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Axiom™ Genotyping Services, Non-Human Catalog 384 Applied Biosystems™

Axiom™ Genotyping Services, Non-Human Catalog 384
Our service lab has genotyped more than one million samples and called about 650 billion genotypes, enabling our customers to complete their genotyping studies quickly and affordably. Our staff uses expert knowledge of best practices to process and analyze your samples, manage your Axiom Genotyping Services project from start to finish, and meet your crucial deadlines. Descriptions of the variety of Axiom Genotyping Services offered are listed below.

Axiom Catalog Array Genotyping Services
Our Axiom Catalog Array Genotyping Services offer hassle-free, high quality data for any existing Axiom Genome-Wide Array Plates or pre-designed arrays. This includes genotyping services using arrays for a variety of organisms and for a range in number of SNPs from 675,000 to two million.

myDesign™ Array Genotyping Services
myDesign Array Genotyping Services enable you to create fully or semi-customized genotyping arrays containing 1,500 to 2.6 million markers and then have them processed by our Research Services Laboratory with the same high-quality and fast turnaround time we provide for our catalog arrays.

For any of the above services, Please inquire for more information.

Axiom™ Buffalo Genotyping Array Applied Biosystems™

Axiom Buffalo Genotyping Array was designed by the Affymetrix Expert Design Program.* The array was developed in collaboration with the International Buffalo Genome Consortia, which included Fondazione Parco Tecnologico Padano in Italy, Iowa State University, and the Agricultural Research Service, United States Department of Agriculture (USDA).

Axiom Buffalo Genotyping Array provides the highest genome-wide coverage of polymorphic SNPs across multiple species and breeds of the water buffalo (Bubalus bubalis bubalis and Bubalus bubalis carabanensis), one of the most important beef and dairy animals in Italy, Brazil, and South Asia.

This array is the only commercially available high-density buffalo genotyping tool.

Features of Axiom Buffalo Genotyping Array:
Comprehensive content – 90,000 common and rare markers selected from sequencing initiatives of the water buffalo (B. bubalis bubalis)
Multiple breeds represented – Mediterranean, Murrah, Jaffarabadi, and Nili-Ravi
Robust assay performance – SNPs demonstrate a ≥99%; call rate and ≥80% conversion rate on Murrah and Mediterranean samples

Applications of Axiom Buffalo Genotyping Array:
Molecular breeding:
   - Genomic biomarker discovery
   - Marker-assisted selection
   - Routine screening
   - DNA fingerprinting for animal tracking

Complex trait research:
   - High-resolution mapping of genetic loci in complex traits such as milk production, percentage of milk fat, and feed conversion efficiency
   - Discovery of genes and pathways underlying simple and complex traits

Conservation and biodiversity:
   - Population diversity studies in river and swamp buffalo
   - Genomic marker-assisted conservation strategies

*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 in the same manner as other catalog products. Through the program, we 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™ Genotyping Services, Non-Human Custom 384 Applied Biosystems™

Axiom™ Genotyping Services, Non-Human Custom384
Our service lab has genotyped more than one million samples and called about 650 billion genotypes, enabling our customers to complete their genotyping studies quickly and affordably. Our staff uses expert knowledge of best practices to process and analyze your samples, manage your Axiom Genotyping Services project from start to finish, and meet your crucial deadlines. Descriptions of the variety of Axiom Genotyping Services offered are listed below.

Axiom Catalog Array Genotyping Services
Our Axiom Catalog Array Genotyping Services offer hassle-free, high quality data for any existing Axiom Genome-Wide Array Plates or pre-designed arrays. This includes genotyping services using arrays for a variety of organisms and for a range in number of SNPs from 675,000 to two million.

myDesign™ Array Genotyping Services
myDesign Array Genotyping Services enable you to create fully or semi-customized genotyping arrays containing 1,500 to 2.6 million markers and then have them processed by our Research Services Laboratory with the same high-quality and fast turnaround time we provide for our catalog arrays.

For any of the above services, Please inquire for more information.

Axiom™ Strawberry Genotyping Array Applied Biosystems™

Axiom Strawberry Genotyping Array was designed through the Affymetrix Expert Design Program in collaboration with the International RosBREED SNP consortium that spans multiple nations, states, and institutions dedicated to genetic improvement of rosaceous crops.* The array offers genome-wide coverage of polymorphic SNPs across the cultivated garden strawberry hybrid (Fragaria ananassa).

Features of Axiom Strawberry Genotyping Array:
Comprehensive content: 95,062 SNPs and indels derived from octoploid and diploid cultivars, including:
   - 1,761 multi-allelic SNPs
   - 3,751 SNPs derived from diploid cultivars; the remaining markers are derived from octoploid cultivars
Multiple cultivars represented: SNP discovery was facilitated with a diverse worldwide breeding germplasm panel that included:    - Holiday, Korona, and F1 seedlings from the cross Holiday x Korona
   - Two likely diploid progenitors, Fragaria mandschurica, F. iinumae
   - One known diploid F. vesca

Applications of Axiom Strawberry Genotyping Array:
Complex trait research
   - QTL discovery
   - Identify traits of economic significance
Molecular breeding
   - Genome-wide scanning
   - Marker-assisted breeding
Release of new cultivars
   - Accelerate and increase efficiency of cultivar development
   - Identify the presence of important markers in existing strawberry germplasm
   - Use genetic information to identify germplasm that will perform well in specific growing regions

Notes about the data analysis: Axiom Strawberry Genotyping Array requires advanced analysis. Genotyping many different varieties together may create multiple clusters during the analysis that interfere with each other and/or blend the clusters together. Genotype calls are not provided for multi-allelic SNPs.

*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™ Porcine Breeders Array, 384 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™ Starter Kit for NIMBUS Applied Biosystems™

The Axiom™ Starter Kit for NIMBUS™ products includes additional equipment and parts necessary to set up the NIMBUS Target Preparation Instrument for Axiom Genotyping Solution.

We have partnered with Hamilton Robotics to provide you with the latest in ultra-compact and precision-based liquid-handling instrumentation. NIMBUS Target Preparation Instrument is industry-recognized for its high-end manufacturing and superior pipetting performance at an affordable price.

Axiom 96-sample automated target preparation
We have automated the target preparation steps for the Axiom 2.0 assay, including DNA amplification, fragmentation, purification, resuspension, hybridization preparation, and stain preparation for the GeneTitan™ MC Instrument.

The Axiom target preparation on the automated liquid-handling workstation helps minimize run-to-run variability and the labor burden associated with complex manual pipetting, helping to improve test reproducibility and laboratory efficiency.

Target preparation for Axiom Genotyping Solution is now effortless with Axiom 96-sample automated target preparation, which offers:
• Small footprint, sleek design, and industry-recognized engineering
• Advanced pipetting technology for precise yet flexible liquid handling
• Workflow designed to accommodate 96 samples
• Laptop with easy-to-use software interface including visual cues for each assay step

Related Links
NIMBUS™ Target Preparation Instrument
Axiom™ Consumables Kit for NIMBUS

Axiom™ 2.0 384HT Reagent Kit Applied Biosystems™

Axiom™ 2.0 384HT Reagent Kit includes all reagents to process one Axiom 384HT Array Plate.

Axiom™ 2.0 Reagent Kit Applied Biosystems™

Axiom™ 2.0 Reagent Kits are designed for use with Axiom pre-designed and Axiom myDesign™ Arrays.

These kits are available in 96-, 384-, and 24- reaction formats. The kits include the reagents and control DNA required to produce hybridization-ready targets for Axiom pre-designed and Axiom myDesign Arrays. Axiom Reagent Kits can be used for genotyping of SNPs and indels on Axiom Genotyping Arrays and for the detection of microbial targets on Axiom Microbiome Arrays.

Axiom™ myDesign™ GW Array Plate, 200K-675K Applied Biosystems™

With the Axiom™ myDesign™ GW Array Plate, 200K-675K, you can create fully customizable genotyping array panels for genome-wide association, replication, fine mapping, and candidate gene studies. Based on the universal workflow of the Genotyping Solution, myDesign Arrays offer unprecedented scale and flexibility to design the most optimal array for your species of interest.

The Array Plate contains one 96-array plate containing between 200K and 675K markers, in a 1x96 configuration (Minimum order size of 480 samples). An example template showing SNP submission can be found here.

The Expert Design Program enables a consortium of researchers to design genotyping arrays for their species of interest with de novo SNPs or SNPs from the Axiom™ Genomic Database. Consortia members interested in developing a new array can contact us for design consultation.

myDesign Custom Arrays feature:
Low minimums – Custom arrays for as few as 480 samples; small repeat orders at attractive prices
Flexible content – Fully customizable panels focused on your SNPs of interest; multiple species on one array supported
Consistent supply – Get 100% identical SNP content at any time and for as long as your research necessitates
High precision – Every SNP is manufactured with a high degree of precision using photolithographic templates
More marker selection freedom – Interfering SNPs can be as close as 10 bases from candidate SNPs
Cost effective – High return on investment; attractive pricing without requiring large consortium volumes

myDesign Arrays are available in formats suitable for the appropriate number of markers:
384HT myDesign Custom Arrays – 1,500 to 50,000 markers per array. 384 arrays per plate
myDesign Targeted Genotyping (TG) Arrays – 1,500 to 200,000 markers per array for targeted genotyping in applications in genotype-trait association, genomic selection, and screening; 96 or 24 arrays per plate
myDesign Genome-Wide (GW) Arrays – 200,000 to 2.6 million SNPs for validation and genome-wide association studies; 96 or 24 arrays per plate; multiple array designs can be used for large studies

myDesign Genotyping Arrays include:
Axiom 2.0 Reagent Kit for automated or manual processing of up to 96 samples or Axiom 2.0 384HT Reagent Kit for processing 384 samples
• 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 a GeneTitan MC Instrument.

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™ Trout Genotyping Array (96 format) Applied Biosystems™

Axiom Trout Genotyping Array (96 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™ 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

Axiom™ Ovine Genotyping Array Applied Biosystems™

The Applied Biosystems Axiom Ovine Genotyping Array 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 11,000 markers on the array facilitate highly accurate imputation up to a higher density panel (e.g., 50K panel) The Axiom Ovine Genotyping Array includes 88 single nucleotide polymorphisms (SNPs) proposed by the International Sheep Genomics Consortium (ISGC) for parentage verification.

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

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

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™ Transplant Genotyping Array Applied Biosystems™

Axiom™ Transplant Genotyping Array, one of the Axiom™ Biobank Genotyping Arrays, is designed for high-powered, genome-wide genotyping of large sample collections such as those screened at biobanks, genome centers, and core labs.

Axiom Transplant Genotyping 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.

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 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. For a list of required Beckman consumables, please see the Axiom™ 2.0 Automated Assay User Guide below.


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