HelixTree provides a graphical user interface (GUI) to the capabilities of the PBAT program, as well as the ability to import from and export to FBAT/PBAT-format and csv-format pedigree and phenotype files. PBAT genotypic data-analysis capabilities are specifically supported by HelixTree using pedigree and phenotype spreadsheets within a HelixTree project. PBAT CNV data-analysis capabilities are supported by HelixTree by reading a LOG2 ratio DSF file and using a matching pedigree spreadsheet to give the pedigree information and, if applicable, a phenotype spreadsheet. The PBAT capability is now current to PBAT version 3.5, with some features from PBAT version 3.6.

As mentioned above, PBAT tools support two scenarios–Pre-study and Post-study. In the Pre-study scenario, you can use the HelixTree PBAT capabilities for power calculations 23.3 to plan family-based association studies for virtually any given study design and ascertainment conditions.

You may assess the power of the family-based association test (FBAT) statistic on a given study plan to decide whether it has sufficient power. Alternatively, HelixTree allows you to easily (and repeatedly) change the family design, the ascertainment conditions, the underlying genetic model (see 23.6) or the mode of inheritance to find what parameters will give the study the best possible power.

For the Post-study scenario, the HelixTree PBAT analysis tools for genotypic data 23.4 provide many useful capabilities for the statistical analysis of family-based genotypic association studies, e.g. simple FBAT or CNV FBAT statistics, multivariate FBAT-statistics (FBAT-GEE and FBAT-PC for genotypic or CNV), FBAT-statistics for time-to-onset data, power estimations for the actually-observed data sets, options to test linkage or association in the presence of linkage, options to use (bi-allelic or multi allelic) marker or haplotype data, single or multiple traits (either separate traits or measurements recorded repeatedly over time) that may be quantitative, qualitative or time to onset, with nuclear families as well as extended pedigrees. Covariates (see 23.6) and gene/covariate interactions in all computed FBAT statistics can be easily handled.

Statistical test results are returned in HelixTree spreadsheets. These spreadsheets allow you to find the most powerful test statistic and to reduce the large pool of traits and markers down to the most promising combinations in terms of the FBAT statistic.

(Please note that there is a glossary 23.6 of terms related to family-based analysis at the end of this chapter.)