Enzymatic Synthesis of M1Gâ Deoxyribose

Adducts formed between electrophiles and nucleic acid bases are believed to play a key role in chemically induced mutations and cancer. M1Gâ dR is an endogenous exocyclic DNA adduct formed by the reaction of the dicarbonyl compound malondialdehyde with a dG residue in DNA. It is an intermediate in the synthesis of a class of modified oligodeoxyribonucleotides that are used to study the mutagenicity and repair of M1G. This unit presents methods for synthesizing M1Gâ dR by enzymatic coupling.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143678/1/cpnc0102.pd

Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study

Abstract Background Although smoking behavior is known to affect body mass index (BMI), the potential for smoking to influence genetic associations with BMI is largely unexplored. Methods As part of the ‘Population Architecture using Genomics and Epidemiology (PAGE)’ Consortium, we investigated interaction between genetic risk factors associated with BMI and smoking for 10 single nucleotide polymorphisms (SNPs) previously identified in genome-wide association studies. We included 6 studies with a total of 56,466 subjects (16,750 African Americans (AA) and 39,716 European Americans (EA)). We assessed effect modification by testing an interaction term for each SNP and smoking (current vs. former/never) in the linear regression and by stratified analyses. Results We did not observe strong evidence for interactions and only observed two interactions with p-values <0.1: for rs6548238/TMEM18, the risk allele (C) was associated with BMI only among AA females who were former/never smokers (β = 0.018, p = 0.002), vs. current smokers (β = 0.001, p = 0.95, pinteraction = 0.10). For rs9939609/FTO, the A allele was more strongly associated with BMI among current smoker EA females (β = 0.017, p = 3.5x10-5), vs. former/never smokers (β = 0.006, p = 0.05, pinteraction = 0.08). Conclusions These analyses provide limited evidence that smoking status may modify genetic effects of previously identified genetic risk factors for BMI. Larger studies are needed to follow up our results. Clinical Trial Registration NCT0000061

Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study.

We performed a Phenome-wide association study (PheWAS) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys (NHANES), conducted by the Centers for Disease Control and Prevention (CDC), and accessed by the Epidemiological Architecture for Genes Linked to Environment (EAGLE) study. We calculated comprehensive tests of association in Genetic NHANES using 80 SNPs and 1,008 phenotypes (grouped into 184 phenotype classes), stratified by race-ethnicity. Genetic NHANES includes three surveys (NHANES III, 1999-2000, and 2001-2002) and three race-ethnicities: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We identified 69 PheWAS associations replicating across surveys for the same SNP, phenotype-class, direction of effect, and race-ethnicity at p0.01, and sample size >200. Of these 69 PheWAS associations, 39 replicated previously reported SNP-phenotype associations, 9 were related to previously reported associations, and 21 were novel associations. Fourteen results had the same direction of effect across more than one race-ethnicity: one result was novel, 11 replicated previously reported associations, and two were related to previously reported results. Thirteen SNPs showed evidence of pleiotropy. We further explored results with gene-based biological networks, contrasting the direction of effect for pleiotropic associations across phenotypes. One PheWAS result was ABCG2 missense SNP rs2231142, associated with uric acid levels in both non-Hispanic whites and Mexican Americans, protoporphyrin levels in non-Hispanic whites and Mexican Americans, and blood pressure levels in Mexican Americans. Another example was SNP rs1800588 near LIPC, significantly associated with the novel phenotypes of folate levels (Mexican Americans), vitamin E levels (non-Hispanic whites) and triglyceride levels (non-Hispanic whites), and replication for cholesterol levels. The results of this PheWAS show the utility of this approach for exposing more of the complex genetic architecture underlying multiple traits, through generating novel hypotheses for future research

Rare variant APOC3 R19X is associated with cardio-protective profiles in a diverse population-based survey as part of the Epidemiologic Architecture for Genes Linked to Environment Study

A founder mutation was recently discovered and described as conferring favorable lipid profiles and reduced subclinical atherosclerotic disease in a Pennsylvania Amish population. Preliminary data have suggested that this null mutation APOC3 R19X (rs76353203) is rare in the general population. To better describe the frequency and lipid profile in the general population, we as part of the Population Architecture using Genomics and Epidemiology I Study and the Epidemiological Architecture for Genes Linked to Environment Study genotyped rs76353203 in 1113 Amish participants from Ohio and Indiana and 19 613 participants from the National Health and Nutrition Examination Surveys (NHANES III, 1999 to 2002, and 2007 to 2008). We found no carriers among the Ohio and Indiana Amish. Of the 19 613 NHANES participants, we identified 31 participants carrying the 19X allele, for an overall allele frequency of 0.08%. Among fasting adults, the 19X allele was associated with lower triglycerides (n=7603; β=-71.20; P=0.007) and higher high-density lipoprotein cholesterol (n=8891; β=15.65; P=0.0002) and, although not significant, lower low-density lipoprotein cholesterol (n=6502; β= -4.85; P=0.68) after adjustment for age, sex, and race/ethnicity. On average, 19X allele participants had approximately half the triglyceride levels (geometric means, 51.3 to 69.7 versus 134.6 to 141.3 mg/dL), >20% higher high-density lipoprotein cholesterol levels (geometric means, 56.8 to 74.4 versus 50.38 to 53.36 mg/dL), and lower low-density lipoprotein cholesterol levels (geometric means, 104.5 to 128.6 versus 116.1 to 125.7 mg/dL) compared with noncarrier participants. These data demonstrate that APOC3 19X exists in the general US population in multiple racial/ethnic groups and is associated with cardio-protective lipid profiles

Related results for PheWAS.

<p>This is a plot of SNP-phenotype associations observed in both NHANES III and Continuous NHANES with p-value <0.01, for SNPs with an allele frequency >0.01, and a sample size >200, for the same race-ethnicity, phenotype-class, and direction of effect. Plotted are results where the significant SNP-phenotype association is closely related to the phenotype of a previously reported SNP-Phenotype association. The first column indicates the chromosome and bp location of the SNP. The second column indicates the SNP ID, the associated phenotype-class, the self-reported race-ethnicity (NHW  =  Non-Hispanic Whites, NHB  =  Non-Hispanic Blacks, or MA  =  Mexican Americans), and the coded-allele. The next column contains a colored box if association results were available for natural log transformed Continuous NHANES phenotypes (Continuous NHANES ln+1), un-transformed Continuous NHANES phenotypes, NHANES III untransformed phenotypes (NHANES III), or transformed NHANES III phenotypes (NHANES III ln+1) (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004678#s4" target="_blank">methods</a> for more details on phenotype transformation). The next column indicates the p-value for each association, and the triangle direction indicates whether the association had a positive (triangle pointed to the left) or negative direction of effect (triangle pointed to the right). The following columns indicate magnitude of the effect (beta), the coded allele frequency (CAF), and the sample size for the association.</p

Novel results.

<p>Novel PheWAS results with the same SNP, phenotype class, and race-ethnicity across NHANES, ordered by these variables. Information on the closest gene and previously reported phenotypes from the PAGE network and GWAS Catalog (with PubMed ID) are included for each SNP. Long phenotype description, along with the corresponding p-value, beta (SE  =  standard error), coded allele frequency (CAF), and sample size for the association are also listed. Significant measures from NHANES III and Continuous NHANES are included, and NHANES Combined was also included when the phenotype was harmonized across both surveys.</p><p>Phenotypes correlated with r>0.6 with any of the significant traits, in either NHANES III or Continuous NHANES for the race/ethnicity of significant PheWAS result.</p><p>Novel results.</p

Overview of the approach for this study.

<p>Genotypic and phenotypic data were collected in NHANES III and Continuous NHANES. The phenotypes for the two studies were matched into phenotype classes. Comprehensive associations were calculated for the genotypes and phenotypes for each survey independently. The results that were found in both surveys, with p<0.01, for the same phenotype-class, and race-ethnicity, and same direction of effect, were maintained for further inspection in this study.</p