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HAPLOTYPE ASSOCIATION OF 49 RARE ALLELES FROM THE NATIONAL MARROW DONOR PROGRAM (NMDP).
Jane Kempenich, Martin Maiers and Michelle Setterholm. Minneapolis MN, National Marrow Donor Program, Scientific Services and Bioinformatics.

The NMDP identified 844,756 allele level HLA-A, B, or DRB1 results in the database. Within this group, 389 rare alleles with a frequency of <1 in 50,000 were analyzed. Strong haplotype associations were found for 49 alleles.
The 49 rare alleles included 8 HLA-A alleles (0219, 0230, 0247, 2423, 2432, 2503, 2618, and 3010), 29 HLA-B alleles (0713, 0719, 0720, 0805, 0807, 0813, 1304, 1544, 1563, 1813, 1814, 3526, 3530, 3541, 4027, 4030, 4031, 4032, 4415, 4417, 4418, 4420, 4421, 4424, 4427, 4429, 4502, 5123, and 5705), and 12 HLA-DRB1 alleles (0306, 0313, 0416, 0433, 0820, 1134, 1136, 1143, 1336, 1441, 1448, and 1607). The data includes the haplotypes, frequencies and the racial or ethnic groups for each allele. Some of these predicted associations may be different than reported in the literature where the allele was first described. For example, DRB1*1143 was described with the haplotype A*24-B*44-DRB1*1143. Of the 13 times reported in the NMDP database, this haplotype was not seen. Similarly, rare alleles such as DRB1*1134 had multiple haplotypes. In other cases, such as the A*0247, one haplotype was predicted for that particular rare allele and matches the previously published information. Examples are shown below;

AlleleHaplotypeAFAAPICAUHISMultiHaplotype Predicted / Allele Reported
A*0247A*0247-B*5301-DRB1*1144/4
B*1544A*3401-B*1544-DRB1*027119/13
DRB1*1134A*02-B*57-DRB1*113455/9
DRB1*1134A*11-B*35-DRB1*113433/9
DRB1*1143A*11-B*18-DRB1*11431111/13
Race Codes: AFA = African American, API = Asian or Pacific Islander, CAU = Caucasian, HIS = Hispanic, Multi = Mixed race

This data should provide valuable reference information in the search process for unrelated stem cell donors when patients carry rare alleles.