Microarray Analysis Software for Population Genomics

Axiom Analysis Suite Software integrates single nucleotide polymorphism (SNP) genotyping, insertion/deletion (indel) detection, multiallele analysis, and off-target variant (OTV) calling of simple and complex genomes as well as copy number detection in an easy-to-use graphical interface.

The software automates Axiom genotyping best-practices workflow to offer accurate results in a single step for export in PLINK, VCF, or TXT formats. Discover and extract copy number information with newly added visualization capabilities.

Improved genotyping, for difficult markers in multiplate batches.

Recent updates include:

• Improved automated SNP quality control checks as well as enhancements to usability and reporting of results
• Tools and visualizations needed to perform copy number variation (CNV) analysis in regions with predetermined boundaries (i.e., fixed-region analysis) and across the entire genome (i.e., discovery analysis)
• New workflows for making high-quality copy number reference files that get the best results for CNV analysis. The new workflows are supported for a subset of copy number-enabled Axiom arrays.

Download the latest version of the Axiom Analysis Suite software below and install by following the instructions in the Axiom Analysis Suite User Guide. This version is compatible with Microsoft Windows 10 (64-bit) Professional operating systems and Quad Core 2.83 GHz systems with a recommended 32 GB RAM. In addition, we recommend a minimum of 150 GB of free space on the C drive to run an analysis. The software cannot be used to analyze data from the Genome-Wide Human SNP Array 6.0 or any other legacy Affymetrix genotyping arrays.

Figure 1. (A) Best Practices Copy Number Reference Creation step 1 batch, marking likely copy neutral samples to make a copy number reference. (B) The step 2 batch tests the new copy number reference on same data. Copy neutral samples should have a MedianLog2Ratio centered at 0.

This software package enables analysis of the CEL files upon scan completion of an Axiom array plate on the GeneTitan MC instrument without user intervention.

Upon completion of plate scanning, a notification is sent to the Application Server Core and sample files are automatically uploaded to a designated folder. The Core alerts the Automated Axiom Analysis Software that CEL files are available for analysis. Automated Axiom then runs the analysis based on the default workflow that has been pre-selected for that specific array type. The results are stored in an Axiom Analysis Suite v5.0 or higher batch folder.

This software package enables creation of SNP-specific priors for your custom array. Benefits of utilizing SNP-specific priors are increased data robustness and batch-to-batch reproducibility.  The Axiom Batch SSP Tool uses an analyzed batch of CEL files as input and produces outputs easily incorporated into subsequent analysis batches.

To access the Axiom Batch SSP Tool, contact your microarray Field Application Specialist.

The Annotation Converter software tool enables you to create custom SQLite format annotations (annot.db) for use with Axiom Analysis Suite. You can customize annotations for Thermo Fisher catalog genotyping arrays or generate annotations for Axiom custom genotyping arrays.

The Axiom Long Export Format Tool (AxLE) is a companion software application to Axiom Analysis Suite software that enables the export of Axiom array genotyping data into long format for easy comparison to legacy arrays.

Features include:

• Separate drop-down sections for Template, Input File and Export Settings
• Enhanced Template functionality
• Ability to save specified Input files, export options and selected Export files in on configuration
• Ability to group samples into separate export files
• Templates for Sample Filter and Sample Grouping

Benefits:

• Easy to use software tool
• Helps reduce the need to change existing bioinformatics pipelines
• For use with both human and non-human Axiom arrays
• Standardized nomenclature for International Society of Animal Genetics (ISAG)
• Enables alignment with breed associations for trait evaluations

The AxLE Tool requires Axiom Analysis Suite software to be installed prior to use. It is supported by 64-bit Microsoft Windows 10 Professional.

The AxLE Tool cannot be used for analyzing data from the Genome-Wide Human SNP Array 6.0 and can only be used for data from Axiom genotyping arrays.

Axiom HLA Analysis is an application for automated high-resolution HLA typing of genotyping array data.  The human leukocyte antigen (HLA) complex is the human version of the major histocompatibility complex (MHC); this complex includes genes responsible for immune function. Variations in these genes affect immune response, including transplant rejection as well as disease susceptibility.  The highly polymorphic nature of this region and the prevalence of pseudogenes create challenges in traditional genotyping methods. Combining the use of direct genotyping with advanced imputation methods over the extended MHC region allows accurate HLA typing from SNP genotype data.

With Axiom HLA Analysis 1.2, you will now be able to produce accurate HLA types from any Applied Biosystems genotyping data set containing high-quality genotypes of a select number of predetermined markers.

Coverage of major HLA genes:

• Determine the HLA type of 11 major MHC Class I and Class II loci with 2-digit and 4-digit resolution
• Integrate HLA typing with genotyping data for insight into immune system variation associations with genome-wide association studies (GWAS)

Direct genotyping and imputation

• Utilize an ancestry-enriched reference panel for populations of interest to improve accuracy of HLA typing. The current reference panel is enriched for Caucasian populations.
• Leverage allele frequency patterns and linkage disequilibrium through imputation and direct genotyping in the extended MHC region to generate accurate HLA haplotypes
• Overcome challenges in multi-ethnic populations for high-accuracy typing of HLA loci

Easy-to-use software

• Select and import a genotyping file in the Axiom HLA Analysis window. The software supports array genotyping output files from Applied Biosystems in .vcf format.
• Analyze HLA loci of interest: select from 11 major MHC Class I and Class II HLA loci
• Export selected loci results for all samples in “Full Report” for 4-digit or 2-digit resolution or for selected samples in “Per Sample Report”

HLA analysis of genotyping data from systems other than genotyping arrays

Research Service Laboratory provides direct HLA analysis of any high-quality genotyping data set with sufficient coverage of markers within the extended MHC region. Please inquire for more information.

Download information and instructions

Download the latest version, Axiom HLA Analysis 1.2 (64-bit), and install the software by following the installation instructions found in the Axiom HLA Analysis User Guide. This version is supported on Microsoft Windows™ 10 Professional (SP 1) with Quad Core Processor and can be used for analyzing data from Axiom Human Genotyping Solution and Genome-Wide Human SNP Array 6.0 genotyping arrays.

Please note that while any population can be analyzed with this software, lower accuracy may be observed for some loci and alleles depending on their frequency in the reference panel. The current reference panel is optimized for Caucasian populations; we are continuing to improve coverage of additional ethnicities to improve call rates and accuracy.

For a list of features and system requirements, please download the latest release notes.

Analysis Power Tools (APT) is a set of cross-platform command line programs that implement algorithms for analyzing and working with GeneChip™ and Axiom arrays. APT programs are intended for "power users" who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality.

Axiom Microbial Analysis Software (MiDAS) is an analysis package for automated high-resolution genomic detection of microbial samples, designed for use with data generated from Axiom Microbiome arrays.

Axiom MiDAS performs single-sample analysis of CEL files from Axiom Microbiome arrays and automatically generates a comprehensive analysis summary in a simple-to-use software package.

Visualize results in Axiom MiDAS Viewer

• View summarized microbial content results that allow intuitive visual comparison of similarities and differences between samples
• Generate a summary table that provides a list of all samples with the number of targets detected in each sample. Summarized block Family and Condensed Family views detail sample granularity in the Family View.
• Filter the Family tile view with the Condensed Family view to show only families detected in at least one sample and provide a cross-sample view of targets present

Quickly search for a target of interest

• View Targets window for table formatted results of all targets detected by Axiom MiDAS in each sample.
• Visualize microbe frequency with a histogram of detected targets detailing the percent of samples where each target was identified and plotted at family or species level.
• Export results in .PNG file formats (for plots) and .TXT (for tabular data).

For a complete list and explanation of features, please download the Axiom Microbiome Solution User Guide.

Download the latest version of Axiom MiDAS, version 1.0 (64-bit), and install the software by following the installation instructions found in the Axiom Microbiome Solution User Guide. This version is supported on Microsoft Windows 10 (64-bit) Professional. The software cannot be used for analyzing data from Axiom Genotyping Arrays.

Detailed analysis is now at the fingertips of every researcher, regardless of access to bioinformatics resources. Transcriptome Analysis Console (TAC) Software, now including the functionality of Expression Console (EC) Software, enables you to go beyond simple identification of differential expression by providing powerful, interactive visualizations.

Designed for the biologist, TAC Software allows you to:

• Perform array QC and data normalization
• Perform statistical tests for differential expression
• Focus on genes or pathways of interest
• Explore interactions between coding and non-coding RNA
• Interpret complex alternative splicing events
• Link out to publicly available annotations
• Obtain sequence information to design validation experiments

New features in TAC Software (version 4.0.1 and subsequent releases):

• Streamlined QC and data analysis with integration of EC Software and TAC Software into a single tool
• Ability to analyze large data sets of 1,000 samples or more
• Integration of established LIMMA package
• Improved alternative splicing analysis

When combined with our comprehensive, high-density microarrays and reagents compatible with challenging and precious samples, you can go from sample to insight in just three days.