When SNP
genotypes
are imputed, genotypes are called with a degree of uncertainty.

Imputed SNP-Trait Association
tests for

association
between various types of

traits
and each individual

SNP
taking into account the probabilities for observing each possible genotype.

Two types of analyses can be performed: a general test based on the probabilities of each SNP genotype or a
regression
testing for a linear trend of SNP

alleles
. Adjustments can be made for quantitative

covariates
and

random effects
or for some trait types,

strata variables
.

P-values
from these tests, with adjustments applied if requested, are plotted along the marker map.

Please refer to the
MIXED
,

GLIMMIX
,

LOGISTIC
, and

PHREG
procedures in the SAS/STAT User's Guide for more information.

One
Input Data Set
, containing all of the marker data and genotypic probabilities, is required for this process.
The

Imputed SNP-Trait Association
process differs from other Genetic Association processes in that the input data set used in this process must be in the stacked format, where there is a row for each SNP/individual combination, as created for example by the

Imputed SNP
input engines. The data set should be sorted by SNP.

The
sample_igp.sas7bdat
data set, shown below, was generated using the

Imputed SNP (Wide Format)
input engine, as described (

Imputed SNP (Wide Format) Input Engine
).

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. This data set is a tall data set; each row corresponds to a different marker.