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The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections., Alexander Immel et al. performed genome-wide analyses of 42 individuals from a collective burial in Niedertiefenbach, Germany from the Wartberg Culture. The authors find that this population had a large hunter-gatherer ancestry component and a distinct HLA pool, which indicates immune defenses against viral pathogens.

Background Stevens–Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening drug-induced dermatologic conditions. SJS/TEN occurs in 1-10 per 10 000 patients taking carbamazepine (CBZ) (Pratt VM, McLeod HL, Rubinstein WS et al. Medical Genetics Summaries. National Center for Biotechnology Information US; 2018: 1-527). The development of SJS/TEN is associated with variable drug metabolism and presence of an at-risk HLA haplotype. HLA-B*15:02 and HLA-A*31:01 haplotypes can produce a hyperimmune response in the setting of CBZ use in patients of Asian and European descent, respectively (Schneider JA, Cohen PR. Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis: A concise review with a comprehensive summary of therapeutic interventions emphasizing supportive measures. Adv Ther. 2017; 34:1235-1244). Objective The US Food and Drug Administration (FDA) and the Canadian pharmacogenomics Network for Drug Safety (CPNDS) recommend that patients with high-risk ethnic backgrounds should be genetic tested before initiating CBZ (Sukasem C, Chaichan C, Nakkrut T et al. Association between HLA-B Alleles and Carbamazepine-induced maculopapular exanthema and severe cutaneous reactions in Thai patients. Journal of Immunology Research. 2018; 1-11).We sought out to assess the awareness of this in prescribing practitioners and their standard of practice. Methods We created a 15-question survey and distributed to pediatric neurologists and pediatricians at the University of Alberta. We hypothesized that there was a discordance between the standard of practice and the recommendation by the FDA and CPNDS. Results The survey results indicated a lack of awareness of the at-risk ethnicities for CBZ-induced SJS/TEN. HLA gene testing was rarely done prior to initiation of CBZ in high-risk patients. In addition, there was a lack of awareness for standard of care for genetic testing in Canada and worldwide. Conclusions Our results demonstrate an evident gap between current prescriber practices and existing FDA and CPNDS recommendations to screen for HLA genotypes. We hope that this study captures the realistic potential to improve patient outcomes.

Background Among the genetic susceptibility factors of Juvenile Idiopathic Arthritis (JIA), the HLA class I and II genes are the most frequently involved. These HLA genes are extensively investigated, highlighting the role of self/non-self-balance in auto-immune and auto-inflammatory diseases. Methods We carried out a retrospective study of HLA class I and/or class II genes (HLA B and HLA DR genes) of 12 children. Genotyping was performed through microlymphocytotoxicity for class I (HLA B5 and B27) and through indirect immunofluorescence and PCR for class II (HLA DR4) Results The summarized results depict: 4 patients have the HLA B27 + 3 patients have the HLA B5+ 1 patient had the HLA DR JIA comprises a broad spectrum influenced by both genetic and environmental factors. The International League of Rheumatology Associations (ILAR) has defined seven categories of JIA consisting of a myriad of pediatric auto-immune and auto-inflammatory diseases. The HLA genomic region is also associated with a wide range of auto-immune diseases, encoding the HLA-DR, HLA-DQ, and HLA-DP proteins involved in the peptide’s presentations to HLA -class II-restricted CD4 + helper T cells. These mechanisms are involved in the pathogenesis of various diseases such as rheumatoid arthritis. Juvenile arthritis has also been associated with a single nucleotide polymorphism in the regulatory region of the interleukin-6 gene, close to the HLA coding region. Conclusion Genetic exploration of the HLA system in JIA, more accessible and less expensive than other targeted genetic typing, can be a helpful tool. Its usage ought to be encouraged and expanded in clinical practice.

New corona virus disease (COVID-19) is a recent worldwide pandemic occurred as a result of SARS-CoV-2 virus, where, it spreads mainly through large respiratory droplets, and probability of other routes of transmission do exist

The Wartberg culture (WBC, 3,500-2,800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We perform a genome-wide analysis of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3,300-3,200 cal. BCE). Our results highlight that the Niedertiefenbach population indeed emerged at the beginning of the WBC. This farming community was genetically heterogeneous and carried a surprisingly large hunter-gatherer ancestry component (40%). We detect considerable differences in the human leukocyte antigen gene pool between contemporary Europeans and the Niedertiefenbach individuals whose immune response was primarily geared towards defending viral infections.

Prediction of different classes within the human leukocyte antigen (HLA) gene family can provide insight into the human immune system and its response to viral pathogens. Therefore, it is desirable to develop an efficient and easily interpretable method for predicting HLA gene class compared to existing methods. We investigated the HLA gene prediction problem as follows: (a) establishing a dataset (HLA262) such that the sequence identity of the complete HLA dataset was reduced to 30%; (b) proposing a feature set of informative physicochemical properties that cooperate with SVM (named HLAPred) to achieve high accuracy and sensitivity (90.04% and 82.99%, respectively) compared with existing methods; and (c) analysing the informative physicochemical properties to understand the physicochemical properties and molecular mechanisms of the HLA gene family.

Human leukocyte antigens (HLAs) have been implicated in rheumatic fever pathogenesis. This pilot whole genome association study compares genotypes of Samoan children with rheumatic fever to unaffected siblings and unrelated healthy controls. No risk-related genotypes were associated with HLA genes. Thirteen Regions of Interest were identified as candidates for further study.

We describe here a novel null allele of human leukocyte antigen gene, A*11:69N, which was initially found in a blood donor from China.

Human Leukocyte Antigen (HLA) plays an important role in the control of self-recognition including defence against microorganisms. The efficient performance of classifying HLA genes facilitates the understanding of the HLA and immune systems. Currently, the classification of HLA genes has been developed by using various computational methods based on codon and di-codon usages. Here, we directly classify the HLA genes by using the k-nearest neighbour (k-NN) classifier. To develop an efficient k-NN classifier, we propose the use of a spectrum kernel to investigate HLA genes. Our approach achieves an accuracy as high as 99.4% of the HLA major classes prediction measured by ten-fold cross-validation. Moreover, we give a maximum accuracy of 99.4% in the HLA-I subclasses. These results show that our proposed method is relatively simple and can give higher accuracies than other sophisticated and conventional methods.

This chapter will present an outline of the structure and functions of the immune system. The approach will differ somewhat from others, as it will not be an exhaustive treatise on the immune system. Our knowledge of the immune system, although far from complete, is already so detailed that such a treatise would be inappropriate (and beyond the capability of this author). Besides, there are excellent comprehensive textbooks that serve this purpose well.1–6 Instead, this chapter will present an overview of the immune system, emphasizing those facts and concepts that will be useful in understanding the material in this book.