The
Haseman-Elston Regression
process tests for
linkage
between genetic markers and a quantitative or
binary trait locus
. Since the original Haseman-Elston approach was introduced (1972), modifications have been proposed to increase its
power
, as discussed by Wang and Elston (2004). These methods use sibling pairs and regress a function of the quantitative
trait
values for the individuals that the pair comprises on the average
allele
-sharing IBD (pi) and the probability of sharing 2 alleles IBD at the markers of interest (z2). When non-independent sib-pairs are included in the sample, a GEE approach is used to account for the
covariance
among pairs from the same family.
The
Haseman-Elston Regression
process is not applied to genetic marker data as are the other JMP Genetic processes. Instead, this
process
analyzes data containing information about the probabilities of pairs of individuals sharing alleles that are
identical-by-descent
(IBD) at the markers of interest. The required input IBD data set must contain one row for each pair of related individuals being analyzed at each marker, with
variables
z0
,
z1
, and
z2
representing the probability of the two individuals in the pair sharing 0, 1, or 2 alleles IBD, respectively. All possible pairwise comparisons within each family should be made. Variables for the
pedigree
or family, the two individual IDs, and the marker are also required in this data set. Pairs of individuals should be grouped by marker rather than by pedigree or family before carrying out these processes.
Two data sets are required to run this process. The first, the
identical by descent (IBD) data set
, contains the marker ID,
pedigree ID, and the IBD probabilities
.
This data set must contain the following variables: a marker ID, a pedigree ID, and the IBD probabilities in columns z0, z1, and z2.The
asp_ibd.sas7bdat
IBD data set is shown below. Note that the required columns are present in this data set.
The second required data set, the
pedigree data set, must contain the pedigree identifiers as well as the
phenotype
information including the quantitative trait being mapped and any
covariates
. The
asp_ped.sas7bdat
pedigree data set is shown below. Individuals in this data set must be listed before their offspring.
A third, 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
annotation data set
used in this example, the
asp_map.sas7bdat
data set, was computer generated and identifies each of the 20 markers in the IBD data set and their locations. This data set is illustrated below. This data set is a tall data set; each row corresponds to a different marker.
The sample data used in the following example is the computer-generated affected sib-pair (ASP) data provided by Gonçalo Abecasis (University of Michigan Center for Statistical Genetics) and is described in
Data Sets Used in JMP Genomics Processes
. This data consists of three associated data sets:
|
2
|
a pedigree data set that lists the family relationships, affected status, and marker
genotypes
for each of the 800 individuals (4 per family) in the data set, and
|
Note
: If you are curious about chromosome 24, recall that these are fictitious data.
All three data sets are included in the
Sample Data
folder that comes 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
.
The output generated by this process is summarized in a Tabbed report. Refer to the
Haseman-Elston Regression
output documentation for detailed descriptions and guides to interpreting your results.