16. Mapping and Characterizing QTL: Outbred Populations
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A correction and a new study concerning
Measures of Informativeness (Pages 492-495). Dr. Yang Da (Department of Veterinary Pathobiology, University of Minnesota) has suggested that parts of our discussion of PIC may not be technically correct.
An extended dicussion of the definition of PIC can be found in
Da, Y. and H.A. Lewin. (1995) Linkage information content and efficiency of fullsib and halfsib designs for gene mapping.
Theoretical and Applied Genetics. 90:699-706.
The Journal of Quantitative Trait Loci (JQTL),, an electronic journal sponsored by the Crop Science Society of America
Identifying And Incorporating Genetic Markers And Major Genes In Animal
Breeding Programs by Brian Kinghorn and Julius van der Werf (pdf file). Notes from a course given in Belo Horizonte (Brazil)
31 May to 5 June 2000.
WWW pages of interest
- There are a huge number of programs for human linkage/association analysis. See the
Bult sites listed above.
QTL Express -- Web-based user-friendly QTL mapping software from Chris Haley,
Mike Kearsey, Sara Knott, George Seaton, and Peter Visscher,
web-based package for QTL analysis using regression interval mapping
techniques. QTL Express currently supports analyses of F2 data from crosses
between inbred or outbred lines, and data from outbred half-sib
populations. Modules allowing analysis of other data-structures and
further enhancements will be added in due course.
Special features include,
- Error checking
- Help files
- Example data files
- Marker segregation distortion test
- Inclusion of fixed effects / covariates
- Permutation tests to set significance thresholds
- Bootstrapping to determine confidence intervals
- Single and linked QTL models
- Hongzhe Li's (UC Davis)
Survival analysis programs (allows for age of onset corrections, etc.)
- List of Pedigree Drawing Programs
PediPet, a small program for assisting the researcher when analyzing genetic data from Claus Thorn Ekstrom. Performs:
- allele frequency estimation at a given marker for general pedigrees by maximum likelihood
- Haseman-Elston regressions (single and multipoint)
- Variance components (single and multipoint)
Statistical Analysis for Genetic Epidemiology (S.A.G.E.) is a software package containing more than 20 programs for use in genetic analysis of
family and pedigree data. The software is available for several platforms.
Here are some of the programs:
AGEON : Estimates the Distribution of Age-of-Onset - in the presence of non-susceptible persons. This information can be used in SIBPAL.
- ASSOC: Marker-Trait Association - allows for estimating and testing the association between a quantitative trait and a genetic marker in pedigree data.
- BCROSS: Genetic Hypothesis Testing from Data on Inbred Strains, their F1 and Backcross(es) - test one locus, two-locus and polygenic hypotheses for quantitative data.
- CLUSTR: Power Transformation to Obtain Normality and Homoscedasticity from Clustered Data - can be used to obtain an appropriate transformation for data that are to undergo analysis with BCROSS.
- DESPAIR: Design of linkage studies that are based on affected pairs of relatives - determines the optimal two-stage study design for such studies.
- FCOR : Familial Correlations - estimates familial correlations for all types of relatives up to third degree, including cross-correlations for up to five traits.
- FSP: Family Structure Program - used to check pedigree data for common structural errors as well as consanguineous
matings and loops,
- LODLINK: Lod Score Linkage Analysis - which performs two-point linkage analysis between a trait and each of a set of markers.
- MAPLOC: Mapping a Disease-Related Trait Relative to a Set of Linked Markers - assumes a fixed map for a set of markers to
find the best relative position for a trait locus.
- REGC, REGD, REGTL,
REGTN: Segregation Analysis Programs - reforms analyses based on regressive models. Information from these programs can
be further processed by LODLINK.
- RELATE : Relationship to Proband - determines, for single proband pedigrees, the relationship of each individual in the
pedigree to the proband.
- RELPAL: Relative Pair Linkage Analysis - which screens for genetic linkage of a continuous trait to markers on the basis of
relative pair relationships.
- SIBPAL : Sib-Pair Linkage Analysis - which screens for genetic linkage on the basis of sib-pair relationships. It can also be
used for ordering marker loci.
- TDTEX : Exact Test for Transmission Disequilibrium - implements several asymptotic and exact versions of the transmission
disequilibrium test (TDT).
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Created 25 February 1995, last updated 8 March 2000
Bruce Walsh. firstname.lastname@example.org .