Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

BMC Genomics

Table 1 Four-digit ambiguous alleles with standard SBT methods and cSBT

Class I exon 2, 3, 4 ambiguous to 4-digit (high freq)
Allele	dbMHC freq
C*07:02:01/07:50	13.20%
C*04:01/04:09 N	11.40%
C*07:01/07:06/07:18	8.20%
C*08:01/08:22	4.90%
B*07:02:01/07:61	4.80%
B*35:01:01/35:42:01	4.50%
16 others	variable
DRB Exon 2 Ambiguous to 4-digit (high freq)
Allele	dbMHC freq
DRB1*11:01/11:100	6.60%
DRB1*14:01:01/14:54	4.10%
6 others	variable
All cSBT ambiguous to 4-digit
Allele	dbMHC freq
A*74:01/74:02	0.90%
C*07:04/07:11	1.70%
B*27:05/27:13	1.50%
DRB1*12:01:01/12:10	1.80%

“Gold Standard” Sanger sequence-based genotyping usually amplifies a minimal number of exons per allele, resulting in a large number of ambiguous allele calls. A non-inclusive list of commonly observed alleles with four-digit ambiguity using exon-based typing methods is shown for class I (exon 2, 3, & 4) and DRB (exon 2) alleles. Also included is a list of all four allele combinations predicted to be four-digit ambiguous using the expanded cSBT method.

ISSN: 1471-2164