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Abstracts / Human Immunology 73 (2012) 49–167
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TNF-A PROMOTER ALLELES WITHIN CONSERVED HLA-HAPLOTYPES. Daniel Fürst, Christine Zollikofer, Hubert Schrezenmeier, Joannis Mytilineos. Transplantation Immunology, IKT Ulm, Ulm, Germany. Aim: Several SNPs within the TNF-a promoter region have been described and the hemizygous combination of SNPs may determine their impact on TNF-a transcription. We hypothesized that the actual number of TNF-a promoter alleles is limited. Our aim was to identify TNF-a alleles and to obtain data about frequency and linkage with classical HLA-genes. Methods: The TNF-a promoter region as well as HLA-A,C,B,DRB1 of 1021 healthy blood donors (German Caucasians) were sequenced by the Sanger technique. Phenotype and genotype frequencies were assessed, and TNF-a promoter alleles and conserved HLA-haplotypes were reconstructed using an EM-algorithm for SNPs with a frequency of greater 1%. (SNP’s detected: 1031, 863, 857, 806, 571, 376, 308, 238,70). Results: 11 TNF-a promoter alleles were identified (Table 1). It was possible to deduce TNF-a promoter allele genotypes in all donors with a high probability. Strong linkage disequilibria with classical HLA genes were found particularly for the most frequent HLA-haplotype (HLA-A⁄01:01/HLA-C⁄07:01/HLA-B⁄08:01/ HLA-DRB1⁄03:01), which contains a less frequent TNF-a promoter allele (allele 3) [Table 1]. Conclusions: Using frequency information it is possible to deduce TNF-a promoter alleles by generic Sanger-sequencing, obviating the need for elaborate allele specific sequencing. This information may enable investigators to take into account the complete TNF-a regulatory region in a phase separated manner in contrast to previous approaches examining only one or few isolated SNPs.
Table 1 TNF-a promoter alleles and their frequencies Allele nr
SNP pos
1 2 3 4 5 6 7 8 9 10 11
T,C,C,C,A,G,G,G,n C,A,C,C,A,G,G,G,n T,C,C,C,A,G,A,G,n T,C,T,C,A,G,G,G,n C,C,C,C,A,G,G,A,n C,A,C,T,A,G,G,G,n T,C,C,C,A,G,A,G,C T,C,C,C,C,G,G,G,n C,C,C,C,A,G,G,G,n C,C,C,C,A,A,G,A,n T,C,C,C,A,A,G,G,n
1031, 863, 857, 806, 571, 376,
308, 238,70
Frequency 0.4922 0.1536 0.1336 0.1186 0.0300 0.0231 0.0117 0.0098 0.0093 0.0082 0.0025
Only alleles with a frequency of >2/1000 are reported. Abbreviations: n (no C insertion).
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INCIDENCE OF THE CLINICALLY SIGNIFICANT NULL ALLELE DRB5⁄01:08N IN THE CANADIAN POPULATION OF SOUTHERN ALBERTA. Charlene Ott, Luz Stamm, Kim Larlee, Noureddine Berka. Tissue Typing, Calary Laboratory Services, Calgary, AB, Canada. Aim: The objective of this study was to identify the frequency of the DRB5⁄01:08N allele in the Canadian population typed by the Tissue Typing Laboratory of Calgary Laboratory Services in Calgary, Alberta, Canada. The DRB5⁄01:08N allele is one of the Common Null Alleles that must be distinguished in external proficiency surveys and routinely in the patient population. DRB5⁄01:08N occurs in the presence of the known haplotype DRB1⁄1502-DQB1⁄05:01. The clinical implication of the presence of a null allele in the bone marrow transplant population is a mismatch that may result in graft vs. host disease or graft rejection. Methods: Our laboratory retrospectively reviewed 627 DRB1⁄ typings performed in the period between January 2011 and March 2012. Testing was performed using One Lambda LABType SSO medium resolution kits on a Luminex platform. Patients were from the renal, bone marrow and disease association populations. Results: DRB1⁄15’s were identified in 7% (42 of 627) of cases. Twenty four per cent of the cases (10 of 42) carried the DRB1⁄15:02-DQB1⁄05:01 haplotype and typed as DRB1⁄01:02/01:08N by SSO low resolution typing. We then tested these 10 cases by One Lambda SSP DRB5 high resolution and the presence of the null allele DRB5⁄01:08N was confirmed in 20% (2 of 10 DRB1⁄15:02-DQB1⁄05:01). The overall incidence of DRB5⁄01:08N in Southern Alberta is 0.3% (2 of 627). Conclusions: The low incidence of DRB5⁄01:08N in our patient population concurs with other studies in the literature. We currently are performing high resolution SSP typing on all DR⁄15:02-DQB1⁄05:01 samples that list DRB5⁄01:08N as a possibility.
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TNF-A PROMOTER ALLELES WITHIN CONSERVED HLA-HAPLOTYPES. Daniel Fürst, Christine Zollikofer, Hubert Schrezenmeier, Joannis Mytilineos. Transplantation Immunology, IKT Ulm, Ulm, Germany. Aim: Several SNPs within the TNF-a promoter region have been described and the hemizygous combination of SNPs may determine their impact on TNF-a transcription. We hypothesized that the actual number of TNF-a promoter alleles is limited. Our aim was to identify TNF-a alleles and to obtain data about frequency and linkage with classical HLA-genes. Methods: The TNF-a promoter region as well as HLA-A,C,B,DRB1 of 1021 healthy blood donors (German Caucasians) were sequenced by the Sanger technique. Phenotype and genotype frequencies were assessed, and TNF-a promoter alleles and conserved HLA-haplotypes were reconstructed using an EM-algorithm for SNPs with a frequency of greater 1%. (SNP’s detected: 1031, 863, 857, 806, 571, 376, 308, 238,70). Results: 11 TNF-a promoter alleles were identified (Table 1). It was possible to deduce TNF-a promoter allele genotypes in all donors with a high probability. Strong linkage disequilibria with classical HLA genes were found particularly for the most frequent HLA-haplotype (HLA-A⁄01:01/HLA-C⁄07:01/HLA-B⁄08:01/ HLA-DRB1⁄03:01), which contains a less frequent TNF-a promoter allele (allele 3) [Table 1]. Conclusions: Using frequency information it is possible to deduce TNF-a promoter alleles by generic Sanger-sequencing, obviating the need for elaborate allele specific sequencing. This information may enable investigators to take into account the complete TNF-a regulatory region in a phase separated manner in contrast to previous approaches examining only one or few isolated SNPs.
Table 1 TNF-a promoter alleles and their frequencies Allele nr
SNP pos
1 2 3 4 5 6 7 8 9 10 11
T,C,C,C,A,G,G,G,n C,A,C,C,A,G,G,G,n T,C,C,C,A,G,A,G,n T,C,T,C,A,G,G,G,n C,C,C,C,A,G,G,A,n C,A,C,T,A,G,G,G,n T,C,C,C,A,G,A,G,C T,C,C,C,C,G,G,G,n C,C,C,C,A,G,G,G,n C,C,C,C,A,A,G,A,n T,C,C,C,A,A,G,G,n
1031, 863, 857, 806, 571, 376,
308, 238,70
Frequency 0.4922 0.1536 0.1336 0.1186 0.0300 0.0231 0.0117 0.0098 0.0093 0.0082 0.0025
Only alleles with a frequency of >2/1000 are reported. Abbreviations: n (no C insertion).
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INCIDENCE OF THE CLINICALLY SIGNIFICANT NULL ALLELE DRB5⁄01:08N IN THE CANADIAN POPULATION OF SOUTHERN ALBERTA. Charlene Ott, Luz Stamm, Kim Larlee, Noureddine Berka. Tissue Typing, Calary Laboratory Services, Calgary, AB, Canada. Aim: The objective of this study was to identify the frequency of the DRB5⁄01:08N allele in the Canadian population typed by the Tissue Typing Laboratory of Calgary Laboratory Services in Calgary, Alberta, Canada. The DRB5⁄01:08N allele is one of the Common Null Alleles that must be distinguished in external proficiency surveys and routinely in the patient population. DRB5⁄01:08N occurs in the presence of the known haplotype DRB1⁄1502-DQB1⁄05:01. The clinical implication of the presence of a null allele in the bone marrow transplant population is a mismatch that may result in graft vs. host disease or graft rejection. Methods: Our laboratory retrospectively reviewed 627 DRB1⁄ typings performed in the period between January 2011 and March 2012. Testing was performed using One Lambda LABType SSO medium resolution kits on a Luminex platform. Patients were from the renal, bone marrow and disease association populations. Results: DRB1⁄15’s were identified in 7% (42 of 627) of cases. Twenty four per cent of the cases (10 of 42) carried the DRB1⁄15:02-DQB1⁄05:01 haplotype and typed as DRB1⁄01:02/01:08N by SSO low resolution typing. We then tested these 10 cases by One Lambda SSP DRB5 high resolution and the presence of the null allele DRB5⁄01:08N was confirmed in 20% (2 of 10 DRB1⁄15:02-DQB1⁄05:01). The overall incidence of DRB5⁄01:08N in Southern Alberta is 0.3% (2 of 627). Conclusions: The low incidence of DRB5⁄01:08N in our patient population concurs with other studies in the literature. We currently are performing high resolution SSP typing on all DR⁄15:02-DQB1⁄05:01 samples that list DRB5⁄01:08N as a possibility.