Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium

The International Pseudomonas aeruginosa Consortium is sequencing over 1000 genomes and building an analysis pipeline for the study of Pseudomonas genome evolution, antibiotic resistance and virulence genes. Metadata, including genomic and phenotypic data for each isolate of the collection, are available through the International Pseudomonas Consortium Database (http://ipcd.ibis.ulaval.ca/). Here, we present our strategy and the results that emerged from the analysis of the first 389 genomes. With as yet unmatched resolution, our results confirm that P. aeruginosa strains can be divided into three major groups that are further divided into subgroups, some not previously reported in the literature. We also provide the first snapshot of P. aeruginosa strain diversity with respect to antibiotic resistance. Our approach will allow us to draw potential links between environmental strains and those implicated in human and animal infections, understand how patients become infected and how the infection evolves over time as well as identify prognostic markers for better evidence-based decisions on patient care

Polymorphisms in Th1/Th2 cytokine Genes, hormone replacement therapy, and risk of non-Hodgkin lymphoma

AbstractWe conducted a population-based case-control study in Connecticut women to test the hypothesis that genetic variations in Th1 and Th2 cytokine genes modify the relationship between hormone replacement therapy (HRT) and risk of non-Hodgkin lymphoma (NHL). Compared to women without a history of HRT use, women with a history of HRT use had a significantly decreased risk of NHL if they carried IFNGR2 (rs1059293) CT/TT genotypes (OR=0.5, 95%CI: 0.3-0.9), IL13 (rs20541) GG genotype (OR=0.6, 95%CI: 0.4-0.9) and IL13 (rs1295686) CC genotype (OR=0.6, 95%CI: 0.4-0.8), but not among women who carried IFNGR2 CC, IL13 AG /AA and IL13 CT/TT genotypes. A similar pattern was also observed for B-cell lymphoma but not for T-cell lymphoma. A statistically significant interaction was observed for IFNGR2 (rs1059293 Pforinteraction=0.024), IL13 (rs20541 Pforinteraction=0.005), IL13 (rs1295686 Pforinteraction=0.008) and IL15RA (rs2296135 Pforinteraction=0.049) for NHL overall; IL13 (rs20541 Pforinteraction=0.0009), IL13 (rs1295686 Pforinteraction=0.0002), and IL15RA (rs2296135 Pforinteraction=0.041) for B-cell lymphoma. The results suggest that common genetic variation in Th1/Th2 pathway genes may modify the association between HRT and NHL risk