- Email: [email protected]
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Abstracts / Human Immunology 74 (2013) 51–173
DIVERSITY OF HLA HAPLOTYPES IN CLINICAL PRACTICE. Pedro Cano 1, Michael Seul 2. 1 HLA Typing Laboratory, Laboratory Medicine, MD Anderson Cancer Center, Houston, TX, USA; 2 BioMolecular Analytics, LLC, Warren, NJ, USA. Aim: To elucidate the composition, abundance and molecular evolution of HLA haplotypes encountered in clinical practice to address the frequent failure to identify exactly matched stem cell grafts for other than the most common haplotypes. Methods: Generated catalog of 6,920 extended haplotypes by family segregation analysis of HLA types for transplant candidates; analyzed haplotype abundance within framework of a stochastic ‘‘birth-death’’ process. Results: rare haplotypes (‘‘hTypes’’): ‘‘shuffling’’ of common alleles – most rare hTypes in our catalog contain COMMON alleles; the more common an allele, the more widely dispersed it is in the hType population; rare alleles, though given much attention in laboratory analysis, play but a minor role in generating rare hTypes; hType diversity: proliferation of unique configurations – alleles in catalog: A : 85 (of which 28, or 32.9%, only once); B: 162 (54 or 33.3%); C: 56 (17 or 30.3%); DRB1: 75 (21 or 28%) vs hTypes: ABC: 1,533 (875 or 57.7%); ABC-DRB1: 3,345 (2,496 or 74.6%); characteristic shape of abundance distributions – ranking hTypes and alleles by abundance yields distributions characteristic of a stochastic ‘‘birth-death’’ process governing hType and allele evolution: the shape of the hType distribution indicates closely matched ‘‘birth’’& ‘‘death’’ rates; abundance fluctuations: evolutionary noise - simulations of random hType pairing under recombination reveal fluctuations in type abundance, reflecting the interplay between the ‘‘death’’ of non-reproducing hType ‘‘species’’ and the ‘‘birth’’ of new species by reciprocal allele exchange. Conclusions: Haplotype rather than allele diversity, and fluctuations in hType abundance define the principal clinical challenge in identifying optimally matched stem cell grafts. Understanding the molecular ‘‘proximity’’ of less common to more common hTypes, and the epitopes they encode, may inform a rational search for grafts that are optimally matched to unusual hType configurations. Seul: BioMolecular Analytics, LLC: Employee.
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RARE ALLELES IN THE SOUTHERN BRAZILIAN PARANA STATE POPULATION. Joandrei Dos Santos Silva, Alessandro Pirri, Jose Samuel Da Silva, Maria Da Graça Bicalho. Genetics, Universidade Federal Do Parana, Curitiba, Parana, Brazil. Aim: Being a HLA genotyping reference laboratory in Southern Brazil, we perform compatibility tests for both related and volunteer bone marrow donors by PCR-Sequence Specific Priming, reverse Sequence Specific Oligonucleotide Probing (low and high definition kits) and Sequence Based Typing. We frequently find alleles listed as rare variants by the NMDP and aimed at presenting them in this study. Methods: 106 537 subjects from the Parana State (Southern Brazil) were genotyped for HLA-A, -B and – DRB1 using LABType SSO tests and or MicroSSP trays (both One Lambda). Genotypings of alleles listed as rare were confirmed through LABType SSO High Definition and Atria SeqR HLA tests, and insTAclone PCR cloning kit (Thermo Scientific) was used in the case of novel alleles. Results: The following rare alleles were found in our sample: A⁄02:52; A⁄02:152; A⁄03:43; A⁄23:13; A⁄24:56; A⁄24:02L; A⁄24:30; A⁄24:71; A⁄26:31; A⁄68:23, B⁄07:20; B⁄07:37; B⁄08:33; B⁄15:151; B⁄18:11; B⁄18:19; B⁄35:62; B⁄37:07; B⁄39:29; B⁄39:37; B⁄40:33/80; B⁄42:05; B⁄42:12; B⁄44:20; B⁄51:29; B⁄55:21; B⁄56:15; B⁄56:25, DRB1⁄04:37; DRB1⁄04:39; DRB1⁄11:25; DRB1⁄11:35; DRB1⁄11:36; DRB1⁄11:42; DRB1⁄11:56; DRB1⁄11:73; DRB1⁄12:10; DRB1⁄12:20; DRB1⁄13:24; DRB1⁄13:25; DRB1⁄13:56; DRB1⁄13:60; DRB1⁄13:63; DRB1⁄13:66; DRB1⁄13:76; DRB1⁄13:80; DRB1⁄13:81; DRB1⁄14:13; DRB1⁄14:17; DRB1⁄14:21; DRB1⁄15:11; DRB1⁄16:09. Up to now, we have described the nine following novel alleles: A⁄03:55, A⁄66:14, B⁄08:48, B⁄18:35, B⁄40:125, B⁄40:129, B⁄51:119, DRB1⁄08:48, DRB1⁄11:130. Specifically, three alleles have frequencies in our population that are significantly higher than the 2x10-5 cut-off established by the NMDP for rarity: A⁄02:52 (0.035%), DRB1⁄13:56 (0.009%) and DRB1⁄14:13 (0.011%). Conclusions: The current policy for solving genotyping ambiguities based on the exclusion of rare allele combinations must be used with caution in populations other than North American. Our allele frequencies suggest that rare alleles lists should be adapted regionally.
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Abstracts / Human Immunology 74 (2013) 51–173
DIVERSITY OF HLA HAPLOTYPES IN CLINICAL PRACTICE. Pedro Cano 1, Michael Seul 2. 1 HLA Typing Laboratory, Laboratory Medicine, MD Anderson Cancer Center, Houston, TX, USA; 2 BioMolecular Analytics, LLC, Warren, NJ, USA. Aim: To elucidate the composition, abundance and molecular evolution of HLA haplotypes encountered in clinical practice to address the frequent failure to identify exactly matched stem cell grafts for other than the most common haplotypes. Methods: Generated catalog of 6,920 extended haplotypes by family segregation analysis of HLA types for transplant candidates; analyzed haplotype abundance within framework of a stochastic ‘‘birth-death’’ process. Results: rare haplotypes (‘‘hTypes’’): ‘‘shuffling’’ of common alleles – most rare hTypes in our catalog contain COMMON alleles; the more common an allele, the more widely dispersed it is in the hType population; rare alleles, though given much attention in laboratory analysis, play but a minor role in generating rare hTypes; hType diversity: proliferation of unique configurations – alleles in catalog: A : 85 (of which 28, or 32.9%, only once); B: 162 (54 or 33.3%); C: 56 (17 or 30.3%); DRB1: 75 (21 or 28%) vs hTypes: ABC: 1,533 (875 or 57.7%); ABC-DRB1: 3,345 (2,496 or 74.6%); characteristic shape of abundance distributions – ranking hTypes and alleles by abundance yields distributions characteristic of a stochastic ‘‘birth-death’’ process governing hType and allele evolution: the shape of the hType distribution indicates closely matched ‘‘birth’’& ‘‘death’’ rates; abundance fluctuations: evolutionary noise - simulations of random hType pairing under recombination reveal fluctuations in type abundance, reflecting the interplay between the ‘‘death’’ of non-reproducing hType ‘‘species’’ and the ‘‘birth’’ of new species by reciprocal allele exchange. Conclusions: Haplotype rather than allele diversity, and fluctuations in hType abundance define the principal clinical challenge in identifying optimally matched stem cell grafts. Understanding the molecular ‘‘proximity’’ of less common to more common hTypes, and the epitopes they encode, may inform a rational search for grafts that are optimally matched to unusual hType configurations. Seul: BioMolecular Analytics, LLC: Employee.
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RARE ALLELES IN THE SOUTHERN BRAZILIAN PARANA STATE POPULATION. Joandrei Dos Santos Silva, Alessandro Pirri, Jose Samuel Da Silva, Maria Da Graça Bicalho. Genetics, Universidade Federal Do Parana, Curitiba, Parana, Brazil. Aim: Being a HLA genotyping reference laboratory in Southern Brazil, we perform compatibility tests for both related and volunteer bone marrow donors by PCR-Sequence Specific Priming, reverse Sequence Specific Oligonucleotide Probing (low and high definition kits) and Sequence Based Typing. We frequently find alleles listed as rare variants by the NMDP and aimed at presenting them in this study. Methods: 106 537 subjects from the Parana State (Southern Brazil) were genotyped for HLA-A, -B and – DRB1 using LABType SSO tests and or MicroSSP trays (both One Lambda). Genotypings of alleles listed as rare were confirmed through LABType SSO High Definition and Atria SeqR HLA tests, and insTAclone PCR cloning kit (Thermo Scientific) was used in the case of novel alleles. Results: The following rare alleles were found in our sample: A⁄02:52; A⁄02:152; A⁄03:43; A⁄23:13; A⁄24:56; A⁄24:02L; A⁄24:30; A⁄24:71; A⁄26:31; A⁄68:23, B⁄07:20; B⁄07:37; B⁄08:33; B⁄15:151; B⁄18:11; B⁄18:19; B⁄35:62; B⁄37:07; B⁄39:29; B⁄39:37; B⁄40:33/80; B⁄42:05; B⁄42:12; B⁄44:20; B⁄51:29; B⁄55:21; B⁄56:15; B⁄56:25, DRB1⁄04:37; DRB1⁄04:39; DRB1⁄11:25; DRB1⁄11:35; DRB1⁄11:36; DRB1⁄11:42; DRB1⁄11:56; DRB1⁄11:73; DRB1⁄12:10; DRB1⁄12:20; DRB1⁄13:24; DRB1⁄13:25; DRB1⁄13:56; DRB1⁄13:60; DRB1⁄13:63; DRB1⁄13:66; DRB1⁄13:76; DRB1⁄13:80; DRB1⁄13:81; DRB1⁄14:13; DRB1⁄14:17; DRB1⁄14:21; DRB1⁄15:11; DRB1⁄16:09. Up to now, we have described the nine following novel alleles: A⁄03:55, A⁄66:14, B⁄08:48, B⁄18:35, B⁄40:125, B⁄40:129, B⁄51:119, DRB1⁄08:48, DRB1⁄11:130. Specifically, three alleles have frequencies in our population that are significantly higher than the 2x10-5 cut-off established by the NMDP for rarity: A⁄02:52 (0.035%), DRB1⁄13:56 (0.009%) and DRB1⁄14:13 (0.011%). Conclusions: The current policy for solving genotyping ambiguities based on the exclusion of rare allele combinations must be used with caution in populations other than North American. Our allele frequencies suggest that rare alleles lists should be adapted regionally.