Shop All Genotyping Arrays & Assays

GeneChip™ Human Mitochondrial Resequencing Array 2.0 (Applied Biosystems™)

The GeneChip™ Human Mitochondrial Resequencing Array 2.0 interrogates the entire 16 kb genome on a single array.

Analysis of mitochondrial mutations is informative for a variety of applications from disease genetics to forensic identification. The GeneChipHuman Mitochondrial Resequencing Array 2.0 provides the most efficient and cost-effective method for detecting germ line and heteroplasmic mutations by delivering the complete mitochondrial genome with minimal PCR in only 48 hours.

Features and Benefits
More Information Per Experiment
The Human Mitochondrial Resequencing Array 2.0 interrogates the entire 16 kb genome on a single array.
Less PCR
The robust Mitochondrial Resequencing Assay amplifies the entire genome in only three PCR reactions.
No Assembly Required
The Mitochondrial Resequencing Array 2.0 delivers completed sequence in 48 hours with minimal alignment.

Array Specifications and Components

Format: 169

Sequence Capacity: 16kb

Feature Size: 8 µm

Instrumentation: GeneChip™ Scanner 3000

Software Support: GeneChip™ Command Console™ Software (AGCC), GeneChip™ Sequence Analysis Software (GSEQ)

Reagents: GeneChip™ Resequencing Reagent Kit

Axiom Canine Genotyping Array Set A (Applied Biosystems™)

Axiom™ Canine Genotyping Array Sets A and B were designed as part of the Expert Array Design program. The arrays offer access to approximately 1.1M markers that were discovered by the National Human Genome Research Institute of the National Institutes of Health. The content, distributed over two arrays, offers dense genotyping for validation and discovery of variants associated with specific phenotypes. All of the new content was discovered through high quality sequencing of over 300 dog genomes. The content on the array was aligned with the CanFam3 reference genome.

Canis Familiaris also serves as a model organism in understanding the human disease drug discovery process. Axiom canine genotyping arrays offer dense genotyping for isolating the variants associated with specific phenotypes. Understanding these genotypes allows breeders to anticipate the phenotypes of potential offspring, maximizing the potential to ensure dogs are mated with minimal inbreeding and to screen for possible genetic disorders.

Features of Axiom Canine Genotyping Array Set A
This array includes over 460,000 markers and includes legacy content from in-market arrays including new rare variants. The legacy content on the array offers the capability to continue your studies while getting access to new functional variants. The array includes:
• Markers from legacy in-market genotyping arrays
• Functional variants of biological relevance
• Intergenic variants based on newly available long non-coding RNA (lnc RNA) data
• miRNA variants
• Breed-specific markers

Learn more about Canine Array Set B ›

Applications of Axiom Canine Genotyping arrays
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• As a model organism to help us understand complex human diseases such as cancer and diabetes

Data from the Axiom Canine Genotyping arrays are analyzed with Axiom Analysis Suite and Axiom CNV Summary Tools Software. Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

Axiom™ Microbiome, 96 array plate (Applied Biosystems™)

Easy, streamlined solution for microbial profiling
Axiom Microbiome Array enables the detection of all known microorganisms in a sample with species- and strain-level identification in a single, scalable assay. Utilizing the robust biochemistry of Axiom 2.0 Assay coupled with manual and automated target preparation methods, this streamlined protocol provides consistent and high-quality results. A simplified, upstream reverse transcriptase reaction enables the detection of RNA virus genomes. Hands-free array processing is performed on GeneTitan Multi-Channel Instrument. The complete solution includes arrays, reagent kits, and free, easy-to-use microbiome analysis software (see Figures 1 and 2).

Highlights:
• Expert design for profiling human and animal microbiomes with a single assay
•Detects greater diversity and higher resolution than 16s rRNA gene sequencing
•Allows genetic profiling of all organisms present in a sample
•Comprehensive coverage of over 11,000 organisms and five microbial domains: archaea, bacteria, fungi, protozoa, and viruses
• Allows identification to the species, strain and sequence level.
•Flexible 24- and 96-array plate formats
•Sample type agnostic: applications in nutrigenomics, agrigenomics, and animal research
•Simplified microbial detection analysis

See also Axiom Microbiome, 24 array plate and Axiom Microbial Detection Analysis Software (MiDAS).

See Figure 2 for target categories represented on Axiom Microbiome Arrays.

Genome-Wide Human SNP Array 6.0 (Applied Biosystems™)

With more than 1.8 million markers, including 946,000 probes for the detection of copy number variants and 906,600 SNPs, the Affymetrix™ Genome-Wide Human SNP Array 6.0 is a powerful tool for a variety of cytogenetic applications.

Pure Power and Performance

The new Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 is the only platform with analysis tools to truly bridge copy number and association, including a new, high-resolution reference map and a copy number polymorphism (CNP) calling algorithm developed by the Broad Institute. The SNP Array 6.0 demonstrates industry-leading performance and represents more genetic variation on a single array than any other product, providing maximum panel power and the highest physical coverage of the genome.

The high price-performance value of the SNP Array 6.0 enables researchers to design association studies with larger sample sizes in the initial scan and replication phases, thereby significantly increasing the overall genetic power of their studies.

Affymetrix Cytogenetics Research Products

Affymetrix Copy Number Solution

Copy Number and LOH analysis tools in Genotyping Console

More than 906,600 SNPs:
•Unbiased selection of 482,000 SNPs; historical SNPs from the SNP Array 5.0
•Selection of additional 424,000 SNPs
           -Tag SNPs
           -SNPs from chromosomes X and Y
           -Mitochondrial SNPs
           -New SNPs added to the dbSNP database
           -SNPs in recombination hotspots

More than 946,000 copy number probes:
•202,000 probes targeting 5,677 CNV regions from the Toronto Database of Genomic Variants
•744,000 probes, evenly spaced along the genome
•Detected 10 times more copy number changes than other SNP/CN platforms
•Three times more coverage of CNPs; only platform with non-polymorphic probes
•GTC 3.0 leverages new, high-resolution reference map and CNP calling algorithm developed by the Broad Institute

More Information:
New Software Tools for Copy Number and LOH Analysis


Axiom™ BreedWheat 35K Genotyping Array (mini-96 format) (Applied Biosystems™)

The Axiom BreedWheat 35K Genotyping Array (Axiom TaBW35K) was designed in the framework of the BreedWheat Project in collaboration with Dr. Etienne Paux, project leader at the National Institute for Agricultural Research, Clermont-Ferrand, France. The BreedWheat Project, a French public-private partnership, aims at strengthening the competitiveness of the French wheat-breeding sector, as well as to address the societal demands for sustainability, quality, and safety in agricultural production. This array is also available in 384 format.

The 34,746 SNPs on this array were derived from the Axiom TaBW280K Genotyping Array (1). Several selection criteria were applied, including clustering profiles, even distribution (based on linkage disequilibrium data rather than physical positions), and known position on the IWGSC RefSeq v1.0.

Information on the SNPs, including physical and genetic positions, context sequences, and statistics derived from a panel of 96 wheat lines representative of the worldwide diversity are also provided.

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

Reference
1. Rimbert H, Darrier B, Navarro J, Kitt J, Choulet F, et al. (2018) High throughput SNP discovery and genotyping in hexaploid wheat. PLOS ONE 13(1): e0186329.

Lettuce (Lactuca sativa) SNP Genotyping Array (1B520367) (Applied Biosystems™)

This lettuce community array is a 6.6M feature GeneChip™ Array that has applications in massively parallel genotyping. The array was designed at UC Davis. The genotyping array uses single feature polymorphism (SFP) markers with applications in quantitative trait loci (QTL) analysis, where whole-genome coverage is desired.

The high-density GeneChip microarray is used to detect SFPs in more than 35,000 lettuce genes.

Please visit http://chiplett.ucdavis.edu/ for more detailed information about the array design, assay, and analysis for use in genotyping.

Research articles:
Schwember A. R., Bradford K. J. Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions. Journal of Experimental Botany 61(15):4423-4436 (2010).

Borevitz, J. O., et al. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Research 13(3):513-523 (2003)

Axiom™ Wheat HD Genotyping Arrays (Applied Biosystems™)

Axiom Wheat HD Genotyping Arrays were designed through Affymetrix Expert Design Program in a collaboration led by Dr. Keith Edwards, project leader and professor of Cereal Functional Genomics at the School of Biological Sciences and member of the Cabot Institute, University of Bristol.*

This product is part of a two array set. Array Plate B can be accessed at 550491 Axiom™ Wheat HD Genotyping Arrays.

The arrays were designed through a public sector pre-breeding program dedicated to accelerating the genetic improvement of modern wheat varieties. Select from one of two formats:
• Axiom; Wheat HD Genotyping Array, a high-density research tool with 817,000 SNPs in a two-array set in the 96-array plate format
• Axiom; Wheat Breeder's Genotyping Array, which includes 35,000 SNPs for worldwide elite wheat lines in the 384-array plate format

Markers on these arrays can be queried on the CerealsDB website (http://www.cerealsdb.uk.net/). This is a searchable database that was created by the Functional Genomics group at the University of Bristol, UK for the purpose of making SNP information available to the worldwide wheat community. It is updated regularly and contains:

• SNP statistics: Map location or contig code, 120 bp flanking sequences. MAF and PIC score are provided for SNPs on Axiom Wheat Breeder's Genotyping Array
• Variety comparison: Select two or more varieties of wheat to see the SNPs in common or SNPs that are different between them

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated by Affymetrix in the same manner as other catalog products. Through the program, Affymetrix continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom Canine Genotyping Array Set B (Applied Biosystems™)

Axiom™ Canine Genotyping Array Sets A and B were designed as part of the Expert Array Design program. The arrays offer access to approximately 1.1M markers that were discovered by the National Human Genome Research Institute of the National Institutes of Health. The content, distributed over two arrays, offers dense genotyping for validation and discovery of variants associated with specific phenotypes. All of the new content was discovered through high quality sequencing of over 300 dog genomes. The content on the array was aligned with the CanFam3 reference genome.

Canis Familiaris also serves as a model organism in understanding the human disease drug discovery process. Axiom canine genotyping arrays offer dense genotyping for isolating the variants associated with specific phenotypes. Understanding these genotypes allows breeders to anticipate the phenotypes of potential offspring, maximizing the potential to ensure dogs are mated with minimal inbreeding and to screen for possible genetic disorders.

Features of Axiom Canine Genotyping Array Set B
This array contains over 670,000 variants that are equally distributed across the chromosomes.

Learn more about Canine Array Set A ›

Applications of Axiom Canine Genotyping arrays
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• As a model organism to help us understand complex human diseases such as cancer and diabetes

Data from the Axiom Canine Genotyping arrays are analyzed with Axiom Analysis Suite and Axiom CNV Summary Tools Software. Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

UK Biobank Axiom™ Array (Applied Biosystems™)

UK Biobank Axiom™ Array was designed by and for thought leaders in the human genetics community for high-throughput, high-value genotyping of large sample cohorts to explore the genetics of complex diseases and translational research with a single comprehensive low-cost solution. This array contains one 96-array plate that allows for genome-wide genotyping of large sample collections such as those screened at biobanks, genome centers, and core labs.

GWAS
• Intelligent marker selection enables imputation of millions of additional SNPs
• The genomic content module of each array is optimized for specific populations and is customizable to any 1000 Genomes population study by adding additional markers of your choosing

Pharmacogenomic markers
• Markers were selected to represent phases of absorption, distribution, metabolism, and excretion (ADME)

Inflammation and HLA
• Contains markers with evidence for association with autoimmune and inflammation
• Covers variants in genes in the HLA and KIR regions known to be important in immune response

Exome
• Rare, non-synonymous coding SNPs and indels in protein coding regions of the genome
• A majority of variants are rare with minor allele frequency (MAF) <1%
• Newly discovered loss-of-function content
• SNPs and indels identified from a sequencing initiative of 26,000 individuals
• Known disease-causing mutations

eQTLs
• Markers that have known associations to RNA expression traits
• Captures unique eQTLs contained in the NCBI Genotype-Tissue Expression (GTEx) eQTL database, GEUVIDAS project, and several other discovery projects

Human disease
• Alzheimer-s disease, including coverage of ApoE
• Blood phenotypes
• Cancer common variants
• Cardiometabolic

Choose your content
• Order the pre-designed array and customize it with markers of your choice
• Custom markers may be de novo or selected from the Axiom Genomic Database of genotype-tested markers

Please note: Reagent kits do not include plastic consumables required to run the assay on the Beckman Biomek™ FXP Target Prep Express System. Please contact us for a list of required plastic consumables.

Axiom™ Bovine-Ovine-Caprine Genotyping Array (Applied Biosystems™)

Axiom Bovine-Ovine-Caprine Genotyping Array (Axiom Ovicap Array) for animal genotyping was designed through the Affymetrix Expert Design Program. The array includes single nucleotide polymorphisms (SNPs) that were identified by the United States Department of Agriculture Agricultural Research Service (USDA ARS), International Sheep Genomics Consortium (ISGC), and the International Goat Genome Consortium for each of the three different species (bovine, ovine, and caprine, respectively. The content for caprine includes SNPs located within the four casein genes implicated in milk production.The array also includes markers for ovine and bovine parentage analysis.

Highlights
• Expert design: developed by key opinion leaders in the community
• Informative, including parentage markers from existing in-market arrays, allowing compatibility with previous studies
• A singe array for three species:
   - Bovine: 54,560 markers.
   - Ovine: 54,236 markers.
   - Caprine: 60,034 markers.

Applications
• Construction of high-resolution genetic maps
• Genetic improvement of pure lines
• Fine mapping of quantitative trait loci (QTL)
• Calculating breeding values
• Parentage analysis

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Ovine Genotyping Array (50K) (Applied Biosystems™)

The Applied Biosystems Axiom Ovine Genotyping Array (50K) provides the power and resolution to enable a wide range of applications in sheep breeding, including breed assignment, parentage verification and discovery, and traceability and monitoring of polymorphisms of known large effect. The Axiom Ovine Genotyping Array includes markers that were selected by the International Sheep Genomics Consortium, with markers derived from three separate sequencing experiments. The array content is augmented with additional markers for parentage testing and traceability in globally diverse breeds of sheep. These include 163 highly informative parentage markers (MAF ≥0.3) in 48 +5 breed groups that enable accurate parentage testing and traceability in many of the world’s sheep breeds.

Features include:
• Expert design—developed in collaboration with Donagh Berry at Teagasc, Animal and Grassland Research and Innovation Center, Ireland
• Exceptionally high quality SNPs with excellent call and concordance rates across platforms and laboratories
• Includes SNPs for parentage as well as other traits including scrapie
• Compatible with Sheep Consortium 15K arrays and thus with previous studies

Applications
• Parentage verification and discovery
• Accurate genomic evaluations
• Genome-wide associations following accurate imputation to higher density panel
• Breed assignment
• Monitoring of major genes
• Aneuploidy detection—early detection of such abnormalities enables identification of animals that are not suitable parents for the next generation
• Measurement of genetic diversity including calculation of genomic inbreeding statistics
• Mating designs
• Traceability

Data from the Axiom Ovine Genotyping Array are analyzed using Axiom Analysis Suite and Axiom CNV Summary Tools software. The data can also be exported into long format using the Axiom Long Format Export Tool (AxLE).

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

PharmacoScan™ Training Kit, 24-Format (Applied Biosystems™)

The PharmacoScan Training Kit includes four 24-format array plates plus reagents, controls, and consumables to process 88 samples and 8 controls. Two DNA training plates containing 22 known samples each are also included.

Note: This includes all consumables and reagents already included with the PharmacoScan Assay Kit (903010TS), but adds two training plates containing known DNA controls.

PharmacoScan Solution is an ideal platform for translational researchers in healthcare, pharma, and research organizations looking to understand how genetic variations affect drug absorption, distribution, metabolism, and excretion (ADME).

By pre-emptively screening for risk factors on a microarray, users in research can precisely and reproducibly analyze 4,627 high- to low-evidence markers* within nearly 1,200 genes* in a single assay. The solution includes copy number variation calling and interrogating predictive markers in complex genes. Unlike solutions that analyze only high-evidence markers, PharmacoScan Solution presents a more comprehensive view for genotyping for pharmacogenomic risk.

*Disclaimer: Number of variants genotyped by default as well as variant to gene mapping is refined over time.

atSNPtilx520433 Arabidopsis Cartridge Array (Applied Biosystems™)

The Arabidopsis thaliana is a small flowering plant that is commonly used as a model organism in plant biology and genetics.

The customized GeneChip™ Arabidopsis SNP Genotyping Array can be used for genotyping and whole-transcript gene expression. The array is a 5 µm array with 249,000 SNPs tiled on the array with 4 probes per SNP. The tiling probes are perfect match (PM) only and omit repetitive sequences. The array is used with Whole-Genome Sampling Assay for Agrigenomics Solutions.

Please visit http://www.ncbi.nlm.nih.gov/pubmed/18369451 and http://www.ncbi.nlm.nih.gov/pubmed/17091126 for more detailed information about the array design, assay, and analysis for use in genotyping.

Research article:
Childs L. H., et al. Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11:188 (2010)

Mouse Diversity Genotyping Array (Applied Biosystems™)

The Mouse Diversity Genotyping Array enables researchers to accurately characterize a broad range of mouse strains and their crosses and uncover genetic changes in mouse models of disease.

With more than 120 times the number of SNPs of competing products, and an average of 4.3 kilobases (kb) between SNPs, the Mouse Diversity Genotyping Array has greater density and distribution than any other publicly available mouse SNP array.

Mouse Diversity Genotyping Array offers:
• More than 120 times the genotyping power of competing products
   - Interrogate more than 623,000 single nucleotide polymorphisms (SNPs)
• More than 100 times the linkage mapping power
   - Map to a resolution of 4.3 kb
• The only array with copy number probes
   - Explore more than 916,000 non-polymorphic regions targeted to functional elements and regions known to harbor segmental duplications
• High performance metrics for 12 classical inbred laboratory strains and their F1 crosses
   - 98.6% call rate
   - 99.9% reproducibility
   - 99.5% concordance
   - < 0.5% error rate
• The broadest coverage of laboratory mouse strains
   - Probes represent SNPs derived from 12 classical inbred strains and 7 wild-derived and wild strains
• The most flexible approach
   - One array for both classical inbred and wild-derived strains for any mouse genetics application
• The lowest cost per genotype
   - Just fractions of a penny per SNP

For more information on the design of the array, please see Yang H., et al. A customized and versatile high-density genotyping array for the mouse. Nature Methods 6(9):663-666 (2009).

Axiom™ Maize Genotyping Array (Applied Biosystems™)

Axiom Maize Genotyping Array was designed by the AgroClustER Synbreed (funded by the German Ministry of Education and Research, BMBF) through a collaboration led by Professor Chris-Carolin Schön, Dr. Eva Bauer, and Sandra Unterseer (Technische Universität München, Germany), and Dr. Georg Haberer and Michael Seidel (Helmholtz Zentrum Mnchen, Germany) through Affymetrix Expert Design Program.* The array interrogates 616,201 carefully selected polymorphic variants to represent the global diversity in the maize genome.

The array overcomes specific challenges caused by a high content of repetitive elements, high genomic and structural diversity, and low linkage disequilibrium (LD) in different cultivars. The SNPs on the array were first discovered through resequencing in a panel of 30 inbred lines that represented global diversity. The array was validated by using a diverse set of European, US, and tropical/semi-tropical lines from various Dent and Flint gene pools.

Features of Axiom Maize Genotyping Array:
Comprehensive content – 616,201 variants including 609,442 SNPs and 6,759 small insertion/deletion variants

Applications of Axiom Maize Genotyping Array:
Complex trait research
   - Genetic diversity analysis
   - Association mapping
   - Genome-wide analysis and selection
   - Haplotype structure in maize varieties
   - LD analysis
   - QTL mapping
Molecular breeding
   - Development of new inbred lines
   - Genomic selection

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated by Affymetrix in the same manner as other catalog products. Through the program, Affymetrix continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument