An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation...

Area of Science:

• Genomics
• Bioinformatics
• Statistical Genetics

Background:

• Affymetrix Axiom SNP arrays are a cost-effective, high-density genotyping solution.
• No public software exists for integrated analysis of hybridization intensities and genotypes on this platform.

Purpose of the Study:

• To develop integrated genomic analysis software for Affymetrix Axiom SNP arrays.
• To enable analysis of allele frequency, allelic imbalance, loss of heterozygosity, and copy number variation.

Main Methods:

• Developed statistical methods for analyzing SNP probe hybridization intensities and genotypes.
• Created a quick circular binary segmentation algorithm for copy number analysis.
• Integrated allele imbalance and LOH/LCSH detection for copy number variation/alteration analysis.

Main Results:

• The developed allele frequency adjustment method improved estimation accuracy.
• The segmentation algorithm reduced computation time by 30-67%.
• The integrated CNV/CNA detection showed promising true positive and controlled false positive rates, validated by qPCR.

Conclusions:

• ALICE software provides a valuable resource for analyzing genomic data from Axiom and other SNP arrays.
• Genomic reference databases are available for download alongside the software.