Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis
© Pendergrass et al; licensee BioMed Central Ltd. 2010
Received: 30 July 2010
Accepted: 16 December 2010
Published: 16 December 2010
Initial genome-wide association study (GWAS) discoveries are being further explored through the use of large cohorts across multiple and diverse populations involving meta-analyses within large consortia and networks. Many of the additional studies characterize less than 100 single nucleotide polymorphisms (SNPs), often include multiple and correlated phenotypic measurements, and can include data from multiple-sites, multiple-studies, as well as multiple race/ethnicities. New approaches for visualizing resultant data are necessary in order to fully interpret results and obtain a broad view of the trends between DNA variation and phenotypes, as well as provide information on specific SNP and phenotype relationships.
The Synthesis-View software tool was designed to visually synthesize the results of the aforementioned types of studies. Presented herein are multiple examples of the ways Synthesis-View can be used to report results from association studies of DNA variation and phenotypes, including the visual integration of p-values or other metrics of significance, allele frequencies, sample sizes, effect size, and direction of effect.
To truly allow a user to visually integrate multiple pieces of information typical of a genetic association study, innovative views are needed to integrate multiple pieces of information. As a result, we have created "Synthesis-View" software for the visualization of genotype-phenotype association data in multiple cohorts. Synthesis-View is freely available for non-commercial research institutions, for full details see https://chgr.mc.vanderbilt.edu/synthesisview.
Significant GWAS findings are being further investigated for replication and characterization, both in the populations in which the initial GWAS findings were discovered (such as European-Americans) as well as in new cohorts and populations. To increase power, meta-analysis is often used to combine results from multiple research sites. Multiple independent and correlated phenotypic measurements may be included in these analyses, such as measurements of cardiovascular disease and related biomarkers (lipids, inflammation, etc). Many of these studies characterize less than 100 SNPs. Visualization of these data an integral part of interpreting as well as sharing the complex and multi-layered results of these follow-up studies. The software "Synthesis-View" has been developed to visually synthesize multiple pieces of information of interest from these studies with the flexibility to perform multiple types of data comparisons.
Synthesis-View was extended from the previous software "LD-Plus" which also uses a flexible data display format of multiple data "tracks" that can be viewed . Within Synthesis-View, through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, is plotted according to user preference. Through these data visualizations, rapid comparisons of multiple forms of information are possible, not easily achievable through reviewing results in tabular form alone.
Synthesis-View plotting options
Title for Synthesis-View plot
Produce a plot with larger sized text than the default
If set to "maximum", axes limits will start and end utilizing the range of the data with tick-marks at regular intervals in-between. If set to "cleaner" the axes will still encompass the range of the data, however the range will begin and end with a multiple of five or ten, and the plot tick-marks will also be a multiple of five or ten.
Additional SNP locations
SNP location information in addition to chromosomal location range.
Offset overlapping points
When points overlap, this setting will include "jitter", whereby overlapping points are offset horizontally to make them more distinguishable.
Phenotype summary plot name
If phenotypic summary data will be incorporated into the Synthesis-View plot, the title for the phenotype summary plot should be specified here.
Include p-value plot
Include plot of p-values
Plot p-values as circles
To plot p-values as circles, instead of triangles that include direction of effect, even if direction of effect information is supplied in the Synthesis-View standard input file.
Draw line at this p-value
Specification of a horizontal red line at a specific p-value of interest.
Maximum y-axis setting for p-value track
Specify the maximum y-axis value for the p-value track in order to limit the range of the y-axis. Any p-value result more significant than this y-axis cutoff value will be plotted at the cutoff value in larger size.
Set points as "diamond shape" for one specific group/substudy
Produce forest plot
To produce a forest plot in Synthesis-View from odds-ratio results
Minimum forest plot x-axis at zero
To set the minimum value of the forest plot x-axis to zero
Plot case/control totals
The total numbers of cases/controls can be plotted either in two separate tracks ("split plot"), or in one track where the total numbers of cases/controls are indicated using open/closed circles ("combined plot").
Plot case/control CAF
The respective coded allele frequency (CAF) for cases/controls can be plotted either as two separate tracks ("split plot"), or in one track where cases/controls are indicated using open/closed circles ("combined plot").
Plot significant odds ratio larger
Plot significant odds-ratio results in larger size
Draw legend for forest plot
Include direction of effect track
Even if direction of effect information is supplied, this setting allows for inclusion/exclusion of a direction of effect track.
Choice of effect size label
Linkage disequilibrium D-prime plot
If linkage disequilibrium information is included as an input file, select this to include a d-prime correlation track.
Linkage disequilibrium R-squared plot
If linkage disequilibrium information is included as an input file, select this to include an R-squared correlation track.
High resolution image (300 dpi)
Select to produce a 300 dpi image, otherwise the image is 72 dpi
Choices of image format include PNG, JPEG, and TIFF
Output file name
Choice of file name for output Synthesis-View plot
One file is necessary to produce a standard Synthesis-View plot. This file contains a column for SNP identification (such as rs number), a column with the corresponding chromosome for each SNP, and a column for SNP genomic location. The rest of the optional information will result in data tracks plotted if data are present, and can include p-values, odds ratios, allele frequencies, and sample size. If additional files are supplied, additional tracks are created including phenotypic summary information for continuous phenotypes, gene summary information, and linkage disequilibrium (LD) data plotted in Haploview style  format as D' or r2.
Availability and requirements
Project name: Synthesis-View
Project home page: http://chgr.mc.vanderbilt.edu/ritchielab/synthesisview
Operating systems(s): Linux, Mac OS X, Windows
Programming language: Ruby
Other requirements: RMagick
License: GNU General Public License
Any restrictions to use by non-academics:
The use of Synthesis-View is restricted to academic and non-profit users
Results and Discussion
Example Standard Output Plot
Physical genome track. Synthesis-View provides information on the relative location of the SNP on a given chromosome and how that position relates to other SNPs in the same study. Lines lead from the chromosome locations to the IDs of each SNP. If the "Additional SNP locations" option is selected, the location of the SNPs within the chromosomal region are indicated. If SNPs are close together, the location of the first SNP in that group is indicated in the plot (to prevent text overlap). When the plot is first generated, an image of the plot is shown within the web browser that includes embedded links. If the results for a SNP are selected within this image, the NCBI SNP database page for that specific SNP is opened in the default web browser of the user.
(2) SNP presence/absence track. Not all SNPs may be available for all associations across study groups or populations. Thus, this track provides information on whether a SNP was used in the test of associations through the presence/absence of a colored box corresponding to the group, study, or phenotype.
Effect size track. The resultant effect size values (beta values here) are plotted. This track allows you to view the similar effect sizes across race/ethnicity in Figure 2. To omit the effect size plot, omit effect size information from the input file.
Coded allele frequency track. The coded allele frequency (CAF), the allele chosen by the user to compare across groups or studies, is optionally plotted so trends and differences in the data can be observed.
Sample size track. Optional plotting of the sample size for each genotype-phenotype association for each group/study/phenotype is available so the relationships between sample size and other results of the study can be explored. To plot without sample size, omit sample size information columns from the input file. If sample size is provided only as entire group summary information, rather than for individual SNP/phenotype regressions, a separate box will appear at the bottom of the plot with this summary information graphically represented.
Phenotype summary plot. Summary information for a single phenotype across several groups is plotted if a separate file of phenotype summary information is included. This is currently a feature for quantitative traits/continuous data. Future versions will incorporate methods to characterize categorical/case-control phenotype summary information.
Other Options for Standard Output Plot
Forest Plot/Odds Ratio options in Synthesis-View
The first track, like with the standard Synthesis-View plot, is a physical genome track, displaying the chromosome and relative location of each SNP used in the association tests.
The next track is an optional significance track, displaying the p-values. A single color represents each group. In this case, a red line has been placed at a p-value of 0.05.
The next three tracks are odds ratio/forest plot tracks. Squares represent the OR point estimate, with lines representing the upper and lower 95% confidence intervals. Here the similarity of the results between Stage 1 and Stage 2 are visible. An additional option, not shown, is available. If a result is significant (the upper or lower boundary of the confidence intervals does not cross 1.0), the square can be plotted in larger size, allowing for quick visual identification of significant results in forest plots with a large number of results.
The second to last track is the CAF track. Colors match those of the groups of the previous tracks, allowing the user to identify trends in allele frequencies between groups which can aid in interpreting replication of results. The option of horizontal separation of overlapping points was also used here as the CAF measurements were very similar between the analyses.
The last track is the sample size track. Case/control sample size can either be plotted in separate tracks, or, as shown here with closed circles indicating cases, and open circles indicating controls in the same track. The colors match those of the groups of the previous tracks. This option is also available when the CAF for cases vs. controls are provided.
An alternative way to view OR results is in stacked tracks where the eye moves from top to bottom, in more of the Synthesis-View standard format. If the forest plot option is not chosen in Synthesis-View, the default data plot is in this format. Unlike the forest plots of Figure 8 ORs are plotted as closed circles. When OR results are significant, the OR closed circle is plotted in a larger size, rendering it easy to discriminate significant results visually.
To date, most replication, meta-analysis, and even top GWAS results, are presented in tabular form. There are additional ways to display these results. We developed and describe here a visualization tool for studies that have data for less than 100 SNPs, which is typical for a targeted genotyping study using thousands to tens of thousands of samples. We emphasize that Synthesis-View is especially effective when data are being investigated across phenotypes, studies, and multiple race/ethnicities. Through visually incorporating results, details of individual SNP-phenotype relationships as well as larger trends in the interplay between information such as SNP location, sample size, data stratification, and allele frequencies can be viewed.
We would like to acknowledge the following individuals for their suggestions and ideas in designing Synthesis-View: Matthew Thomas Oetjens, Janina Jeff, Logan Dumitrescu, Fredrick Schumacher, Chris Haiman. This work was funded in part by the following grants: LM010040 and HG004798.
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