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A novel DQB1*03 allele revealed by rSSOP and identified by SBT
S30
Abstracts
3 35-P
A NOVEL DQB1*03 ALLELE REVEALED BY rSSOP AND IDENTIFIED BY SBT Dong-Feng Chen, Angelica DeOliveira, Sharon Peplinski, Walter Herczyk, Nancy L. Reinsmoen, Pathology, Duke University Medical Center, Durham, NC, USA HLA genes are highly polymorphic and the number of alleles increases continuously. Recently, in two individuals of a potential stem cell recipient’s family, we observed unusual DQB1 rSSOP typing patterns indicating existence of a potential novel DQB1*03 allele. This potential novel allele was demonstrated in the samples from the father and sister of the patient by Luminex-rSSOP (OneLambda), while a homozygous DQB1*0301 was assigned to the patient by Dynal SSP. However, the family haplotype analysis indicated that the patient might also carry this potential novel allele. DQB-SSP from OneLambda and Dynal were also performed on the sample from the father. An unusual SSP pattern was revealed by OneLambda’s SSP but not by Dynal’s SSP. To identify this potential novel DQB1*03 allele (local name DQB1*03COR), we performed SBT on the samples from the patient and his father and sister using single-allele sequencing reagent from Protrans. The sequence data obtained from these individuals verified the existence of a novel DQB1*03 allele which is identical to the DQB1*030101 with an exception of one base substitution at codon 55 changing from CCG to CAG resulting in an amino acid change from Proline to Glutamine. This polymorphic motif distinguishes the novel DQB1*03COR from all other known DQB1 alleles. The sequence of DQB1*03COR has been submitted to the GenBank (accession: DQ026226) and WHO for official nomenclature. Based on the family analysis the haplotype carrying the DQB1*03COR has been established as following: A*2301, Cw*1505, B*0702, DRB1*1303, DRB3*0202, DQB1*03COR. The DQB1*03COR explained the unexpected DQB1 rSSOP and SSP patterns observed and may have important clinical consequence due to the amino acid substitution identified.
3 36-P
DETERMINATION OF HLA HAPLOTYPES IN THE INTERPRETATION OF HLA TYPING Pedro Cano, Marcelo Fernandez-Vina, Laboratory Medicine, M.D. Anderson Cancer Center, Houston, TX, USA HLA typing should not be interpreted as the independent allele assignment in different genetic loci. Linkage disequilibrium is strong enough to consider HLA-B-C as one block and HLA-DRB1-DRB3/4/5-DQB1 as another block. Allele assignment for these blocks should be carried out as a single step. A weaker linkage disequilibrium exists between the other loci and these blocks. Knowledge of the extent and nature of these associations between genes and gene blocks is essential in the interpretation of HLA typing results. The meaning of an HLA phenotype is conveyed by the inference of two haplotypes from the phenotype and the description of these haplotypes in terms of their position in the distribution of all haplotypes in a given reference population. The distinction must be made between “haplotypes in full linkage disequilibrium” and haplotypes resulting from random recombination. Only if a rare allele is encountered in a haplotype in full linkage disequilibrium there is hope of finding a match. Many described alleles have not been documented sufficiently to be considered in the interpretation of genetic typing reaction patterns. Their inclusion can also lead to unfortunate decisions in the design of typing reagents. Contrary to what might be believed, the polymorphic universe of HLA genes is rather limited. After typing more than 22,000 samples, 203 B-C blocks, 151 DRB1-DRB3/4/5-DQB1 blocks; and 56 A, 111 B, 36 Cw, 59 DRB1, 22 DRB3/4/5, 22 DQB1, and 20 DPB1 alleles were identified. Knowledge of the boundaries of the HLA polymorphic universe is essential in the interpretation of HLA typing. Haplotype frequencies, rather than allele frequencies, are also the key to determine reliable genetic distances between populations.
Abstracts
3 35-P
A NOVEL DQB1*03 ALLELE REVEALED BY rSSOP AND IDENTIFIED BY SBT Dong-Feng Chen, Angelica DeOliveira, Sharon Peplinski, Walter Herczyk, Nancy L. Reinsmoen, Pathology, Duke University Medical Center, Durham, NC, USA HLA genes are highly polymorphic and the number of alleles increases continuously. Recently, in two individuals of a potential stem cell recipient’s family, we observed unusual DQB1 rSSOP typing patterns indicating existence of a potential novel DQB1*03 allele. This potential novel allele was demonstrated in the samples from the father and sister of the patient by Luminex-rSSOP (OneLambda), while a homozygous DQB1*0301 was assigned to the patient by Dynal SSP. However, the family haplotype analysis indicated that the patient might also carry this potential novel allele. DQB-SSP from OneLambda and Dynal were also performed on the sample from the father. An unusual SSP pattern was revealed by OneLambda’s SSP but not by Dynal’s SSP. To identify this potential novel DQB1*03 allele (local name DQB1*03COR), we performed SBT on the samples from the patient and his father and sister using single-allele sequencing reagent from Protrans. The sequence data obtained from these individuals verified the existence of a novel DQB1*03 allele which is identical to the DQB1*030101 with an exception of one base substitution at codon 55 changing from CCG to CAG resulting in an amino acid change from Proline to Glutamine. This polymorphic motif distinguishes the novel DQB1*03COR from all other known DQB1 alleles. The sequence of DQB1*03COR has been submitted to the GenBank (accession: DQ026226) and WHO for official nomenclature. Based on the family analysis the haplotype carrying the DQB1*03COR has been established as following: A*2301, Cw*1505, B*0702, DRB1*1303, DRB3*0202, DQB1*03COR. The DQB1*03COR explained the unexpected DQB1 rSSOP and SSP patterns observed and may have important clinical consequence due to the amino acid substitution identified.
3 36-P
DETERMINATION OF HLA HAPLOTYPES IN THE INTERPRETATION OF HLA TYPING Pedro Cano, Marcelo Fernandez-Vina, Laboratory Medicine, M.D. Anderson Cancer Center, Houston, TX, USA HLA typing should not be interpreted as the independent allele assignment in different genetic loci. Linkage disequilibrium is strong enough to consider HLA-B-C as one block and HLA-DRB1-DRB3/4/5-DQB1 as another block. Allele assignment for these blocks should be carried out as a single step. A weaker linkage disequilibrium exists between the other loci and these blocks. Knowledge of the extent and nature of these associations between genes and gene blocks is essential in the interpretation of HLA typing results. The meaning of an HLA phenotype is conveyed by the inference of two haplotypes from the phenotype and the description of these haplotypes in terms of their position in the distribution of all haplotypes in a given reference population. The distinction must be made between “haplotypes in full linkage disequilibrium” and haplotypes resulting from random recombination. Only if a rare allele is encountered in a haplotype in full linkage disequilibrium there is hope of finding a match. Many described alleles have not been documented sufficiently to be considered in the interpretation of genetic typing reaction patterns. Their inclusion can also lead to unfortunate decisions in the design of typing reagents. Contrary to what might be believed, the polymorphic universe of HLA genes is rather limited. After typing more than 22,000 samples, 203 B-C blocks, 151 DRB1-DRB3/4/5-DQB1 blocks; and 56 A, 111 B, 36 Cw, 59 DRB1, 22 DRB3/4/5, 22 DQB1, and 20 DPB1 alleles were identified. Knowledge of the boundaries of the HLA polymorphic universe is essential in the interpretation of HLA typing. Haplotype frequencies, rather than allele frequencies, are also the key to determine reliable genetic distances between populations.