Example phenotype-classes and binned subphenotypes within phenotype-classes.

<p>Presented below are examples of phenotypes binned into three phenotype classes, “Asthma”, “BMI”, and “CRP”. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003087#pgen.1003087.s002" target="_blank">Table S2</a> contains the complete list of matched phenotypes across studies within phenotype-classes, for all phenotype-classes used within this study.</p

PheWAS associations for rs4420638 near <i>APOC1</i>.

<p>SNP rs4420638 has previously been associated with LDL cholesterol levels, triglycerides, Alzheimer's disease, coronary artery disease, and sporadic late onset Alzheimer's. The length of the lines correspond to –log10(p-value), and the lines are plotted clockwise starting at top for the association with the smallest p-value. Lines are labeled with the study-specific phenotype, the PAGE study, racial/ethnic group, and direction of effect (+ or −). Red lines represent associations at p<0.01. “LN1” indicates the phenotype had 1 added to the variable, and then the variable was natural log transformed. The PheWAS phenotypes significantly associated with this SNP varied, with known associations for LDL cholesterol levels, as well as the related phenotypes “Total cholesterol (mmol/l)” and “Dietary cholesterol (mg)”, and novel phenotypes such as “Baseline glucose (mg/dl)”.</p

Workflow for phenotype matching, to develop the 105 phenotype classes.

<p>A MySQL database was used to filter the data from five studies for any results with p<0.01 to generate lists of the unique phenotypes for each individual PAGE study. The number of phenotypes that passed this significance threshold for each of the four groups was 604 (ARIC), 331 (CHS), 63 (MEC), 324 (EAGLE), 1,342 (WHI). Note that during the binning process, a smaller number of phenotypes are listed in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003087#pgen-1003087-g006" target="_blank">Figure 6</a> than the total number of phenotypes referred to in the manuscript for the actual associations, in the phenotype matching process we only took into account distinct phenotypes regardless of whether or not they were transformed or untransformed or if they were categorical phenotypes binned into case/control phenotypes. Next, resulting phenotypes were then manually matched up between ARIC, CHS, MEC, EAGLE and WHI using and knowledge about the phenotypes and the known focus of specific PAGE study questions (such as arterial measurements including degree of arterial stenosis). In the last step, phenotypes from all studies, regardless of significance from genotype-phenotype tests of association, were matched to the already-defined phenotype classes using the criteria described above.</p

PheWAS Tests of Association: Novel Associations.

<p>Novel associations that met the criteria for PheWAS significance are given here, sorted by the most to least number of PAGE study sites available. Related associations were defined as SNPs significantly associated in this PheWAS with phenotype-classes closely related to phenotypes among known associations. Significance was defined as a test of association with p<0.01 observed in two or more PAGE studies for the same SNP, phenotype class, and race/ethnicity and consistent direction of effect when relevant. For each, the nearest gene(s), the SNP rs number, coded allele (CA) and frequency (CAF), associated phenotypes, phenotype-class, race/ethnicity, p-values, genetic effect/beta values (standard error; SE), sample sizes, substudies, number of substudies with results passing our p-value cutoff, the previously associated phenotype for that SNP, and references for the previously associated phenotypes are given.</p>1<p>Coded Allele.</p>2<p>Coded allele frequency.</p>3<p>Associated phenotypes.</p>4<p>Phenotype-class.</p>5<p>Race/ethnicity for association, abbreviations: African American (AA), European American (EA), Mexican American/Hispanic (H).</p>6<p>P-Values of results that passed p = 0.01 threshold in order of the associated phenotypes.</p>7<p>Beta and standard error in order of the associated phenotypes.</p>8<p>Sample size in order of the associated phenotypes.</p>9<p>Studies with the significant result, in order of the associated phenotypes.</p>10<p>Total number of studies with at least one result passing p-value threshold for specific phenotype class and SNP.</p>11<p>Previously reported associated phenotypes for the SNP.</p>12<p>Pubmed ID's for previously associated phenotypes.</p

PheWAS Tests of Association: Related Associations.

<p>Related associations that met the criteria for PheWAS significance are given here, sorted by the number of PAGE site replications for a given phenotype-class. Related associations were defined as SNPs significantly associated in this PheWAS with phenotype-classes closely related to phenotypes among known associations. Significance was defined as a test of association with p<0.01 observed in two or more PAGE studies for the same SNP, phenotype-class, and race/ethnicity and consistent direction of effect when relevant. For each, the nearest gene(s), the SNP rs number, coded allele (CA) and frequency (CAF), associated phenotypes, phenotype-class, race/ethnicity, p-values, genetic effect/beta values (standard error; SE), sample sizes, substudies, number of substudies with results passing our p-value cutoff, the previously associated phenotype for that SNP, and references for the previously associated phenotypes are given.</p>1<p>Coded Allele.</p>2<p>Coded allele frequency.</p>3<p>Associated phenotypes for individual results.</p>4<p>Phenotype-class.</p>5<p>Race/ethnicity for association, abbreviations: African American (AA), European American (EA), Mexican American/Hispanic (H).</p>6<p>P-Values of results that passed p = 0.01 threshold in order of the associated phenotypes.</p>7<p>Beta and standard error in order of the associated phenotypes.</p>8<p>Sample size in order of the associated phenotypes.</p>9<p>Studies with the significant result, in order of the associated phenotypes.</p>10<p>Total number of studies with at least one result passing p-value threshold for specific phenotype-class and SNP.</p>11<p>Previously reported associated phenotypes for SNP.</p>12<p>Pubmed ID's for previously associated phenotypes.</p

The number of SNP–Phenotype tests of association for phenotype-classes varies by PAGE study site genotype and phenotype overlap.

1<p>Number of PAGE study sites where both the SNP and phenotype were available for a given phenotype class.</p>2<p>Total number of tests of association, by number of PAGE study sites, where both the SNP and phenotype were available for a given phenotype class.</p>3<p>Number of tests of association that was significant (p<0.01) for two or more PAGE study sites for a single phenotype class and SNP, taking into account matching direction of effect when phenotypically relevant.</p>*<p>Three results where two or more of the groups had a SNP–phenotype association p<0.01 for a single phenotype class across 5 groups represented. The most replicated novel results across studies were for SNPs rs599839, rs10923931, and rs2228145 with hematologic traits.</p

Study Descriptions.

<p>Abbreviations: European American (EA), African American (AA), Hispanic/Mexican American (H), Asian/Pacific Islander (API).</p>1<p>Data from PAGE studies available for this PheWAS include: Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS), Epidemiologic Architecture for Genes Linked to Environment (EAGLE), Multiethnic Cohort (MEC), and Women's Health Initiative (WHI). PAGE study sites and study design descriptions are in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003087#pgen.1003087.s005" target="_blank">Text S1</a>.</p>2<p>Pubmed ID of study description manuscript for each study.</p>3<p>Maximum sample size and Minimum sample size are dependent both on who was genotyped and who had a specific phenotype measured. Not all phenotypic measurements were available for all participants within each study.</p>4<p>This is the total number of SNPs available for each study. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003087#pgen.1003087.s001" target="_blank">Table S1</a> has the list of these SNPs for each study, genotyped across two or more studies.</p>5<p>This includes the number of phenotypes transformed and untransformed, as well as categorical phenotypes divided into binary phenotypes, full description in Materials and Methods.</p>6<p>Total number of tests of association calculated for each study, in parenthesis is the total number of associations with p<0.01.</p

PheWAS associations for rs2144300 within <i>GALNT2</i>.

<p>The previously published associations for this SNP were with triglyceride and HDL cholesterol levels. Genotype-phenotype associations are plotted clockwise starting at top for the association with the smallest p-value. The length of the line corresponds to –log10(p-value), the longer the line the more significant the result. The study race/ethnicity/and phenotype for each tests of association are listed. Red lines represent associations at p<0.01, and results with p<0.05 are also plotted in grey to show trends for additional phenotypes. The novel PheWAS phenotypes significantly associated with this SNP varied, including white blood cell counts, forced vital capacity at three seconds (FEV3), and serum calcium levels.</p

PheWAS results for blood cell counts and hemoglobin levels.

<p>Eleven novel genotype-phenotype-class associations were identified for white blood cell counts and hemoglobin levels collectively. The top track indicates the chromosomal location of each SNP, below that track is a SNP/Phenotype identification track containing the SNP ID, as well as the phenotype, phenotype transformation if present (LN1 = ln(1+variable)), and the race-ethnicity for the test population (AA or EA). The next track is a “presence/absence” track, box presence indicates if the SNP was present for ARIC (blue), CHS (red), WHI (orange), or EAGLE (purple). The next tracks are as follows: –log10(p-value), where the each p-value is plotted, the direction of the triangle indicates the direction of effect (triangle pointed up is positive, triangle pointed down is negative), base of the triangle corresponds to the location of the p-value, solid red line is positioned at p-value = 0.01; The next track is magnitude of effect (beta) dotted grey line is positioned at the null; Next are coded allele frequencies (CAF) for each study; Final track is sample size for each test of association.</p

Additional file 2: of Genetic architecture of lipid traits in the Hispanic community health study/study of Latinos

Supplementary Figures. (DOCX 112 kb