Genomic landscape and fine-scale population structure of Helicobacter pylori across China.

Appreciating lifetime risk of gastric cancer through established risk factors is one simple way to promote preventive behavior. We have estimated cumulative risks (CRs) of gastric cancer by genetic and environmental risk factors, PSCA-rs2294008 polymorphism, Helicobacter Pylori (HP) infection and smoking, based on a case-control study involving 697 cases and 1372 controls at Aichi Cancer Center. We estimated odds ratio (OR) and 95% confidence interval (CI) for groups by these factors using logistic regression model after adjustment for age, sex, family history of gastric cancer and intake of fruit and vegetable. The ORs were combined with gastric cancer incidence rates in Japan to calculate CRs using the Peto's method. The CRs by age of 75 varied according to the risk groups, from 0.9% (95% CI, 0.3%-3.3%) for never smokers without both HP infection and risk allele of rs2294008 to 13.4% (95% CI, 13.3%-13.4%) for ever smokers with HP infection and 1-2 risk alleles. Among those with 1-2 risk alleles, the CRs were reduced to 2.0% (95% CI, 1.9%-2.0%) in those without both smoking history and HP infection, 3.9% (95% CI, 3.8%-3.9%) for ever smokers without HP infection, 9.4% (95% CI, 9.4%-9.5%) for never smokers with HP infection, although it was 13.4% in those with both smoking history and HP infection. In conclusion, the findings based on genetic and environmental risk factors in this study would be important information for promoting primary and secondary prevention of gastric cancer. Citation Format: Hidemi Ito, Isao Oze, Satoyo Hosono, Miki Watanabe, Hideo Tanaka, Keitaro Matsuo. Cumulative risks of gastric cancer by PSCA polymorphism, Helicobacter Pylori infection and smoking history in Japan. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2210. doi:10.1158/1538-7445.AM2014-2210

ObjectiveBoth variations in the interleukin-10 (IL10) gene and environmental factors are thought to influence inflammation and gastric carcinogenesis. Therefore, we investigated the associations between IL10 polymorphisms, Helicobacter pylori (H. pylori) infection, and smoking in noncardia gastric carcinogenesis in Koreans.MethodsWe genotyped three promoter polymorphisms (-1082A>G, -819T>C, and -592 A>C) of IL10 in a case-control study of 495 noncardia gastric cancer patients and 495 sex- and age-matched healthy controls. Multiple logistic regression models were used to detect the effects of IL10 polymorphisms, H. pylori infection, and smoking on the risk of gastric cancer, which was stratified by the histological type of gastric cancer.ResultsThe IL10-819C and -592C alleles were found to have complete linkage disequilibrium, and all three IL10 polymorphisms were associated with an increased risk of intestinal-type noncardia gastric cancer. These associations were observed only in H. pylori-positive subjects and current smokers. A statistically significant interaction between the IL10-592 genotype and H. pylori infection on the risk of intestinal-type gastric cancer was observed (P for interaction = 0.047). In addition, H. pylori-positive smokers who were carriers of either the IL10-1082G (OR [95% CI] = 17.76 [6.17−51.06]) or the -592C (OR [95% CI] = 8.37 [2.79−25.16]) allele had an increased risk of intestinal-type gastric cancer compared to H. pylori-negative nonsmokers homozygous for IL10-1082A and -592A, respectively. The interaction between the IL10-1082 polymorphism and the combined effects of H. pylori infection and smoking tended towards significance (P for interaction = 0.080).ConclusionsInflammation-related genetic variants may interact with H. pylori infection and smoking to increase the risk of noncardia gastric cancer, particularly the intestinal-type. These findings may be helpful in identifying individuals at an increased risk for developing noncardia gastric cancer.

Understanding the scale of marine population connectivity is critical for the conservation and sustainable management of marine resources. For many marine species adults are benthic and relatively immobile, so patterns of larval dispersal and recruitment provide the key to understanding marine population connectivity. Contrary to previous expectations, recent studies have often detected unexpectedly low dispersal and fine-scale population structure in the sea, leading to a paradigm shift in how marine systems are viewed. Nonetheless, the link between fine-scale marine population structure and the underlying physical and biological processes has not been made. Here we show that patterns of genetic structure and population connectivity in the broadcast-spawning and long-distance dispersing sea urchin Centrostephanus rodgersii are influenced by physical oceanographic and geographic variables. Despite weak genetic differentiation and no isolation-by-distance over thousands of kilometers among samples from eastern Australia and northern New Zealand, fine-scale genetic structure was associated with sea surface temperature (SST) variability and geography along the southeastern Australian coast. The zone of high SST variability is characterized by periodic shedding of eddies from the East Australian Current, and we suggest that ocean current circulation may, through its influence on larval transport and recruitment, interact with the genetic consequences of large variance in individual reproductive success to generate patterns of fine-scale patchy genetic structure. If proven consistent across species, our findings suggest that the optimal scale for fisheries management and reserve design should vary among localities in relation to regional oceanographic variability and coastal geography.

Regulation of Gastric Carcinogenesis by InflammatoryCytokines.

Antimicrobial susceptibility testing of Helicobacter pylori comparison of E-test, broth microdilution, and disk diffusion for ampicillin, clarithromycin, and metronidazole

Several polymorphisms of the IL1B and IL10 gene promoters have been reported to be associated with gastric cancer risk in Caucasians. However, studies in other populations have shown differing results. We aimed to test for associations between polymorphisms in IL1B (-31 and +3954), IL10-592 and IL1RN variable number of tandem repeats (VNTR) and risk of gastric cancer in a Mexican population. DNA was extracted from sera of 183 gastric adenocarcinoma patients and 377 controls. The IL1B-31, IL1B+3954 and IL10-592 biallelic polymorphisms were discriminated using 5' Nuclease (TaqMan) assays and Pyrosequencing. The IL1RN penta-allelic VNTR polymorphism was genotyped using PCR followed by GeneScan analysis. A significant interaction was found between IL1B-31 and CagA status for the risk of intestinal-type gastric cancer (p = 0.023). Among CagA positive subjects, those with IL1B-31CC genotype had an increased risk of intestinal-type gastric cancer (OR 3.19, 95%CI = 1.05-9.68), compared to carriers of IL1B-31TT genotype. In contrast, among CagA negative subjects, no significant association of IL1B-31CC genotype with gastric cancer was observed. The IL10-592CC genotype was associated with more than doubling of the risk of the intestinal-type gastric cancer (OR, 2.20, 95%CI = 1.04-4.65). A nonsignificantly increased risk for intestinal-type gastric cancer was found in IL1RN*2 carriers (OR 1.49, 95%CI = 0.89-2.50). None of these polymorphisms was significantly related to the risk of diffuse-type gastric cancer. No significant association was found between risk of gastric cancer and the IL1B+3954 polymorphism. Individuals carrying 2 or more of the risk-associated alleles (IL1B-31C, IL1RN *2 and IL10-592C) were at increased risk for intestinal-type gastric cancer, compared to those with 0 or 1 risk-associated allele. The risk from multiple risk-associated alleles was especially high in subjects infected with CagA positive H. pylori. Our results support the identification of the IL1B-31 promoter polymorphism as a useful marker for risk of intestinal type gastric cancer in persons with CagA positive H. pylori infections.

Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.

Decision letter: ODELAM, rapid sequence-independent detection of drug resistance in isolates of Mycobacterium tuberculosis

Evaluating vancomycin susceptibility in Staphylococcus aureus Marcelo J Mimica, Alessandra Navarini Department of Pathology, Division of Microbiology, Santa Casa de São Paulo School of Medicine, São Paulo, BrazilWe read the report by Phillips et al1 with great interest and would like to discuss it in comparison with our previous published data on the subject.2,3We have also studied a number of Staphylococcus aureus clinical isolates (n=125), comparing different vancomycin susceptibility tests, including microdilution, Etest® (bio-Mérieux, Marcy-l’Étoile, France), and brain heart infusion vancomycin screening plates. We found only one isolate with reduced susceptibility with a minimum inhibitory concentration (MIC) =4 mg/L when tested with Etest and 2 mg/L when tested with microdilution.2,3 Our results showed a tendency of higher lethality when higher MICs were present, even within the susceptible range,3 as some previous studies have shown.4,5Concordant to Phillips et al1 and other authors,6,7 we also reported a poor correlation between different tests. Comparing Etest and microdilution (approximating an Etest MIC value between two twofold dilutions up to the highest value), 58% of the isolates had similar MICs, whereas 38% had an MIC by Etest one dilution higher than microdilution. One isolate had an Etest MIC twofold higher and four isolates an Etest MIC onefold lower than microdilution.2However, in our study, a brain heart infusion screening plate with 2.0 mg/L of vancomycin showed a sensitivity of 100% to detect isolates with an MIC ≥2.0 by Etest and 91% to detect an MIC ≥2.0 by microdilution, making this test an interestingoption for initial screening of S. aureus isolates for reduced vancomycin susceptibility. Specificities were 63% and 38%, respectively, which would still make necessary the further testing with an MIC method, but in a much smaller number of isolates.2 This approach would be suitable for a large number of laboratories throughout the world where the routine MIC testing of all S. aureus isolates is not feasible.View original paper by Phillips et al.

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

In migratory animals, high mobility may reduce population structure through increased dispersal and enable adaptive responses to environmental change, whereas rigid migratory routines predict low dispersal, increased structure, and limited flexibility to respond to change. We explore the global population structure and phylogeographic history of the bar-tailed godwit, Limosa lapponica, a migratory shorebird known for making the longest non-stop flights of any landbird. Using nextRAD sequencing of 14,318 single-nucleotide polymorphisms and scenario-testing in an Approximate Bayesian Computation framework, we infer that bar-tailed godwits existed in two main lineages at the last glacial maximum, when much of their present-day breeding range persisted in a vast, unglaciated Siberian-Beringian refugium, followed by admixture of these lineages in the eastern Palearctic. Subsequently, population structure developed at both longitudinal extremes: in the east, a genetic cline exists across latitude in the Alaska breeding range of subspecies L. l. baueri; in the west, one lineage diversified into three extant subspecies L. l. lapponica, taymyrensis, and yamalensis, the former two of which migrate through previously glaciated western Europe. In the global range of this long-distance migrant, we found evidence of both (1) fidelity to rigid behavioural routines promoting fine-scale geographic population structure (in the east) and (2) flexibility to colonise recently available migratory flyways and non-breeding areas (in the west). Our results suggest that cultural traditions in highly mobile vertebrates can override the expected effects of high dispersal ability on population structure, and provide insights for the evolution and flexibility of some of the world's longest migrations.

After the dissemination of penicillin and oxacillin resistance in Staphylococcus aureus, vancomycin-intermediate and vancomycin resistant isolates have been reported. Even between isolates with minimum inhibitory concentrations (MICs) within the susceptible range, some authors have demonstrated that higher MICs correlate with higher lethality. To test this hypothesis in our setting, we compared vancomycin MICs evaluated by two methods and clinical outcomes in hospitalized patients with S. aureus bacteremia. We compared lethality in patients infected with isolates that had MICs under or over 2 mg/L. Among patients infected with isolates that had microdilution MICs <2 mg/L, the lethality was 25%; among patients infected with strains that had microdilution MICs ≥2 mg/L, 33% died. Among patients infected with isolates that had Etest MICs <2 mg/L, 23% died; in comparison, patients infected with strains that had Etest MICs ≥2 mg/L had a lethality of 44%. Our results showed a slight tendency of higher lethality when higher MICs were present. However, this difference did not reach statistical significance, possibly due to the relatively small number of patients included in the study. Future prospective studies are needed to further evaluate this correlation and to help clinicians guide antimicrobial therapy.

Allium vegetable intake associated with the risk of incident gastric cancer: a continuous follow-up study of a randomized intervention trial

Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure. Our work addresses multiple areas where substantial progress is being made: improved statistics and models for better capturing differentiation, admixture, and the spatial distribution of variation; computational speed-ups that allow methods to scale to modern data; and advances in haplotypic modeling that have wide ranging consequences for the analysis of population structure. We conclude by outlining four important open challenges: the limitations of discrete population models, uncertainty in individual origins, the incorporation of both fine-scale structure and ancient DNA in parametric models, and the development of efficient computational tools, particularly for haplotype-based methods.

Background: Genetic variations of interleukin-10 (IL-10) and environmental factors are assumed to influence inflammation and gastric carcinogenesis. Therefore, we aimed to investigate the association between IL-10 polymorphisms, smoking, and Helicobacter pylori (H. pylori) infection on the noncardia gastric carcinogenesis in Koreans. Methods: We genotyped 3 promoter polymorphisms (−1082 A&amp;gt;G, -819T&amp;gt;C, -592A&amp;gt;C) on the IL-10 gene in 495 noncardia gastric cancer patients and 495 sex- and age-matched controls. Multiple logistic regression models were used to detect the effects of IL-10 genetic variants, smoking, and H. pylori infection on gastric cancer risk, stratified by histological type of gastric cancer. Results: The IL-10-819C allele and -592C allele are in complete linkage disequilibrium, and IL-10-819C/-592C carriers are associated with a higher risk of noncardia gastric cancer, particularly with a risk of intestinal type cancer (OR [95% CI] = 1.50 [1.08−2.08]), than those with the wild type homozygote genotypes. Compared to nonsmokers carrying the wild type homozygotes, current smokers carrying IL-10-1082G and -819C/-592C showed 4.91 (95% CI = 2.49−9.69) and 6.82 (95% CI = 2.94−15.84) times increased risk of intestinal type gastric cancer, respectively. In addition, smokers with H. pylori infection were in the highest risk of intestinal gastric cancer compared with non-smokers without H. pylori infection, and this association was particularly stronger among IL-10-1082G carriers than AA carriers (OR [95% CI] = 15.54 [5.52−43.72]). Conclusion: Inflammation-related genetic variants may interact with smoking and H. pylori infection on the risk of noncardia gastric cancer, particularly intestinal type. Therefore, high risk group may reduce the risk of gastric cancer by modifying their lifestyles. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3745. doi:10.1158/1538-7445.AM2011-3745