HLA-E coding and 3′ untranslated region variability determined by next-generation sequencing in two West-African population samples

Castelli, Erick C.; Mendes-Junior, Celso Teixeira; Sabbagh, Audrey; Porto, Iane O. P.; Garcia, André; Ramalho, Jaqueline; Lima, Thálitta H. A.; Massaro, Juliana Doblas; Dias, Fabrício C.; Collares, Cristhianna V. A.; Jamonneau, Vincent; Bucheton, Bruno; Camara, Mamadou; Donadi, Eduardo Antônio

doi:10.1016/j.humimm.2015.06.016

Cited by 32 publications

(51 citation statements)

References 54 publications

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“…We know that the interaction KIR-HLA has two sides of KIR and HLA. For example overexpression of HLA-E on surface of colorectal cancer cells can result in inhibition of NKs [53] and such patients have better survival from the disease [54]; of course the receptor of HLA-E is CD94/NKG2a [55], [56]. KIR2DL1 and 2DS1 interact with HLA-C2, and KIR2DL2, 2DL3 and 2DS2 interact with HLA-C1 [57]; so every mathematical predict do not occur.…”

Section: Resultsmentioning

confidence: 99%

Colorectal cancer and the KIR genes in the human genome: A meta-analysis

et al. 2016

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Colorectal cancer is one of the most common types of inflammation-based cancers and is occurred due to growth and spread of cancer cells in colon and/or rectum. Previously genetic association of cell cycle genes, both proto-oncogenes and the tumor suppressors has been proved. But there were few studies about association of immune related genes such as killer-cell immunoglobulin-like receptors (KIRs). Thus we intend to perform a meta-analysis to find the association of different genes of KIR and susceptibility to be affected by colorectal cancer. The overall population of the four studies investigated in our meta-analysis was 953 individuals (470 individuals with colorectal cancer and 483 individuals in control groups). After the analyses, we concluded that colorectal cancer is affected by KIR2DS5 and also there were no protecting gene. This result shows the inflammatory basis of this cancer. In other words, in contrast to leukemia and blood cancers, colorectal cancers seem to be affected by hyper activity of natural killer-cells (NKs). Whys and therefore of this paradox, is suggested to be investigated further.

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Section: Resultsmentioning

confidence: 99%

Colorectal cancer and the KIR genes in the human genome: A meta-analysis

et al. 2016

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“…We used VCFx software (Castelli et al. ) to convert our Ensifer genus vcf file of combined E. meliloti and E. medicae SNPs to an aligned fasta file—the input format for ClonalFrame. We performed two runs of ClonalFrame with 100,000 iterations and removed 50,000 as the burn‐in.…”

Section: Methodsmentioning

confidence: 99%

“…We used the program ClonalFrame (Didelot and Falush 2007) to estimate ρ/θ (number of recombination events/number of mutation events). We used VCFx software (Castelli et al 2015) to convert our Ensifer genus vcf file of combined E. meliloti and E. medicae SNPs to an aligned fasta file-the input format for ClonalFrame. We performed two runs of ClonalFrame with 100,000 iterations and removed 50,000 as the burn-in.…”

Section: Structurementioning

confidence: 99%

Geographically structured genetic variation in theMedicago lupulina–Ensifermutualism

et al. 2017

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Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.

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“…For instance, whole-genome sequencing (WGS) was successfully used to type HLA-A alleles at full resolution in 1070 healthy Japanese individuals [12] and to fully evaluate HLA-E variability in West African populations [13]. However, the main problem with MHC sequencing using current technologies is the relatively short read lengths, which limit the amount of allelic data that can be generated at a high resolution.…”

Section: Advances In Mapping Susceptibility Variants In the Mhc Locusmentioning

confidence: 99%

The MHC locus and genetic susceptibility to autoimmune and infectious diseases

et al. 2017

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In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1207-1) contains supplementary material, which is available to authorized users.

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HLA-E coding and 3′ untranslated region variability determined by next-generation sequencing in two West-African population samples

Cited by 32 publications

References 54 publications

Colorectal cancer and the KIR genes in the human genome: A meta-analysis

Colorectal cancer and the KIR genes in the human genome: A meta-analysis

Geographically structured genetic variation in theMedicago lupulina–Ensifermutualism

The MHC locus and genetic susceptibility to autoimmune and infectious diseases

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