The
Genetics Rare Variants Workflow
process runs a
workflow
for performing
association
testing on both common and rare variants, automatically coding rare variants according to a dominant
model
, and optionally combining rare variants within a gene or other defined set of
SNPs
into a single
locus
. Association tests can then be performed on each single locus, or combined tests can be performed on all common and rare variants within a gene or SNP set. Both the Combined Multivariate and Collapsing (CMC) method described by Li and Leal (2008) and the Rare Variant Test 2 (RVT2) described by Morris and Zeggini (2009) can be implemented using this workflow.
For
binary
or
continuous traits
, the
Sequence Kernel Association Test (SKAT)
is also an option.
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1
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2
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Recode Genotypes
, to code common variants using numbers representing an additive model and rare variants using numbers representing a dominant model, optionally combining rare variants within a gene together,
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and several processes for performing association testing of
SNPs
with the
trait
variables specified:
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3
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Case-Control Association
, to perform Pearson
chi-square
and Fisher's exact test on the numeric
genotypes
,
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4
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5
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Multiple SNP-Trait Association
, to combine rare and common variants within a gene into either a single regression model, a
radial basis machine
, or for
Hotelling's T-squared test
when the trait is binary.
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One wide-formatted input SAS data set that contains all of the marker data is
required
to run the
Genetic Rare Variants Workflow
process. This data set must be formatted like those using the
Affymetrix SNP CHP Input Engine
or
Illumina SNP Input Engine
:
marker variables
contain “
/
”
-delimited genotypes (such as
A/A
,
A/B
).
The
morocco_snps1exp.sas7bdat
data set represents the data from a study of gene
expression
variation and SNP associations in southern Morocco (Idaghdour, Czika,
et al
., 2010), and serves as an example.
(Note: The data was modified slightly to preserve anonymity of subjects.)
It lists genotype data at 4746 SNPs in 193 individuals. Marker data is presented in the one-column format. This data set is partially shown below. Note that this is a wide data set; markers are listed in columns, whereas individuals are listed in rows.
A second,
optional
, data set is the
Annotation Data Set
. This data set contains information such as gene identity or chromosomal location, for each of the markers. The
morocco_anno.sas7bdat
annotation data set
serves as an example. It identifies markers, location, and gene identities. A portion of this data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.
Note
: The top-to-bottom order of the rows in the annotation data set matches the left-to-right order of the columns in the input data set. This correspondence is required for markers to be matched appropriately.
Both the
morocco_snps1exp.sas7bdat
data set and the
morocco_anno.sas7bdat
annotation data set
are located in the
Sample Data\Genetics
directory included with JMP Genomics.
For detailed information about the files and data sets used or created by JMP Life Sciences software, see
Files and Data Sets
.
When you click
, the
Genetics Rare Variants Workflow
process begins by opening the
Workflow Builder
. The
Workflow Builder
builds a
settings file
for each process, containing the information from the data sets and parameters specified in the
Genetics Rare Variants Workflow
dialog
. Once the setting files are generated and saved, the individual processes in the workflow are sequentially opened, populated, and run. The results of the processes are saved in the specified output folder. Finally, a JMP
journal
, providing links to the workflow dialog and the results of each process, is generated.
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Click
.
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The
Workflow Builder
dialog shows the settings for each of the processes in the workflow. You can select and edit individual settings to adjust your analysis.
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Clicking each of the
buttons on the journal brings up the output of each of the processes. This enables you to examine each set of output so that adjustments can be made to the individual settings, as needed. For your convenience, links to the default
Genetics Rare Variants Workflow
processes are given below.
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