HLA Haplotypes In 250 Families: The Baylor Laboratory Results And A Perspective On A Core NGS Testing Model For The 17th International HLA And Immunogenetics Workshop.

Since their inception, the International HLA & Immunogenetics Workshops (IHIW) served as a collaborative platform for exchange of specimens, reference materials, experiences and best practices. In this report we present a subset of the results of human leukocyte antigen (HLA) haplotypes in families tested by next generation sequencing (NGS) under the 17th IHIW. We characterized 961 haplotypes in 921 subjects belonging to 250 families from 8 countries (Argentina, Austria, Egypt, Jamaica, Germany, Greece, Kuwait, and Switzerland). These samples were tested in a single core laboratory in a high throughput fashion using 6 different reagents/software platforms. Families tested included patients evaluated clinically as transplant recipients (kidney and hematopoietic cell transplant) and their respective family members. We identified 486 HLA alleles at the following loci HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, -DPB1 (77, 115, 68, 69, 10, 6, 4, 44, 31, 20 and 42 alleles, respectively). We also identified nine novel alleles with polymorphisms in coding regions. This approach of testing samples from multiple laboratories across the world in different stages of technology implementation in a single core laboratory may be useful for future international workshops. Although data presented may not be reflective of allele and haplotype frequencies in the countries to which the families belong, they represent an extensive collection of 3rd and 4th field resolution level 11-locus haplotype associations of 486 alleles identified in families from 8 countries.

Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop.

The 17th International HLA and Immunogenetics Workshop (IHIW) organizers conducted a Pilot Study (PS) in which 13 laboratories (15 groups) participated to assess the performance of the various sequencing library preparation protocols, NGS platforms and software in use prior to the workshop. The organizers sent 50 cell lines to each of the 15 groups, scored the 15 independently generated sets of NGS HLA genotyping data, and generated "consensus" HLA genotypes for each of the 50 cell lines. Proficiency Testing (PT) was subsequently organized using four sets of 24 cell lines, selected from 48 of 50 PS cell lines, to validate the quality of NGS HLA typing data from the 34 participating IHIW laboratories. Completion of the PT program with a minimum score of 95% concordance at the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 loci satisfied the requirements to submit NGS HLA typing data for the 17th IHIW projects. Together, these PS and PT efforts constituted the 17th IHIW Quality Control project. Overall PT concordance rates for HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRB1, HLA-DRB3, HLA-DRB4 and HLA-DRB5 were 98.1%, 97.0% and 98.1%, 99.0%, 98.6%, 98.8%, 97.6%, 96.0%, 99.1%, 90.0% and 91.7%, respectively. Across all loci, the majority of the discordance was due to allele dropout. The high cost of NGS HLA genotyping per experiment likely prevented the retyping of initially failed HLA loci. Despite the high HLA genotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software.

Association of DRB1 and DQB1 HLA class II polymorphisms in high-grade and neoplastic cervical lesions of women from Argentina.

OBJECTIVES: To investigate associations between HLA-DRB1 and HLA-DQB1 polymorphisms with low- and high-grade cervical lesions in Argentine population and the role human papillomavirus status in these associations. MATERIALS AND METHODS: Cervical biopsies and peripheral blood samples were taken from 32 patients with cervical intraepithelial neoplasia grade 1 (CIN 1) and 44 patients with cervical CIN 3 or invasive squamous cell carcinomas. Cervical cells and peripheral blood samples from 40 healthy women were included as control group. Human papillomavirus detection and typing were done by polymerase chain reaction (PCR) MY09, 11-restriction fragment length polymorphisms, or PCR 5+, 6+ dot-blot hybridization, and HLA DR/DQ typing by the PCR-sequence-specific oligonucleotide probes method. RESULTS: HLA-DRB1*04 and HLA-DQB1*0302 were found to be positive associated with the CIN 3/invasive squamous cell carcinomas subgroup, whereas HLA-DRB1*13 and HLA-DQB1*02 were negatively associated with the same group, when comparing to the control group. CONCLUSIONS: The data support the hypothesis that HLA-DRB1*04 and HLA-DQB1*0302 may be considered risk factors for malignant progression, whereas HLA-DRB1*13 and HLA-DQB1*02 may have a protective role. Further studies with a larger group are needed to confirm these susceptibility and protective roles in disease progression in Argentine population.

Determinación del polimorfismo de los genes KIR en la población argentina normal / Determination of the polymorphism of kir genes in a normal argentine population

The "Natural Killer" cells play an important roll in the immune response to tumoral cells and viral infections, and also they particpate in the rejection processes in allogeneic bone marrow transplantation. The interaction of natural killer cells and their receptors, with special reference to human diversity in killer cell inhibitory receptor genes, are described in this article with consideration to a normal Argentine population