Category » PBAT

There were 22 articles found in this category:

1. Alternative Rapid Extended Pedigree Algorithm
   As of SVS version 6.3, Golden Helix PBAT includes an option when doing family-based SNP analysis to use a new Alternative Rapid Extended Pedigree Algorithm (available under the Phenotype and Haplotype Parameters tab). The greatest benefit of this new algorithm is that it's significantly faster ...
2. Why are there negative signed p-values in the PBAT output?
   In Golden Helix SVS 6.3 there is an option under the PBAT Test Statistic and Computational tab to output "signed" p-values for SNP, haplotype and copy number analysis (Figure 1). Choosing this option will provide positive and negative p-values for the pvalue(FBAT) column in the output table. NOT ...
3. Family-Based Association Test Principal Components (FBAT-PC)
   This definition of FBAT-PC is courtesy of Jessica Lasky-Su from the following publication: Lasky-Su J, Faraone SV, Lange C, Biederman J, Tsuang M, Doyle AE, Smoller J, Laird N, Sklar P. Family based association of statistically derived quantitative traits for ADHD reveal an association in DRD4 w ...
4. Does PBAT support repeated measures?
   Yes, PBAT supports repeated measurements. You will notice when running PBAT that in the third tab there is an option for the FBAT-GEE, FBAT-PC, and Logrank options. Logrank is only applicable with time to onset analysis, so ignore that for this situation. It will handle this "under the hood for ...
5. Difference between FBAT-PC and FBAT-GEE
   FBAT-PC and FBAT-GEE are two approaches for handling multiple phenotypes in PBAT. Each has pros and cons depending on your specific situation. FBAT-GEE is a generalized estimation equation and you are running a multivariate test. The biggest benefit to FBAT-GEE is that you can run multiple phen ...
6. Haplotype construction in PBAT
   Based on the observed offspring haplotypes, a possible set of parental haplotypes are constructed. Only those parental haplotypes that are consistent with the offspring haplotypes (for example, if the offspring haplotypes are unphased, only parental haplotypes that produce unphased offspring hap ...
7. Hardy Weinberg Equilibrium (HWE) differences between HelixTree and PBAT
   1. There are two HWE columns in PBAT. The "main" HWE column is for patients only and the other for parents only. HelixTree calculates HWE for all samples (not including deactivated rows.) 2. PBAT uses 2 degrees of freedom and HelixTree only one for its HWE calculations.
8. Can PBAT handle multi-allelic markers?
   No, PBAT will not handle multi-allelic markers. It will allow them to be used, but what it really does is take the first two alleles and just uses those.
9. How does PBAT handle extended pedigrees?
   When extended pedigrees are used in PBAT, the founders are used in the conditional mean model for the screening process. If siblings and other extended families members are genotyped and phenotyped, then they are used in the calculation on the FBAT statistic (i.e. not the screening procedure). I ...
10. Is the format where all founders are missing genotypes a problem?
    In a case in which parental (founder) genotypes are missing, the only way to extract information from that pedigree is if you have multiple offspring. If you have individuals with no siblings and missing parental genotypes, that patient should be coded as a founder (don't create dummy parents/f ...
11. When parents/founders are missing, do they contribute to allele frequency estimation/HW tests in the parents/non-founders?
    When founders are missing, they will not contribute to either the allele frequency or HW estimation in allele freq (parents) or HWE (parents) columns. This is why the pvalues were all 1 and allele frequencies were 0 in the parents.
12. How are pedigrees broken up when the number of non-founders is exceeded?
    The pedigrees are broken across generations, starting with the top (the founders) of the pedigree structure. For example, if there are one set of grandparents, three sets of parents, and 9 grandchildren (3 grandchildren per set of parents), the grandparents/parents would be broken into a pedigre ...
13. How does PBAT define and use informative families?
    When using PBAT, the number of informative families depends on genotypic information and what genetic model you are using. PBAT defines an informative family as "Having at least one parent contributing to the variance of the offspring genotype during transmission." This is based on the assumptio ...
14. How does PBAT handle Mendelian errors?
    On a SNP by SNP basis, Mendelian errors are evaluated for each family. If there is a Mendelian error in that family, all genotypes on all family members for that SNP will be removed. Note that PBAT does this "under the hood" and doesn't give the explicit results. We recommend first running the ...
15. Heritability calculations in PBAT
    Heritability is how much of the variance in Y (trait) is explained by the marker. It is the ratio of two variances. The long answer: For example, let Y=BMI (body mass index). The variance of BMI is just each individuals BMI - mean BMI in the group. Next, we introduce the marker and calculate a b ...
16. PBAT - dominant and recessive model give the exact opposite results?
    Suppose that the SNP we are looking at has 2 alleles, A and B Select allele A to model. The following is true: 1. A recessive model is coded as 1 for the homozygous AA genotype and 0 otherwise (i.e. AA = 1, AB, BB = 0) 2. A dominant model is coded as 1 for any genotype that contains an A allel ...
17. PBAT Options: Offsets, Empirical Distributions and Dichotomous Traits
    All FBAT tests in PBAT are an extension of the Transmission Disequilibrium Test (TDT). For the TDT to be run, you can only have perfect trios with a single affected individual - and only a dichotomous outcome. Through the use of offsets and generalizing the TDT, PBAT allows for a much more robus ...
18. Definition of offset
    Definition of Offset The offset is simply a weight that is assigned to each individual depending on his/her disease status - and it is an inverse weight. This means that if you were performing analysis and 10% of your individuals were affected, these 10% would be weighted with a 0.9 in the analy ...
19. Jiang vs. Murphy methods
    No matter what you choose for your empirical distribution (continuous, Jiang, Murphy, etc.) you will get the same P-Value in your results. However, since the conditional power calculations are calculated based on a linear regression, if you choose continuous as your distribution you will only ge ...
20. How PBAT splits extended pedigrees can give disparate analysis results.
    Getting disparate results in PBAT when running the exact same analysis is most likely the result of how PBAT handles extended pedigrees. The “Maximal Number of Non-Founders” parameter and the sorting of the spreadsheet can influence this. PBAT splits up pedigrees if they have a larger number o ...