statistical analysis system procedures haplotype, mixed and  (SAS institute)

Journal:

Article Title: The long (and winding) road to gene discovery for canine hip dysplasia

doi: 10.1016/j.tvjl.2009.02.008

Figure Lengend Snippet: Association tests between the Norberg angle and 40 simulated single nucleotide polymorphism (SNP) markers spaced 2 cM apart across an 80 centimorgan (cM) length chromosome. The strength of association was measured as the log (1/probability [P]) on the Y-axis for each individual SNP genotype and the haplotype of two adjacent markers. The haplotype model considers the contribution of flanking marker genotypes beginning with the two markers flanking the quantitative trait locus (QTL) and eventually including the haplotype over multiple markers. Advantages of haplotype analysis are that interactions among QTLs are revealed and the power of detection for QTLs that are not superimposed on markers is increased. The threshold for the level of significance would be determined based on the number of association tests. The simulated QTL was located at 50 cM where the peak is revealed. The additional power to detect the QTL with the flanking haplotypes compared to the single SNP genotype is clear. A centimorgan (cM) is equivalent to a megabase (Mb) over short intervals. The cM is the unit of measurement for a linkage study because cM is a measure of recombination distance. The Mb is the physical genetic distance used in a true association study of unrelated dogs where recombinations are not observed.

Article Snippet: All the analyses were carried out using the Statistical Analysis System (SAS) procedures HAPLOTYPE, MIXED and SAS.

Techniques: Marker

Journal:

Article Title: The long (and winding) road to gene discovery for canine hip dysplasia

doi: 10.1016/j.tvjl.2009.02.008

Figure Lengend Snippet: Distribution of P values under the null hypotheses of no association between the quantitative trait locus (QTL) and the marker genotype. A broken straight diagonal line drawn in black is expected if there is no association with the lowest type I error rate, i.e. calling the presence of a QTL when in fact the null hypothesis of no association holds. The mixed model with the relationship matrix based on markers (Marker) is the closest to the expected relationship. The model excluding background QTLs (Fixed) is the worst relationship. The mixed model with relationship based on the true Cornell pedigrees (Pedigree) is intermediate. All the analyses were carried out using the Statistical Analysis System (SAS) procedures HAPLOTYPE, MIXED and SAS. The SAS procedure HAPLOTYPE was used to estimate the haplotype probability by maximum likelihood using the expectation maximization (EM) algorithm. The procedure MIXED tests for both fixed and random effects (Littell et al., 1996). To make the polygenic effect a correlated random effect, the variance and covariance structure was constructed before using the procedure. A computer program LORG in the form of a SAS macro was developed to facilitate the applications. The macro automatically constructs a SAS dataset that defines the variance and covariance structure of genetically correlated random effects. The SAS dataset can be imported by the SAS procedure MIXED with the option of GDATA or LDATA.

Article Snippet: All the analyses were carried out using the Statistical Analysis System (SAS) procedures HAPLOTYPE, MIXED and SAS.

Techniques: Marker, Construct