Golden Helix PBAT

Cutting-edge tools for family-based association studies

Golden Helix PBAT is an advanced statistical package for the design and analysis of family-based SNP and copy number variation (CNV) association studies. In addition to its extensive array of analysis methods, PBAT is acclaimed for its ability to overcome the multiple testing problem in whole genome association studies using cutting-edge screening methods.

Golden Helix PBAT is developed in collaboration with Dr. Christoph Lange of the Harvard School of Public Health.

  • What's New
  • Overview
  • Getting Started

New Analysis Capabilities Make PBAT more Powerful and Comprehensive

Family-Based Copy Number Association Analysis
PBAT now supports the testing for copy-number variation (CNV) in a family-based setting as discussed in [Ionita-Laza 2008]. In conjunction with the Copy Number Analysis Module (CNAM), you can quickly:

  • Normalize copy number intensity data
  • Correct for batch effects using Eigenstrat-based PCA
  • Filter out "poor quality" markers
  • Join log2 ratios with pedigree/phenotype information
  • Perform whole genome association tests

All robustness properties of the FBAT approach are maintained as in PBAT for SNP analysis. In addition, all previously-developed FBAT extensions, including FBATs for time-to-onset, multivariate FBATs, and FBAT-testing strategies, can be directly transferred to the analysis of copy number variations.
›› Learn more about PBAT & Copy Number Variation

 PBAT CNV Webinar

View PBAT Copy Number Overview

Faster Extended Pedigree Analysis
A new optional algorithm is available that can make PBAT 10-100 times faster than the original implementation when analyzing large extended pedigrees. It can be applied to SNP, haplotype and copy number analysis.

See the following knowledge base article for more information:

Golden Helix PBAT Helps to Find a Whole Genome Age-Dependent Association between SNP rs1455832 and obesity

American Journal of Human GeneticsIn a recent whole genome association study using the Affymetrix
100K scan of the Framingham Heart Study (FHS), Dr. Jessica
Lasky-Su et al used Golden Helix PBAT to find an age-dependent
association between SNP rs1455832 and obesity. The finding was
replicated in five of eight followup studies.

The paper titled On the Replication of Genetic Association: Timing Can Be Everything was published in the April 11, 2008 edition of American Journal of Human Genetics.
›› Read the abstract

What is Golden Helix PBAT?

Golden Helix PBAT provides tools for the design and analysis of family-based SNP and copy number association studies. It incorporates virtually all functionality of the family-based association tests (FBAT) package, but also provides additional options for designing association/linkage studies, analyzing data with multiple continuous traits, and screening for the most "promising" combinations of markers and phenotypes.

 

Explore Further

Get Started Accelerating Your Quest for Significance!

The following resources are available to help you get started:

A more complete copy number association workflow

The following processing, analysis, and quality control measures have
been added recently to make the copy number association workflow more complete:

  • Download Free Trial
  • Whole Genome Association Tutorial
  • Documentation
  • Tutorials and Webinars