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Agrigenomics Research Community

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Featured articles

Norwegian Salmon Breeders to use new Affy genotyping chips to select for disease-resistant fish
Use of SNP arrays to identify markers associated with resistance to diseases and parasites that affect salmon.

Futuristic fish and chips
Aquaculture is rapidly adapting genomic methods first used in livestock to characterize and select for traits in marine species.

Array and NGS integration in genomics

Development of an Axiom High Density Porcine Genotyping Array

Development of an Axiom High Density Porcine Genotyping Array

Martien Groenen, Wageningen University
Dr. Martien Gorenen from Wageningen University discusses the design and preliminary data from a custom-designed high density porcine genotyping array. SNPs were selected to represent domestic pigs and wild boars in Europe and Asia.

Microarray resources for genetic and genomic studies in chicken: A review

Microarray resources for genetic and genomic studies in chicken: A review

Geyas A. A., et al. Genesis DOI:10.1002/dvg.22387 (2013).
This review discusses how the relative strengths of microarray and NGS technologies are best applied in genomics of livestock animals and experimental models.

de novo marker selection strategies

Development of a high-density 600K chicken SNP genotyping array

Development of a high-density 600K chicken SNP genotyping array

Prof. Dave Burt, Roslin Institute, UK
Robust marker selection from NGS data is non-trivial. Here, using bioinformatic and empirical filtering, high-value markers are identified from NGS discovery data.

Development of a high density 600K SNP genotyping array for chicken

Development of a high density 600K SNP genotyping array for chicken

Kranis A., et al. BMC Genomics 14:59 (2013).
The strategy outlined in Professor Burt’s presentation above is described here in detail to select high-value, validated markers from putative SNPs discovered by NGS.

Development of a high-throughput high-density SNP genotyping array for bovine

Development of a high-throughput high-density SNP genotyping array for bovine

Ali Pirani, Bioinformatics, Affymetrix.
Incomplete data, errors, and marker redundancy can be managed by post-NGS bioinformatic and empirical filtering of de novo SNPs.

Marker selection from NGS data: avoiding errors, monomorphs, and redundancy

Marker selection from NGS data: avoiding errors, monomorphs, and redundancy

Affymetrix Genomics Scientists
A marker panel with optimized coverage ensures maximum power for any downstream genotyping application. Our bioinformaticians share their expertise.

Axiom genotyping of markers with nearby secondary polymorphisms

Axiom® genotyping of markers with nearby secondary polymorphisms

Laurent Bellon, Product Development, Affymetrix.
Axiom® Genotyping Solution is uniquely suited to genotyping of highly polymorphic genomes as it is permissive to secondary variants as close as 10 bp from the target variant.

Learn more about Axiom myDesign Arrays

Learn more about Axiom myDesign™ Arrays

Custom Axiom® myDesign™ Arrays enable de novo marker validation and downstream genotyping for whole-genome or focused panels.

Automation and best practice for (non)diploid genotype calling

Automated analysis of complex genomes with Axiom Genotyping

Automated analysis of complex genomes with Axiom® Genotyping

Laurent Bellon, Product Development, Affymetrix.
Manual genotype clustering for polyploid species is very time consuming. Learn how the Axiom® automated genotyping software enables polyploid analysis in ~1 hour.

Best practices for genotyping analysis of plant and animal genomes

Best practices for genotyping analysis of plant and animal genomes

Ali Pirani, Bioinformatics, Affymetrix.
Overview of the best workflow to get from data to results in the shortest time.

Allopolyploid genotyping algorithm on Affymetrix Axiom Arrays

Allopolyploid genotyping algorithm on Affymetrix Axiom® Arrays

Hong Gao, Bioinformatics, Affymetrix.
An automated algorithm that reduces genotype analysis to ~1 hour is described and applied to hexaploid wheat data.

Statistical methods for off-target variant genotyping on Axiom Arrays

Statistical methods for off-target variant genotyping on Axiom® Arrays

Teresa Webster, Bioinformatics, Affymetrix.
Automated clustering and calling of "Off-Target Variants," atypical cluster patterns caused by secondary variants in the probe hybridization region.

High throughput and low cost for routine genotyping applications

High throughput and low cost for routine genotyping applications

Michael Shapero, Product Development, Affymetrix.
Outline of the development and performance of the new Axiom® 384 high-throughput format for low-cost genotyping of up to 50,000 SNPs.

High throughput and low cost for routine genotyping applications

High throughput and low cost for routine genotyping applications

Shantanu Kaushikkar, Genotyping Business Unit, Affymetrix.
For high-throughput processing, the new Axiom® 384 high-throughput format enables low-cost processing of up to 50,000 SNPs in 3,000+ samples per week.

Learn more about Affymetrix genomics solutions

Axiom Genotyping Solution for agrigenomics

Axiom® Genotyping Solution for agrigenomics

Download an overview to see how you can use the Axiom® platform.

Axiom Genotyping Solution for agrigenomics

Axiom® Genotyping Solution for agrigenomics

Visit the web page to learn about the arrays available and the custom flexibility and scalability that make the Axiom® platform ideal for research and commercial uses.

Axiom myDesign™ Arrays for custom agrigenomics

Axiom myDesign™ Arrays for custom agrigenomics

The Axiom® myDesign™ platform enables high-density de novo marker validation and scalable whole-genome or focused panels for downstream genotyping.

"For Research Use Only. Not for use in diagnostic procedures."

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Archived Webinars +

Plant Genomics Webinar

Validating Complex Biology Webinar

Translating Genetic Biomarkers to the Clinic Webinar

Clinical Validation of Cancer Biomarker Signatures using Array Technology Webinar

Cancer Genomics Webinar

Circulating Tumor Cells Webinar

Warning! The earliest signals for cancer - miRNA regulation

The Hunt for Missing Heritability