HLAreporter: a tool for HLA typing from next generation sequencing data

Huang, Yazhi; Yang, Jing; Ying, Dingge; Zhang, Yan; Shotelersuk, Vorasuk; Hirankarn, Nattiya; Sham, Pak Chung; Lau, Yu Lung; Yang, Wanling

doi:10.1186/s13073-015-0145-3

Table 1 HLA predictions of class I and class II genes

From: HLAreporter: a tool for HLA typing from next generation sequencing data

	HLAminer	HLAreporter	HLAminer	HLAreporter	HLAminer	HLAreporter	HLAminer	HLAreporter	DRB1	HLAminer	HLAreporter	DQB1
ID ^(SRR)a	HLA-A	HLA-A	HLA-B	HLA-B	HLA-C	HLA-C	HLA-DRB1	DRB1(exon 2)	(exon 2&3) ^b	HLA-DQB1	DQB1 (exon 2)	(exon 2&3) ^b
359102	30:01; 30:02; 30:04; 66:01	30:02:01G; 66:01:01G	15:83; 18:01; 18:26; 41:01; 45:01; 50:01	18:01:01G; 41:02:01	05:01; 17:01	05:01:01G; 17:01:01G	03:01; 07:01	*03:01:01G	*03:01:01	*02:01	*02:01:01G	*02:01:01
359103	01:01; 01:03; 02:01; 02:03; 11:02; 68:08	01:01:01G; 02:01:01G	18:01; 18:03; *57:01	18:01:01G; 57:01:01G	*07:01	*07:01:01G	03:01; 07:01	03:01:01G; 07:01:01G	03:01:01; 07:01:01	02:01; 03:03	02:01:01G; 03:03:02G	02:01:01; 03:03:02
359108	-	03:01:01G; 68:02:01G^p	-	35:01:01G; 53:01:01	*04:01	*04:01:01G	-	04:05:01; 08:04:01	04:05:01; 08:04:01	-	03:01:01G; 03:02:01G	03:01:04; 03:02:01
359298	11:01; 11:02; 11:50; 24:02; 24:07; 24:20^c	11:02:01G; 24:07^p	27:04; 27:25; 39:34; 40:02; *40:06	27:04:01G; 39:05:01	08:01; 08:21; 12:02; 12:03	08:01:01G; 12:02:01G^p	04:03; 08:03; 12:01; 14:54^c	08:03:02; 12:02:01	08:03:02; 12:02:01	03:01; 06:01	03:01:01G; 06:01:01G	03:01:01; 06:01:01
359295	02:03; 03:01	02:03:01G; 03:01:01G^p	35:01; 35:03; 37:01; 55:02; 55:48; 56:01	35:03:01G; 55:02:01G^p	01:02; 04:01; 04:03; 12:03; 15:02; 15:16^c	04:01:01G; 12:03:01G	04:03; 07:01; 08:03; 14:05	08:02:01; 14:05:01	08:02:01; 14:05:01	03:02; 03:03; 03:05; 05:03	04:02:01; 05:03:01G	04:02:01; 05:03:01
360655	30:01; 30:02; 30:04; 32:01; 74:01; 74:11	30:02:01G; 74:01:01G	15:03; 57:01; 57:06; 57:11	15:03:01G; 57:03:01^p	02:02; 02:11; *07:01	02:10; 07:01:01G^p	07:01; 08:03; 11:01; 13:02	11:01:02; 13:02:01	11:01:02; 13:02:01	05:01; 05:03; *06:09	05:02:01G; 06:09:01	05:02:01; 06:09:01
360288	*02:01	02:01:01G; 02:11:01G	15:01; 15:07; 15:32; 35:14; *58:01	15:04; 35:05:01	01:02; 04:01; 04:03; 04:06	01:02:01G; 04:01:01G	04:03; 07:01	04:11:01; 09:01:02	04:11:01; 09:01:02	*03:02	03:02:01G; 03:03:02G	03:02:01; 03:03:02
360391	02:01; 02:48; *68:01	02:01:01G; 68:01:02G^p	07:02; 40:02; *40:06	07:02:01G; 40:02:01G^p	03:03; 03:04; *07:02	03:04:01G; 07:02:01G^p	01:01; 07:01	01:03; 09:01:02	01:03; 09:01:02	03:03; 05:01	03:03:02G; 05:01:01G	03:03:02; 05:01:01
360148	01:01; 02:01; *36:01	02:01:01G; 36:01	07:02; 35:01; 35:41; 40:01; 40:79; 53:01^c	35:01:01G; 40:01:01G^p	03:02; 03:04; 04:01; 04:03; 15:02; 15:17^c	03:04:01G; 04:01:01G	01:01; 01:02; 07:01; 15:01	01:01:01G; 15:01:01G	01:01:01; 15:01:01	05:01; 06:02	06:02:01G; 05:01:01G	06:02:01; 05:01:01
359301	02:03; 11:02; 31:01; 32:01; 74:01; 74:11	02:03:01G; 31:01:02G^p	13:01; 48:01	13:01:01G; 48:01:01G	03:03; 03:04	03:03:01G; 03:04:01G	07:01; 08:03; *11:01	11:01:01G; 13:12:01	11:01:01; 13:12:01	*03:01	*03:01:01G	*03:01:01
359098	-	03:01:01G; 68:02:01G^p	-	35:01:01G; 53:01:01	*04:01	*04:01:01G	-	04:05:01; 08:04:01	04:05:01; 08:04:01	-	03:01:01G; 03:02:01G	03:01:04; 03:02:01

^a‘SRR’ is the prefix of each sample name, which is not explicitly shown in the table due to space limitations. ^bAll alleles with identical exon 2 and 3 sequences are reported. For example, after examining exons 2 and 3 of allele DQB1*03:03:02G, HLAreporter reports alleles 03:03:02:01/03:03:02:02/03:03:02:03. Since the last two digits out of eight digit-based HLA nomenclature are determined by intronic sequences, we only present the first six digits *03:03:02 in the table after examining the minor exon. ^cAdditional ambiguity at four-digit resolution is not shown. ^pPhase was reported.

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	HLAminer	HLAreporter	HLAminer	HLAreporter	HLAminer	HLAreporter	HLAminer	HLAreporter	DRB1	HLAminer	HLAreporter	DQB1
ID ^(SRR)a	HLA-A	HLA-A	HLA-B	HLA-B	HLA-C	HLA-C	HLA-DRB1	DRB1(exon 2)	(exon 2&3) ^b	HLA-DQB1	DQB1 (exon 2)	(exon 2&3) ^b
359102	30:01; 30:02; 30:04; 66:01	30:02:01G; 66:01:01G	15:83; 18:01; 18:26; 41:01; 45:01; 50:01	18:01:01G; 41:02:01	05:01; 17:01	05:01:01G; 17:01:01G	03:01; 07:01	*03:01:01G	*03:01:01	*02:01	*02:01:01G	*02:01:01
359103	01:01; 01:03; 02:01; 02:03; 11:02; 68:08	01:01:01G; 02:01:01G	18:01; 18:03; *57:01	18:01:01G; 57:01:01G	*07:01	*07:01:01G	03:01; 07:01	03:01:01G; 07:01:01G	03:01:01; 07:01:01	02:01; 03:03	02:01:01G; 03:03:02G	02:01:01; 03:03:02
359108	-	03:01:01G; 68:02:01G^p	-	35:01:01G; 53:01:01	*04:01	*04:01:01G	-	04:05:01; 08:04:01	04:05:01; 08:04:01	-	03:01:01G; 03:02:01G	03:01:04; 03:02:01
359298	11:01; 11:02; 11:50; 24:02; 24:07; 24:20^c	11:02:01G; 24:07^p	27:04; 27:25; 39:34; 40:02; *40:06	27:04:01G; 39:05:01	08:01; 08:21; 12:02; 12:03	08:01:01G; 12:02:01G^p	04:03; 08:03; 12:01; 14:54^c	08:03:02; 12:02:01	08:03:02; 12:02:01	03:01; 06:01	03:01:01G; 06:01:01G	03:01:01; 06:01:01
359295	02:03; 03:01	02:03:01G; 03:01:01G^p	35:01; 35:03; 37:01; 55:02; 55:48; 56:01	35:03:01G; 55:02:01G^p	01:02; 04:01; 04:03; 12:03; 15:02; 15:16^c	04:01:01G; 12:03:01G	04:03; 07:01; 08:03; 14:05	08:02:01; 14:05:01	08:02:01; 14:05:01	03:02; 03:03; 03:05; 05:03	04:02:01; 05:03:01G	04:02:01; 05:03:01
360655	30:01; 30:02; 30:04; 32:01; 74:01; 74:11	30:02:01G; 74:01:01G	15:03; 57:01; 57:06; 57:11	15:03:01G; 57:03:01^p	02:02; 02:11; *07:01	02:10; 07:01:01G^p	07:01; 08:03; 11:01; 13:02	11:01:02; 13:02:01	11:01:02; 13:02:01	05:01; 05:03; *06:09	05:02:01G; 06:09:01	05:02:01; 06:09:01
360288	*02:01	02:01:01G; 02:11:01G	15:01; 15:07; 15:32; 35:14; *58:01	15:04; 35:05:01	01:02; 04:01; 04:03; 04:06	01:02:01G; 04:01:01G	04:03; 07:01	04:11:01; 09:01:02	04:11:01; 09:01:02	*03:02	03:02:01G; 03:03:02G	03:02:01; 03:03:02
360391	02:01; 02:48; *68:01	02:01:01G; 68:01:02G^p	07:02; 40:02; *40:06	07:02:01G; 40:02:01G^p	03:03; 03:04; *07:02	03:04:01G; 07:02:01G^p	01:01; 07:01	01:03; 09:01:02	01:03; 09:01:02	03:03; 05:01	03:03:02G; 05:01:01G	03:03:02; 05:01:01
360148	01:01; 02:01; *36:01	02:01:01G; 36:01	07:02; 35:01; 35:41; 40:01; 40:79; 53:01^c	35:01:01G; 40:01:01G^p	03:02; 03:04; 04:01; 04:03; 15:02; 15:17^c	03:04:01G; 04:01:01G	01:01; 01:02; 07:01; 15:01	01:01:01G; 15:01:01G	01:01:01; 15:01:01	05:01; 06:02	06:02:01G; 05:01:01G	06:02:01; 05:01:01
359301	02:03; 11:02; 31:01; 32:01; 74:01; 74:11	02:03:01G; 31:01:02G^p	13:01; 48:01	13:01:01G; 48:01:01G	03:03; 03:04	03:03:01G; 03:04:01G	07:01; 08:03; *11:01	11:01:01G; 13:12:01	11:01:01; 13:12:01	*03:01	*03:01:01G	*03:01:01
359098	-	03:01:01G; 68:02:01G^p	-	35:01:01G; 53:01:01	*04:01	*04:01:01G	-	04:05:01; 08:04:01	04:05:01; 08:04:01	-	03:01:01G; 03:02:01G	03:01:04; 03:02:01

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