNWASQIY	260	271	CTL	✓	8	1117	B*1501	B62		-	-	+
			KLNWASQIY	263	271	CTL	✓		1376	A*3002	A01		-	-	-
		18	WEFVNTPPLVKLWYQ	414	428	TH			65	DRB10101, DRB10401, DRB10405, DRB10701, DRB10802, DRB10901, DRB11101, DRB11302, DRB11501, DRB50101			+	+	+
		19	GAETFYVDGA	436	445	CTL			11	A*6802	A03		+	+	+
		20	IVTDSQYAL	495	503	CTL	✓	9	471	Cw*0802			-	-	-
			VTDSQYALGI	496	505	CTL	✓		857	B*1503	B27			+
	RT-Integrase	21	LFLDGIDKA	560	8	CTL	✓	10	557	B*81	B07		+	+	+
	Integrase	22	LKTAVQMAVFIHNFK	172	186	TH	✓	11	1172				-	-	-
			KTAVQMAVF	173	181	CTL	✓		1279	B*5701	B07		+	+	+
			KTAVQMAVFIHNFKR	173	187	TH	✓		1041	DRB10101, DRB10405, DRB11101, DRB11302			+	+	+
			AVFIHNFKRK	179	188	CTL	✓		631	A0301, A1101	A03		+	+	+
			FKRKGGIGGY	185	194	CTL	✓		195	B*1503	B27		-	+	-
		23	VPRRKAKII	260	268	CTL	✓	12	15	B*42	B07		+	+	+
			RKAKIIRDY^#	263	271	CTL			0	B*1503	B27		-	+	-
Env		24	PIPIHYCAPA^#	212	221	Ab			0	110.1			-	-	-
		25	IKQI	420	423	Ab			5	E51			-	-	-
Nef		26	VGFPVRPQ	66	73	TH	✓	13	72	DR1, DRw15(2)			-	-	-
			RPQVPLRPM	71	79	CTL			7	B*4201	B07		+	+	+
		27	FLKEKGGL	90	97	CTL	✓	14	258	B*0801	B08	B50	+	-	-

Out of the 44 epitopes included in the association rule mining, 41 were found to be part of association rules. Non-overlapping genomic regions and HLA alleles corresponding to each epitope are also shown.
^# Epitopes not involved in any association rule
^@ Amino acid coordinates are given with respect to the corresponding gene/protein in the HIV-1 HXB2 reference sequence (GenBank Accession no: K03455)
^ Epitopes involved in association rules with 2 types and 3 genes
^$ HLA allele/MAb data given where available (from HIV database & IEDB)
*As per Frahm et al., 2007 [56]

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ISSN: 1471-2180

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