Next‐generation sequencing of <i>HLA‐G</i> based on long‐range polymerase chain reaction

Nilsson, Line; Funck, Tina; Kjersgaard, Nina Dahl; Hviid, Thomas Vauvert F.

doi:10.1111/tan.13342

Cited by 7 publications

(6 citation statements)

References 27 publications

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“…Moreover, NGS is ideal to detect new HLA variants. Researchers now routinely identify novel HLA alleles ( Nilsson et al, 2018 ; Ralazamahaleo et al, 2019 ; Loginova et al, 2020 ; Ananeva et al, 2021a ; Ananeva et al, 2021b ; Cheranev et al, 2021 ; Loginova et al, 2021 ) using NGS and confirm them using SBT with PCR-SBT error often responsible for non-concordance between the two. NGS-based sequencing of multiple exons and introns has led to increases in the growth of the IPD-IMGT-HLA Database collection ( Robinson et al, 2015 ; Robinson et al, 2019 ).…”

Section: Generating and Working With Hla Datamentioning

confidence: 99%

Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

et al. 2021

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The current SARS-CoV-2 pandemic era launched an immediate and broad response of the research community with studies both about the virus and host genetics. Research in genetics investigated HLA association with COVID-19 based on in silico, population, and individual data. However, they were conducted with variable scale and success; convincing results were mostly obtained with broader whole-genome association studies. Here, we propose a technical review of HLA analysis, including basic HLA knowledge as well as available tools and advice. We notably describe recent algorithms to infer and call HLA genotypes from GWAS SNPs and NGS data, respectively, which opens the possibility to investigate HLA from large datasets without a specific initial focus on this region. We thus hope this overview will empower geneticists who were unfamiliar with HLA to run MHC-focused analyses following the footsteps of the Covid-19|HLA & Immunogenetics Consortium.

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Section: Generating and Working With Hla Datamentioning

confidence: 99%

Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

et al. 2021

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“…The HLA-G gene region extending from positions −1550 to 3404, relative to the start codon, was analyzed using long-range PCR. Specific primers were designed in relation to HLA-G RefSeqGene version NG_029039.1 (NCBI database), as previously described ( 58 ). The libraries were prepared starting from 1 ng of PCR product using the Nextera XT DNA Library Preparation Kit.…”

Section: Methodsmentioning

confidence: 99%

The double-sided of human leukocyte antigen-G molecules in type 1 autoimmune hepatitis

et al. 2022

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The immunomodulatory effects of HLA-G expression and its role in cancers, human liver infections and liver transplantation are well documented, but so far, there are only a few reports addressing autoimmune liver diseases, particularly autoimmune hepatitis (AIH).Method and materialsWe analyzed the genetic and phenotypic characteristics of HLA-G in 205 type 1 AIH patients (AIH-1) and a population of 210 healthy controls from Sardinia (Italy).ResultsAnalysis of the HLA-G locus showed no substantial differences in allele frequencies between patients and the healthy control population. The HLA-G UTR-1 haplotype was the most prevalent in both AIH-1 patients and controls (40.24% and 34.29%). Strong linkage was found between the HLA-G UTR-1 haplotype and HLA-DRB1*03:01 in AIH-1 patients but not controls (D’ = 0.92 vs D’ = 0.50 respectively; P = 1.3x10-8). Soluble HLA-G (sHLA-G) levels were significantly lower in AIH-1 patients compared to controls [13.9 (11.6 – 17.4) U/mL vs 21.3 (16.5 – 27.8) U/mL; P = 0.011]. Twenty-four patients with mild or moderate inflammatory involvement, as assessed from liver biopsy, showed much higher sHLA-G levels compared to the 28 patients with severe liver inflammation [33.5 (23.6 – 44.8) U/mL vs 8.8 (6.1 – 14.5) U/mL; P = 0.003]. Finally, immunohistochemistry analysis of 52 liver biopsies from AIH-1 patients did not show expression of HLA-G molecules in the liver parenchyma. However, a percentage of 69.2% (36/52) revealed widespread expression of HLA-G both in the cytoplasm and the membrane of plasma cells labeled with anti-HLA-G monoclonal antibodies.ConclusionThis study highlights the positive immunomodulatory effect of HLA-G molecules on the clinical course of AIH-1 and how this improvement closely correlates with plasma levels of sHLA-G. However, our results open the debate on the ambiguous role of HLA-G molecules expressed by plasma cells, which are pathognomonic features of AIH-1.

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“…Typing to identify the HLA-G alleles has mainly been performed in the framework of population and evolutionary studies and studies on reproduction, infection and disease associations, often limited to sequencing of exons 2-4 (230,235,236), sometimes combined with identification of the 14 bp insertion/deletion in the 3' UTR region (237)(238)(239). Recently, also NGS has been used to identify the HLA-G alleles present (212,215,(240)(241)(242). A high linkage disequilibrium was found between the HLA-G allele type and the polymorphism in the 3' UTR region (241).…”

Section: Non-classical Hla Class I Determinationmentioning

confidence: 99%

HLA Class I Molecules as Immune Checkpoints for NK Cell Alloreactivity and Anti-Viral Immunity in Kidney Transplantation

et al. 2021

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Natural killer (NK) cells are innate lymphocytes that can kill diseased- or virally-infected cells, mediate antibody dependent cytotoxicity and produce type I immune-associated cytokines upon activation. NK cells also contribute to the allo-immune response upon kidney transplantation either by promoting allograft rejection through lysis of cells of the transplanted organ or by promoting alloreactive T cells. In addition, they protect against viral infections upon transplantation which may be especially relevant in patients receiving high dose immune suppression. NK cell activation is tightly regulated through the integrated balance of signaling via inhibitory- and activating receptors. HLA class I molecules are critical regulators of NK cell activation through the interaction with inhibitory- as well as activating NK cell receptors, hence, HLA molecules act as critical immune checkpoints for NK cells. In the current review, we evaluate how NK cell alloreactivity and anti-viral immunity are regulated by NK cell receptors belonging to the KIR family and interacting with classical HLA class I molecules, or by NKG2A/C and LILRB1/KIR2DL4 engaging non-classical HLA-E or -G. In addition, we provide an overview of the methods to determine genetic variation in these receptors and their HLA ligands.

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Next‐generation sequencing of HLA‐G based on long‐range polymerase chain reaction

Cited by 7 publications

References 27 publications

Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

Approaching Genetics Through the MHC Lens: Tools and Methods for HLA Research

The double-sided of human leukocyte antigen-G molecules in type 1 autoimmune hepatitis

HLA Class I Molecules as Immune Checkpoints for NK Cell Alloreactivity and Anti-Viral Immunity in Kidney Transplantation

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