Prevalence gradients of Friedreich's ataxia and R1b haplotype in Europe co-localize, suggesting a common Palaeolithic origin in the Franco-Cantabrian ice age refuge.

Combining data from epidemiological studies in Friedreich's Ataxia (FRDA) and patient organization membership lists, shows that FRDA prevalence exhibits large regional differences in Europe with a prevalence gradient from west to east. Highest levels are observed in northern Spain, south of France and Ireland, lowest levels in Scandinavia and Russia. The observed distribution of FRDA in Europe co-localizes with the gradient of the chromosomal R1b marker as detected within west Europe. This gradient is either derived from Palaeolithic migrations out of the Franco-Cantabrian Ice age refuge or from Neolithic migrations entering west Europe with the advance of agriculture. FRDA prevalence may have been increased in this population anytime after its separation from the closely related R1a carrying group. East European populations with a high frequency of the R1a marker show 10 fold lower prevalence of FRDA, indicating that the FRDA mutation was present in the common ancestor and was increased in the R1b carrying group. The FRDA carrying population went through a Palaeolithic population bottleneck supporting the view that the observed FRDA distribution and potentially the R1b distribution are derived from Palaeolithic migrations out of the Franco-Cantabrian ice age refuge.

Practical Considerations and Workflow in Utilizing KIR Genotyping in Transplantation Medicine.

This chapter is intended to serve as a practical guide for establishing a workflow using sequence-specific polymorphism PCR (SSP-PCR) for killer cell immunoglobulin-like receptor (KIR) genotyping in a clinical setting, especially in allogeneic hematopoietic stem cell transplantation (HSCT). As clinical evidence accumulates on the application of KIR and HLA genetics to guide donor selection in HSCT, there is an increasing need for KIR genotyping in clinical settings, and thus medical institutes may need to build this capability. Among the various KIR genotyping approaches now available, SSP-PCR methods are well-established and are the most cost-effective and will likely be the method of choice especially when expenses will be passed on to the patient. The protocol described in this chapter developed by Vilches et al. features small amplicon PCR and is suitable for KIR genotyping using FFPE-derived DNA as well as DNA extracted from blood samples. Setting up a laboratory workflow for in-house KIR genotyping is relatively straightforward; in this chapter, considerations for KIR genotyping to guide clinical decisions are discussed.In HSCT, a main objective of KIR genotyping is to apply the genetic analysis to predict donor and recipient combinations that have the most potential to produce NK cell alloresponses either through the missing-self mechanism or by action associated with activating KIR. The desired effects are reduction in acute GVHD and relapse rates and enhancement of overall survival. The information herein may also be useful to clinical laboratories considering the application of KIR genotyping in areas such as solid organ transplantation, NK cell-based treatment in other forms of cancer and autoimmune diseases, humanized antibody treatment, regenerative medicine, and reproductive medicine. Some background knowledge on KIR genetics will be necessary in managing a KIR genotyping platform. This chapter aims to address the main difficulties often encountered by physicians in understanding the KIR system, such as basic aspects of the nomenclature of KIR genes and haplotypes, genotypes, and determining presence/absence of KIR ligands in the patient and donor from the extensively diversified HLA class I allotypes. In describing the workflow, emphasis has been placed on the processes after genotype PCR and gel image acquisition: haplotype inference, generating B content scores, deduction of KIR ligands from HLA typing results, and the emerging algorithms for donor selection based on KIR and HLA genetics.

Ovine ß-globin gene: A new qPCR for rapid haplotype identification and association with susceptibility to Haemonchus contortus infection.

Two ß-globin allelic haplotypes (A and B) were identified in domestic sheep, wherein animals which are homozygous for ßB allele (BB haplotype) have a deletion of pre-adult ßC-globin and consequently are less tolerant to anemia and hypoxia. Since Haemonchus contortus infection, is associated with severe anemia, studies performed from 1960s to 1990s investigated the association between ß-globin haplotype and resistance against this parasite. However, the findings were controversial, pointing out from increased resistance in animals harboring the ßA allele to inexistence of association. Thus, our study aimed to develop a qPCR for ß-globin haplotype identification, and to evaluate the association between ß-globin haplotype and resistance against H. contortus in a group of sheep submitted to artificial infection with this parasite. A total of 286 lambs of Morada Nova breed were experimentally challenged with 4000 H. contortus L3 and monitored for 112 days from weaning. Significantly improved (p < 0.05) phenotypic profiles (lower fecal egg counts, higher packed cell volume and birthweight) were observed for AA haplotype animals, especially when compared to BB animals, while AB animals were similar to BB. This is the first report of a qPCR assay for ovine ß-globin haplotype identification. In view of significant differences of phenotypic profiles between haplotype groups, the developed qPCR may constitute an important tool for sheep producers to improve genetic selection of parasite resistant animals.

Comparison of ovine ß-globin haplotype sequences and a new multiplex PCR for identification.

Deletion of pre-adult ßC-globin in sheep harboring BB haplotype of ß-globin was associated to decreased tolerance to anemia and hypoxia, and consequently, reduced resistance to Haemonchus contortus infection, which is closely related to severe anemia. Recently, a qPCR using hydrolysis probe was successfully developed for ß-globin haplotype identification, and association between resistance against H. contortus and presence of ßA allele was observed in Morada Nova sheep. Thus, this study aimed to better investigate the differences between ß-globin haplotypes and to develop a conventional multiplex PCR, as an alternative to qPCR assay for ß-globin haplotype identification. A total of 333 Morada Nova lambs had their blood collected and tested by both qPCR and new multiplex PCR, and 100 % of agreement was observed between the results. Since different primers were designed for such assay development, including different target genes, high specificity of both methods may be also highlighted. Three A haplotype samples were submitted to DNA Sanger sequencing of ß-globin gene and compared to sequences previously deposited in Genbank. One nucleotide deletion in intronic region was observed only in AA haplotype of Morada Nova animals, while in BB animals the nucleotide remained present. To the best of our knowledge, this is the first report of multiplex conventional PCR for ovine ß-globin haplotype identification. The advantages of the developed conventional PCR are reduced reagents costs (less than a half price) and wider reachability, since even labs without real time PCR thermocyclers are able to offer this assay. Therefore, it may become an important tool for sheep producers to improve genetic selection of parasite resistant animals.

Human Leukocyte Antigen (HLA) Class I Susceptible Alleles Against COVID-19 Increase Both Infection and Severity Rate.

Introduction Each country's difference in the severity rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be explained by the difference in human leukocyte antigen (HLA) class I molecules, which affects the reactivity of cytotoxic T lymphocyte (CTL). Methods To clarify the relationship between HLA class I and the severity rate, the binding repertoires of each HLA class I allele to SARS-CoV-2 peptides and the allele frequencies of HLA-A, -B, and -A/B haplotypes in each country were quoted. Results HLA-A1 and the number of deaths per million population (severity rate) in each country had an exponential approximation correlation with correlation coefficient R=0.4879. In addition, the correlation between the infected cases per million (infection rate) and the severity rate was linearly approximated, with R=0.7422. Weak HLA-A alleles with a repertoire of under 300 also had an exponential approximation correlation with the severity rate (R=0.5972), whereas there was a linear approximation with the infection rate (R=0.6808). Weak HLA-B alleles of 30 repertoires or less had no correlation with the severity rate (R=-0.1530). The weak HLA-A/B haplotype has a stronger effect on the severity rate than the weak HLA-A alone. Therefore, the simple HLA class I susceptibility index was calculated, and a strong correlation (R=0.7388) of an exponential approximation with the severity rate was obtained. Conclusions HLA class I susceptible alleles against COVID-19 increase both infection and severity rate. The weak HLA-A is a major factor of severity rate, whereas the weak -B alone has no correlation. However, the weak HLA-A/B haplotype has a stronger effect on the severity rate than the weak -A alone.

Activating KIR Haplotype Influences Clinical Outcome Following HLA-Matched Sibling Hematopoietic Stem Cell Transplantation.

Natural killer cells are thought to influence the outcome of hematopoietic stem cell transplant (HSCT), impacting on relapse, overall survival, graft versus host disease and the control of infection, in part through the complex interplay between the large and genetically diverse killer immunoglobulin-like receptor (KIR) family and their ligands. This study examined the relationship between KIR gene content and clinical outcomes including the control of opportunistic infections such as cytomegalovirus in the setting of human leucocyte antigen (HLA)-matched sibling HSCT in an Australian cohort. The presence of the KIR B haplotype which contain more activating receptors in the donor, in particular centromeric B haplotype genes (Cen-B), was associated with improved overall survival of patients with acute myeloid leukemia (AML) undergoing sibling HSCT and receiving myeloablative conditioning. Donor Cen-B haplotype was also associated with reduced acute graft versus host disease grades II-IV whereas donor telomeric-B haplotype was associated with decreased incidence of CMV reactivation. In contrast, we were not able to demonstrate a reduced rate of relapse when the donor had KIR Cen-B, however relapse with a donor Cen-A haplotype was a competing risk factor to poor overall survival. Here we show that the presence of donor activating KIR led to improved outcome for the patient, potentially through reduced relapse rates and decreased incidence of acute GvHD translating to improved overall survival. This article is protected by copyright. All rights reserved.

Macrophages from disease resistant B2 haplotype chickens activate T lymphocytes more effectively than macrophages from disease susceptible B19 birds.

Resistance to respiratory pathogens, including coronavirus-induced infection and clinical illness in chickens has been correlated with the B (MHC) complex and differential ex vivo macrophage responses. In the current study, in vitro T lymphocyte activation measured by IFNγ release was significantly higher in B2 versus B19 haplotypes. AIV infection of macrophages was required to activate T lymphocytes and prior in vivo exposure of chickens to NP AIV plasmid enhanced responses to infected macrophages. This study suggests that the demonstrated T lymphocyte activation is in part due to antigen presentation by the macrophages as well as cytokine release by the infected macrophages, with B2 haplotypes showing stronger activation. These responses were present both in CD4 and CD8 T lymphocytes. In contrast, T lymphocytes stimulated by ConA showed greater IFNγ release of B19 haplotype cells, further indicating the greater responses in B2 haplotypes to infection is due to macrophages, but not T cells. In summary, resistance of B2 haplotype chickens appears to be directly linked to a more vigorous innate immune response and the role macrophages play in activating adaptive immunity.

Establishment of six homozygous MHC-B haplotype populations associated with susceptibility to Marek's disease in Chinese specific pathogen-free BWEL chickens.

The highly polymorphic chicken major histocompatibility complex (MHC) is associated with different levels of immunologic responses to certain avian pathogens. MHC-B haplotype chickens are an important genetic resource for studying the genetic determination of pathogen resistance and susceptibility. The BWEL chicken population is the only specific pathogen-free (SPF) chickens bred and developed by the State Center of Poultry Genetic Resources of Laboratory Animals in China. In this study, we successfully established six homozygous MHC-B haplotype populations from the BWEL chickens using microsatellite marker technology, named as BW/G(1, 2, 3, 5, 6, 7) lines, and their molecular genotypes were matched to six serologically defined MHC-B haplotypes, B13, B15, B2, B5, B21 and B19, respectively. The sequences of BF genes exons 2 and 3 from four successive generations (F1-F4) of the BW/G(n) lines were completely consistent with those of serologically defined MHC-B haplotypes. Subsequently, six BW/G(n) line specific allo-antisera were prepared by immunization with red blood cells (RBCs) and hemagglutination tests results showed the BW/G(n) SPF chickens could be serologically differentiated. Additionally, susceptibility to Marek's disease (MD) in the BW/G3 (B2 haplotype) and BW/G7 (B19 haplotype) lines were determined by comparing mortality, macroscopic and histopathological lesions, and viral loads in feather pulp. The BW/G7 line showed greater genetic susceptibility to the very virulent MD virus (MDV) strain than the BW/G3 line. The establishment of MHC-B haplotype chicken populations associated with susceptibility to MD will be helpful for studying host immune responses and further developing the more effective vaccines in the context of MHC specificities, and they are also very useful for an understanding of MHC genes architecture and function.