Polymorphisme nucléotidique

Résumé

vignette|La molécule d'ADN 1 diffère de la 2 par un seul nucléotide (polymorphisme C/T). Le polymorphisme nucléotidique (PN, ou polymorphisme d'un seul nucléotide, PSN ; single nucleotide polymorphism, SNP) est, en génétique, la variation (polymorphisme) d'une seule paire de bases du génome entre individus d'une même espèce, ou entre un individu et la séquence de référence de l'espèce. La variation doit être située à un endroit spécifique du génome et apparaître sur une proportion supérieure à 1 % de la population pour être caractérisée comme PSN. Ces variations sont très fréquentes (environ une paire de bases sur mille dans le génome humain). Les PSN représentent 90 % de l'ensemble des variations génétiques humaines, et des PSN avec une fréquence allélique supérieure à 1% sont présents toutes les cent à trois cents paires de bases en moyenne dans le génome humain, où deux PSN sur trois substituent la cytosine avec la thymine. Les PSN peuvent être causes directes de diverses maladie

Source officielle

https://fr.wikipedia.org/wiki/Polymorphisme_nucl%C3%A9otidique

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Host genetic predictors of the kynurenine pathway of tryptophan catabolism among treated HIV-infected Ugandans

Yunfei Huang

Objective: Plasma kynurenine/tryptophan ratio, a biomarker of indoleamine 2,3-dioxygenase-1 (IDO) activity, is a strong independent predictor of mortality in HIV-infected Ugandans initiating antiretroviral therapy (ART) and may play a key role in HIV pathogenesis. We performed a genome-wide study to identify potential host genetic determinants of kynurenine/tryptophan ratio in HIV-infected ART-suppressed Ugandans. Design/methods: We performed genome-wide and exome array genotyping and measured plasma kynurenine/tryptophan ratio during the initial 6-12 months of suppressive ART in Ugandans. We evaluated more than 16 million single nucleotide polymorphisms in association with log(10) kynurenine/tryptophan ratio using linear mixed models adjusted for cohort, sex, pregnancy, and ancestry. Results: Among 597 Ugandans, 62% were woman, median age was 35, median baseline CD4(+) cell count was 135 cells/mu l, and median baseline HIV-1 RNA was 5.1 log(10) copies/ml. Several polymorphisms in candidate genes TNF, IFNGR1, and TLR4 were associated with log(10) kynurenine/tryptophan ratio (P < 5.0 x 10(-5)). An intergenic polymorphism between CSPG5 and ELP6 was genome-wide significant, whereas several others exhibited suggestive associations (P < 5.0 x 10(-7)), including genes encoding protein tyrosine phosphatases (PTPRM and PTPRN2) and the vitamin D metabolism gene, CYP24A1. Several of these single nucleotide polymorphisms were associated with markers of inflammation, coagulation, and monocyte activation, but did not replicate in a small US cohort (N = 262; 33% African-American). Conclusion: Our findings highlight a potentially important role of IFN-gamma, TNF-alpha, and Toll-like receptor signaling in determining IDO activity and subsequent mortality risk in HIV-infected ART-suppressed Ugandans. These results also identify potential novel pathways involved in IDO immunoregulation. Further studies are needed to confirm these findings in treated HIV-infected populations. Copyright (C) 2016 Wolters Kluwer Health, Inc. All rights reserved.

Lippincott Williams & Wilkins2016

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Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient

Chloé Christiane Laurence Jollivet, Stéphane Mauger

Temperature is one of the most important range-limiting factors for many seaweeds. Driven by the recent climatic changes, rapid northward shifts of species' distribution ranges can potentially modify the phylogeographic signature of Last Glacial Maximum. We explored this question in detail in the cold-tolerant kelp species Saccharina latissima, using microsatellites and double digest restriction site-associated DNA sequencing ( ddRAD-seq) derived single nucleotide polymorphisms (SNPs) to analyze the genetic diversity and structure in 11 sites spanning the entire European Atlantic latitudinal range of this species. In addition, we checked for statistical correlation between genetic marker allele frequencies and three environmental proxies (sea surface temperature, salinity, and water turbidity). Our findings revealed that genetic diversity was significantly higher for the northernmost locality (Spitsbergen) compared to the southern ones (Northern Iberia), which we discuss in light of the current state of knowledge on phylogeography of S. latissima and the potential influence of the recent climatic changes on the population structure of this species. Seven SNPs and 12 microsatellite alleles were found to be significantly associated with at least one of the three environmental variables. We speculate on the putative adaptive functions of the genes associated with the outlier markers and the importance of these markers for successful conservation and aquaculture strategies for S. latissima in this age of rapid global change.

MDPI2020

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Background: Kaposi's sarcoma, the most common AIDS-related cancer, represents a major public concern in resource-limited countries. Single nucleotide polymorphisms within the Interferon lambda 3/4 region (IFNL3/4) determine the expression, function of IFNL4, and influence the clinical course of an increasing number of viral infections. Objectives: To analyze whether IFNL3/4 variants are associated with susceptibility to AIDS-related Kaposi's sarcoma among MSM enrolled in the Swiss HIV Cohort Study (SHCS). Methods: The risk of developing Kaposi's sarcoma according to the carriage of IFNL3/4 SNPs rs8099917 and rs12980275 and their haplotypic combinations was assessed by using cumulative incidence curves and Cox regression models, accounting for relevant covariables. Results: Kaposi's sarcoma was diagnosed in 221 of 2558 MSM Caucasian SHCS participants. Both rs12980275 and rs8099917 were associated with an increased risk of Kaposi's sarcoma (cumulative incidence 15 versus 10%, P=0.01 and 16 versus 10%, P=0.009, respectively). Diplotypes predicted to produce the active P70 form (cumulative incidence 16 versus 10%, P=0.01) but not the less active S70 (cumulative incidence 11 versus 10%, P=0.7) form of IFNL4 were associated with an increased risk of Kaposi's sarcoma, compared with those predicted not to produce IFNL4. The associations remained significant in a multivariate Cox regression model after adjustment for age at infection, combination anti retrovi ral therapy, median CD4(+) T-cel I count nadir and CD4(+) slopes (hazard ratio 1.42, 95% confidence interval 1.06-1.89, P=0.02 for IFLN P70 versus no IFNL4). Conclusion: This study reports for the first time an association between IFNL3/4 polymorphisms and susceptibility to AIDS-related Kaposi's sarcoma. Copyright (C) 2018 Wolters Kluwer Health, Inc. All rights reserved.

LIPPINCOTT WILLIAMS & WILKINS2018

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Host genetic predictors of the kynurenine pathway of tryptophan catabolism among treated HIV-infected Ugandans

Yunfei Huang

Lippincott Williams & Wilkins2016