Shop All Genotyping Arrays & Assays

Axiom™ Cotton Genotyping Array (Applied Biosystems™)

Axiom Cotton Genotyping Array was designed through Affymetrix- Expert Design Program, and the markers on the array were selected from public databases in collaboration with the National Botanical Research Institute, India. The array includes 35,550 markers that were discovered in G. hirsutum and G. barbadense.

Axiom Cotton Genotyping Array can be used to analyze samples from different populations by adding up to 380,000 custom markers or by transferring polymorphic markers with 100%; fidelity on to the Axiom 384HT myDesign™ breeders array. The Axiom GT1 algorithm can automatically cluster, assign genotypes, and classify the markers into six different categories for easy visualization.

Features of Axiom Cotton Genotyping Array
Comprehensive content:
The Axiom Cotton genotyping array includes a total of 35,550 markers:
• 28,158 intra-specific markers identified using gene-enriched genomic sequences of G. hirsutum.
• 7,392 markers discovered using genome reduction methodology that is based on restriction site conservation (GR-RSC).
   - 5,286 markers were discovered in an inter-specific assembly of G. hirsutum and G. barbadense.
   - 2,106 markers are intra-specific to G. hirsutum.

Applications of Axiom Cotton Genotyping Array
Complex trait research and molecular breeding:
• GWAS and QTL mapping
• Identification of economically-important traits
• Improved accuracy marker-assisted selection programs through genomic selection

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Pepper (Capsicum) SNP Genotyping Array (B520549) (Applied Biosystems™)

This pepper array is a 6.4M feature GeneChip™ Array that has applications in massively parallel genotyping. The array design was supported by seven companies and the UC Discovery grant. This design is based on the public pepper ESTs and genetic information from GeneBank™ and the EST information of 21 libraries from Seoul National University (S. Korea). 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 30,000 pepper genes.

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

Research articles:
Ashrafi H., et al. Genome-Wide SNP Discovery from de novo Assemblies of pepper (Capsicum annuum) Transcriptomes. International Conference on the Status of Plant and Animal Genome Research Poster presentation (Poster P0480) January 14-18, 2012, San Diego, CA.

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

Axiom™ Trout Genotyping Array (384 format) (Applied Biosystems™)

Axiom Trout Genotyping Array (384 format) was designed under the Affymetrix Expert Design Program in collaboration with the National Center for Cool and Cold Water Aquaculture, USDA-ARS, USA, and AquaGen, Trondheim, Norway. The array includes 57,501 markers and is available in both 96 format and 384 format.

Axiom Trout Genotyping Array offers a standard high-throughput, cost-effective, and robust genotyping technology to conduct genome-wide association studies (GWAS), to study genetic architecture, perform marker-trait association, and to increase accuracy of breeding programs. The high marker density on the array ensures a broad coverage of the trout genome to provide representation of all regions in the genome.

Features of Axiom Trout Genotyping Array
Comprehensive content: The array includes 57,501 markers spaced across the genome as follows:
    - 17,000 markers that are unique to SNPs discovered in a previous USDA study1
    - 20,000 markers unique to an outbred Norwegian commercial population
    - Amino acid shifting SNPs
    - SNPs preferentially located within a gene and with minor allele frequency (MAF) >0.2
    - Y chromosome-specific SNPs near the sdY gene (male-specific in rainbow trout)2

Applications of Axiom Trout Genotyping Array
Complex trait research and molecular breeding
    - GWAS and quantitative trait locus (QTL) mapping
    - Identification of economically important traits
    - Improved accuracy in aquaculture breeding programs through genomic selection

Population and evolutionary genetics
    - Development of new breeding populations
    - Differentiation between fish of different origins
    - Gender determination via sdY chromosome-specific probes
    - Differentiation of farmed and wild populations

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

Axiom™ Genome-Wide ASI 1 Array Plate (Applied Biosystems™)

Axiom Genome-Wide Population-Optimized Human Arrays are genotyping panels that offer the best genetic coverage of rare and common variants for genome-wide disease association studies.

The Axiom Genome-Wide ASI 1 Array Plate is the first array designed to maximize genomic coverage of rare alleles (MAF >1%) of a consensus East Asian (JPT+CHB) genome

Benefits of Axiom Genome-Wide Population-Optimized Arrays
Each array plate was designed to achieve ˜90% genomic coverage (r2 >0.8) in each target population, while covering markers with MAF of 1-5% in areas such as:
• Critical biological categories (e.g., coding SNPs)
• Biological processes (e.g., drug metabolizing genes)
• Disease categories (e.g., cardiovascular disease, cancer, immunity/inflammation, MHC, and CNS)
• Common and rare SNPs and insertions/deletions (indels) from the International HapMap Project, 1000 Genomes Project, and published disease associations
• Genotype-tested genomic content proven to give informative and reliable results
• Markers preselected for coverage in critical biological categories, such as coding SNPs, and biological pathways, such as drug metabolizing or cardiovascular genes
• High sample pass rate, call rate, and reproducibility
• Compatible with the Axiom 2.0 Reagent Kit, GeneTitan™ MC Instrument, automated or manual workflow, and Genotyping Console™ Software

Other Maximum Genome-Wide Coverage Arrays
These array plates are designed to maximize whole-genome coverage of common and rare alleles, including SNPs within 10 kb of genes.
Axiom Genome-Wide CEU 1 Array Plate - The first cost-effective array to maximize coverage of rare variants (MAF >1%) for European populations
The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle - This set bundle contains the Axiom Genome-Wide CHB 1 Array Plate and the Axiom Genome-Wide CHB 2 Array Plate. The Axiom Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome. The Axiom Genome-Wide CHB 2 Array Plate is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate
The Axiom Genome-Wide CHB 2 Array Plate - This array is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate. The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle enables the most comprehensive commercially available genome-wide coverage in CHB populations.

• The Axiom Genome-Wide PanAFR Array Plate Set - The first array to offer pan-African genomic coverage, with ≥90% genetic coverage of common and rare variants (MAF >2%) of the Yoruba (West African) genome and >85% coverage of common and rare variants (MAF >2%) of the Luhya and Maasi (East African) genomes. This array set also offers high genomic coverage (>85%) in admixed populations with West African ancestry.

Please visit our NetAffx Analysis Center for more information on microarray analysis

Don't see what you're looking for? Learn how to create an Axiom myDesign™ Array Plate tailored for your study.

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

Axiom™ Biobank Plus Genotyping Array (Applied Biosystems™)

The Axiom™ Biobank Plus Genotyping Arrays were 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.

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

Transplant
• Content specific for transplantation research including functional variants, loss-of-function markers, and copy number
• Immune function, including content covering the major histocompatibility complex (MHC), human leukocyte antigen (HLA), and killer-cell immunoglobulin-like receptors (KIR)

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 mutationseQTLs

• 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 Applied Biosystems 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™ Apple Genotyping Array (Applied Biosystems™)

Axiom Apple Genotyping Array (Axiom_Apple480) was designed through the Affymetrix Expert Design Program in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.com). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights
• Very high diversity
• Includes markers discovered in 63 worldwide M. domestica cultivars• High resolution to address rapid decay of LD   - 487,249 markers on the array
   - Bias towards common variants with minor allele frequency (MAF) >0.05
   - Includes 21,463 previously validated markers: 19,990 markers from an existing in-;market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS)
• Absence of paralogous variants through the use of double haploid accessions in SNP discovery

Applications of Axiom Apple Genotyping Array
• Construction of high-resolution genetic maps
• Fine mapping of quantitative trait loci
• Genome-wide association studies

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel InstrumentAxiom Apple Genotyping Array (Axiom_Apple480) was designed through the Expert Design Program at Affymetrix in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.com). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita- Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom™ Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights
  • Very high diversity
  • Includes markers discovered in 63 worldwide M. domestica cultivars
  • High resolution to address rapid decay of LD
    • 487,249 markers on the array
    • Bias towards common variants with minor allele frequency (MAF) >0.05
    • Includes 21,463 previously validated markers: 19,990 markers from an existing in-market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS)
  • Absence of paralogous variants through the use of double haploid accessions in SNP discovery
Applications of Axiom Apple Genotyping Array
  • Construction of high-resolution genetic maps
  • Fine mapping of quantitative trait loci
  • Genome-wide association studies

Table 1: The country of origin and the number of cultivars used in the SNP discovery process for Axiom Apple Genotyping Array.
Country of origin Number of cultivars
Australia 1
Central Europe 39
Canada 1
Iran 1
Simmental 16
Japan 1
New Zealand 1
Northern Europe 4
Russia 9
Tunisia 1
United States 5
 



Axiom™ Genome-Wide Chicken Array Kit (Applied Biosystems™)

Axiom Chicken Genotyping Array was developed in collaboration with leading academic institutions and commercial poultry companies including the Roslin Institute, Aviagen Ltd, Hy-Line International under BBSRC LINK funding and the German Synbreed project funded by the BMBF.

This genotyping array detects genetic variants in white egg layers, brown egg layers, broilers and outbred non-commercial breeds. The parental high-density information from the array is useful for poultry breeding while markers associated with wild out-bred lines are useful for analysis of genetic diversity among indigenous chicken populations.

Features and benefits of Axiom Chicken Genotyping Array:
Comprehensive content: Over 580,000 common and rare markers selected from 1.8M tested variants
Genome-wide coverage: Well-annotated markers uniformly distributed across the genome in layers and broilers
Designed for your breed: Over 24 breeds represented including commercial layers and broilers and non-commercial outbred lines
Affordable: High return on investment and lowest available cost per marker
Robust assay performance: Includes genotype-tested SNPs that are highly polymorphic and demonstrate a >99% call rate

Applications of Axiom Chicken Genotyping Array:
Genome-wide association studies
High-resolution genetic mapping
Mendelian trait mapping
Diversity analysis in indigenous chickens
Selection signature analysis
Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Porcine Breeders Array, mini-96 format (Applied Biosystems™)

The Applied Biosystems Axiom Porcine Breeders Array includes markers focused on genomic selection of commercial porcine breeds, including Large White, Landrace, Duroc, and Pietrain. Core markers for the array were selected from markers on the Axiom Porcine High-Density Array that were evaluated using samples from multiple commercial and domestic breeds, including European wild boars. The inclusion of the most informative and well-performing markers from existing porcine arrays ensures that this array can be used for comparison with data generated by previous studies. With the availability of the Axiom Long Format Export Tool, which converts Axiom array data into long format, the array also provides the ability to continue existing projects with no change to the current bioinformatics infrastructure and pipeline.

Features include:
• 55,150 markers for genomic and trait selection
• 42 trait-specific markers selected by United States Department of Agriculture
• 64 parentage markers, including ISAG core markers
• Evenly distributed SNPs across the porcine genome
• Marker annotations aligned to Sscrofa10.2/susScr3 genome and dbSNP 148
• Targeted for commercial breeds including Large White, Landrace, Duroc, and Pietrain

Applications
• Parentage analysis
• Identification of economically important traits
• Genetic improvement of pure lines

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

Axiom™ Genome-Wide CHB 1 & CHB 2 Array Set Bundle (Applied Biosystems™)

Axiom Genome-Wide Population-Optimized Human Arrays are genotyping panels that offer the best genetic coverage of rare and common variants for genome-wide disease association studies.

The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle contains the Axiom Genome-Wide CHB 1 Array Plate and the Axiom Genome-Wide CHB 2 Array Plate. The Axiom Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome. The Axiom Genome-Wide CHB 2 Array Plate is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate. The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle enables the most comprehensive commercially available genome-wide coverage in CHB populations.

Benefits of Axiom Genome-Wide Population-Optimized Arrays
Each array plate was designed to achieve ˜90% genomic coverage (r2 >0.8) in each target population, while covering markers with MAF of 1-5% in areas such as:
• Critical biological categories (e.g., coding SNPs)
• Biological processes (e.g., drug metabolizing genes)
• Disease categories (e.g., cardiovascular disease, cancer, immunity/inflammation, MHC, and CNS)
• Common and rare SNPs and insertions/deletions (indels) from the International HapMap Project, 1000 Genomes Project, and published disease associations
• Genotype-tested genomic content proven to give informative and reliable results
• Markers preselected for coverage in critical biological categories, such as coding SNPs, and biological pathways, such as drug metabolizing or cardiovascular genes
• High sample pass rate, call rate, and reproducibility
• Compatible with the Axiom 2.0 Reagent Kit, GeneTitan™ MC Instrument, automated or manual workflow, and Genotyping Console™ Software

Other Maximum Genome-Wide Coverage Arrays
These array plates are designed to maximize whole-genome coverage of common and rare alleles, including SNPs within 10 kb of genes.
Axiom Genome-Wide CEU 1 Array Plate - The first cost-effective array to maximize coverage of rare variants (MAF >1%) for European populations
Axiom Genome-Wide ASI 1 Array Plate - The first array designed to maximize genomic coverage of rare alleles (MAF >1%) of a consensus East Asian (JPT+CHB) genome
Axiom Genome-Wide PanAFR Array Plate Set - The first array to offer pan-African genomic coverage, with ≥90% genetic coverage of common and rare variants (MAF >2%) of the Yoruba (West African) genome and >85% coverage of common and rare variants (MAF >2%) of the Luhya and Maasi (East African) genomes. This array set also offers high genomic coverage (>85%) in admixed populations with West African ancestry.

Please visit our NetAffx Analysis Center for more information on microarray analysis

Don't see what you're looking for? Learn how to create an Axiom myDesign™ Array Plate tailored for your study.

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

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).

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™ Equine Genotyping Array (Applied Biosystems™)

Axiom Equine Genotyping Array (Axiom MNEC670) for equine genotyping was designed through the Expert Design Program by Affymetrix in collaboration with the University of Minnesota and members of the Equine Genetic Diversity Consortium.*

Axiom Equine Genotyping Array is a novel array and the only array that can be used for genotyping 20 different breeds. It offers maximum utility for research in equine genetics. It features 670,796 markers that were selected through a screening of 2 million markers for optimal genomic coverage of known genetic diversity among domestic horse breeds.1 Powered by Axiom Genotyping Solution, the array offers the highest data completeness, call rates, and reproducibility of any technology available today.

Features of Axiom® Equine Genotyping Array:
• Expert design: developed by key opinion leaders in the equine community
• High resolution: available in 96 format; supporting a wide range of genotyping applications for equine research

Highlights
Content:
• Axiom Equine Genotyping Array includes a total of 670,796 markers:
   - Approximately 400,000 markers between population tag SNPs
   - Approximately 200,000 markers within population tag SNPs
   - Approximately 70,000 SNPs from legacy arrays
   - Additional SNP density within the equine major histocompatibility complex

Diversity:
Axiom Equine Genotyping Array includes markers that were selected to maximize accuracy of imputation up to 1.8 million markers both within and across 20 breeds(Fig. 1). An emphasis was placed on breeds with high commercial relevance.

Applications of Axiom Equine Genotyping Array:
• Complex trait research
   - Genome-wide analysis and fine mapping
   - Diversity analyses
   - Genomic prediction of disease risk
• Molecular breeding
   - Association mapping
   - Improved efficiency of breeding programs
   - Selection signature analyses

*The Equine Genetic Diversity Consortium (EGDC) led by the University of Minnesota represents a collaborative international community of equine researchers who are working to build a comprehensive understanding of genetic diversity among equine populations across the world. (http://www.cvm.umn.edu/equinegenetics/egdc/)

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Bovine Genotyping v3 Array (384 format) (Applied Biosystems™)

The Applied Biosystems Axiom Bovine Genotyping v3 Array has >63,000 markers and is designed for genomic and trait selection and parentage verification of cattle. The single-nucleotide polymorphisms (SNPs) on the array were selected based on their position in the bovine genome, ensuring even spacing. These include VIP trait-associated SNPs that are publically available, ISAG core parentage markers, and 44,000 markers from the Council on Dairy Cattle Breeding (CDCB). SNPs optimized for STR imputation (1) are also included in the array content. This array is also available in mini-96 format.

Traits associated with fertility are on the Y-chromosome, so over 500 markers on the Y-chromosome are included in this array. The array also contains >10,000 Bos indicus markers of approximate equal coverage across the Bos indicus genome to avoid gaps.

Applications
• Parentage analysis
• Identification of economically important traits
• Dairy evaluation
• Genetic improvement of pure lines

Required products
Axiom Long Format Export Tool
Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

Reference
1. McClure MC, Sonstegard TS, Wiggans GR, et al. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Front Genet. 2013;4:176.

Eureka™ Bovine Parentage Panel (Applied Biosystems™)

Eureka™ Bovine Parentage Panel was developed in collaboration with key scientists from Agricultural Research Services-U.S. Meat Animal Research Center (ARS-USMARC). The panel includes 122 SNPs, one hundred of which overlap with the International Society of Animal Genetics (ISAG) core markers. Eureka Bovine Parentage Panel offers an affordable, high-throughput, and robust targeted genotyping by sequencing (GBS) technology to parentage studies to increase accuracy of bovine breeding programs. The low marker density panel ensures accurate interrogation of all the bovine parentage markers in all regions of the genome.

Features of Eureka Bovine Parentage Panel
Content: The panel consists of 100 core SNPs and an additional set of 22 markers that can be used internationally to make results comparable between laboratories.

Applications of Eureka Bovine Parentage Panel
• Molecular breeding
    -Identification of economically important traits
    -Improved accuracy in bovine breeding programs through genomic selection

Axiom™ Exome 319 Array Plate (Applied Biosystems™)

Streamline your causal variant studies by enriching genome-wide association studies (GWAS) datasets with an extensive set of novel, rare, putative functional variants. The content was discovered in 16 major exome sequencing projects spanning a total of 12,000 samples.

With the Axiom Exome 319 Array Plate, you get:
Comprehensive content for highest discovery power
   - More than 300,000 coding SNPs including non-synonymous and synonymous SNPs as well as variants in splice and stop codons.
   - Approximately 30,000 single-base and complex indels from the draft Phase 1 1000 Genomes Project exome calls.
Informative markers to enable integrated data analysis
   - AIMs: Ancestry informative markers to measure Latino and African American ancestry. All markers have low linkage disequilibrium (LD) and span all autosomes and chromosome X.
   - >GWAS tags: Includes over 5,000 SNPs reported in the NHGRI Catalog of Published Associations (August 2011) and additional unpublished hits from scientific collaborations.
   - High value: Contains other markers of interest, including DNA fingerprinting SNPs, human leukocyte antigen (HLA) genes, chromosome Y, mitochondrial DNA, and microRNA sequences.
Customization to include your candidate genes
   - Include an additional 100,000 SNPs from your own candidate genes to meet your research needs. Choose from the Axiom Genomic Database of 11M genotype-tested markers, or include variants of your own choosing.
Proven performance
   - The panel has been fully genotype-tested against stringent QC criteria to ensure high-quality data.
   - Every marker has been tested against approximately 1,200 samples to ensure high sample pass, call rate, and reproducibility.

Axiom Exome Genotyping Array Plates include:
   - Axiom 2.0 Reagent Kit for automated or manual processing of up to 96 samples per array plate.
   - A fully automated workflow with validated robotics methods for target preparation and array processing, based on the Beckman Biomek™ FXP Target Prep Express System and the GeneTitan™ MC Instrument.
   - A manual target preparation protocol for lower-throughput users.
   - Axiom Analysis Suite for automated allele calling and easier quality assessment of called genotypes.

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