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Axiom™ HLA Typing Analysis Services (Applied Biosystems™)

High-resolution HLA typing on large-scale sample sets over thousands of markers
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.

4-digit HLA types for 11 major loci
•With Axiom HLA Analysis 1.2, you will now be able to produce accurate HLA types from any genotyping data set from Affymetrix 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 (see Fig. 1) 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 (see Fig. 2) 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, see the publication on Multi-Population Classical HLA Type Imputation.

Easy-to-use software
•Select and import a genotyping file in the Axiom HLA Analysis window (see Fig. 3). The software supports our array genotyping output files 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 our genotyping arrays
Affymetrix Research Service Laboratory (ARSL) 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 of the 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®7 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.

Click here to download a copy of Axiom™ HLA Analysis software.
Download software

Additional software files and analysis solutions from Affymetrix
Axiom™ Analysis Suite
Affymetrix Power Tools (APT)
Genotyping Console™ (GTC) Software
SNPolisher

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.

Eureka™ Genotyping Services, Catalog Panels (Applied Biosystems™)

Eureka™ Genotyping Services™ Catalog Panels
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 Eureka Genotyping Services project from start to finish, and meet your crucial deadlines. Descriptions of the variety of Eureka Genotyping Services offered are listed below.

Eureka Catalog Panel Genotyping Services for Agrigenomics
Our Eureka Catalog Panel Genotyping Services work collaboratively with customers, providing a personal touch to achieve your research goals. Using state-of-the-art technology, you can fast-track your genomic selection program.

Eureka™ myDesign™ Panel Genotyping Services for Agrigenomics
Our Eureka myDesign Panel Genotyping Services enable you to customize your genotyping panel containing 100 to 3,000 markers. They will be processed by our Research Services Laboratory with the same high-quality and fast turnaround time we provide for our Eureka catalog panels.

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

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.

OncoScan™ CNV FFPE Services (Applied Biosystems™)

Discover new biomarkers for diagnosis, prognostics, or predictive research by looking at whole genome copy number changes Tumors usually arise from normal cells with tissue-specific acquired mutations or aberrations in their genomic materials. Copy number variation (CNV) is one of the most important somatic aberrations (Beroukhim R., et al. The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899-905 (2010)). As it turns out, cancer top classes are dominated by either mutations (M class)-quality of a gene, or copy number changes (C class)-quantity of a gene. Cancer is driven by either mutation (M class) or copy number (C class) (Ciriello G., et al. Emerging landscape of oncogenic signatures across human cancers. Nature Genetics 45(10):1127-1133 (2013)).

In order to fully maximize cancer discoveries from formalin fixed, paraffin embedded (FFPE) samples, one will have to look at both copy number and somatic mutations in FFPE samples. With OncoScan services, you can easily assess the copy number status in your samples. We offer two outstanding options:

1.    OncoScan CNV FFPE Services: high-resolution, genome-wide copy number profiling
2.    OncoScan FFPE Services: same outstanding copy number coverage as OncoScan CNV Services, plus a somatic mutation panel of 74 mutation in 9 genes (BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS, and TP53).

This robust solution offers

Unbeatable whole-genome copy number coverage for large and small copy number changes
   •Additional data as compared to targeted gene panels
       - Whole-genome coverage vs. targeted-coverage
       - Ability to detect large aberration (Mb scale) that are missed by targeted panels
   •High-resolution (50-125 kb) copy number detection in priority cancer genes
       - Integrated analysis of whole-genome copy number changes and copy-neutral loss of heterozygosity (LOH)
       - Linear dynamic range: 0-60 copies

High-quality data from 80 ng of input DNA

Rapid data analysis
   •Visualize copy number data for hundreds of samples in minutes
   •We partnered with BioDiscovery, an industry-leading software provider, to enable a more comprehensive data analysis solution. Learn more about Nexus Copy Number™ Software at www.biodiscovery.com.

Convenience and Quality
Experience the convenience of the Affymetrix Research Services Laboratory (ARSL)-just send in your DNA. ARSL has processed thousands of the most challenging FFPE samples with a pass rate of greater than 92 percent, and our lab has the quality systems in place to handle your project with the highest standard of care and excellence. Take advantage of our expertise and receive data of the highest quality with the OncoScan FFPE and CNV FFPE Services (see Fig. 1). Please inquire for more information

Learn how scientists are using OncoScan CNV assays
•Evidence of clinical utility of copy number in solid tumors using the OncoScan™ FFPE Assay Kit
•Copy number alterations and breast cancer: retrospective results from archived FFPE samples based on OncoScan™ solution
•Whole-genome copy number analysis in stratification and differential diagnosis of brain tumor patients: experiences in more than 600 FFPE brain tumor biopsies

Axiom™ Genotyping Services, Non-Human Custom 96 (Applied Biosystems™)

Axiom™ Genotyping Services, Non-Human Custom 96
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 emailtechsupport@thermofisher.com for more information.

OncoScan™ FFPE Services (Applied Biosystems™)

Applied Biosystems OncoScan Assay Services accelerate your projects. Discover new biomarkers for diagnosis, prognostics, or predictive research by looking at whole genome copy number changes. OncoScan Assay service providers work collaboratively with you to achieve your research objectives. We consistently provide reliable, on-time services at a reasonable cost.

Key benefits:
• Tailored services to meet your research goals
• Reliable, rapid, on-time results
• High-quality data

Maximize cancer discoveries from formalin fixed, paraffin-embedded (FFPE) samples, by easily assessing their copy number status. We offer two service options:

1. OncoScan CNV Assay Services: high-resolution, genome-wide copy number profiling
2. OncoScan CNV Plus Assay Services: the same copy number coverage as OncoScan CNV Assay Services, plus a somatic mutation panel of 74 mutation in 9 genes (BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS, and TP53).

This robust solution offers:
• Unbeatable whole-genome copy number coverage for large and small copy number changes, loss of heterozygosity (LOH), and copy neutral LOH
• Linear dynamic range: 0–60 copies
• High-quality data from 80 ng of input DNA
• Rapid data analysis—visualize copy number data for hundreds of samples in minutes

Convenience and quality
Experience the convenience of OncoScan Assay Services—just send in your DNA. Our services laboratory has processed thousands of the most challenging FFPE samples with a pass rate of greater than 92 percent, and our lab has the quality systems in place to handle your project with the highest standard of care and excellence. Take advantage of our expertise and receive data of the highest quality with the OncoScan CNV Assay and CNV Plus Assay services (Figure 1). Please inquire for more information.

Axiom™ Genotyping Services, Human Custom 96 (Applied Biosystems™)

Axiom™ Genotyping Services, Human Custom 96
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™ Genotyping Services, Non-Human Catalog 96 (Applied Biosystems™)

Axiom™ Services non-Human Catalog 96
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™ Genotyping Services, Human Catalog 96 (Applied Biosystems™)

Axiom™ Services Human Catalog 96
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.

FFPE DNA Extraction Services (Applied Biosystems™)

Maximize cancer discoveries from FFPE samples with FFPE Express 2.0 Services. The FFPE Express Service offers high-quality copy number and genotype data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.

This robust solution offers:

High-resolution, cancer-relevant, whole-genome coverage
    • Enhanced coverage developed in collaboration with world-renowned cancer scientists
    • Reveals the genomic complexity of cancer with:
       • Integrated analysis of whole-genome copy number changes and copy-neutral loss of heterozygosity (LOH)
       • Linear dynamic range: 0-60 copies
    • Interrogates the entire genome
    • More than 335,000 markers

High-quality data from 75 ng of input DNA
    • More than 6,000 samples processed by our Research Services Laboratory
    • Average pass rate of 92 percent
    • Successful on samples as old as 28 years

Advanced data analysis
    • We have partnered with BioDiscovery, an industry-leading software provider, to enable a more comprehensive data analysis solution.

Convenience and quality
Experience the convenience of our Research Services Laboratory—just send in your DNA to FFPE Express Services and visualize the results. Our Research Services Laboratory has processed thousands of the most challenging FFPE samples with a pass rate of greater than 92 percent, and our lab has the quality systems in place to handle your project with the highest standard of care and excellence. Take advantage of our expertise and receive data of the highest quality with the FFPE Express 2.0 Service.

Learn how scientists are using MIP technology and FFPE Express 2.0 Services
Molecular inversion probes: a novel microarray technology and its application in cancer research
View a list of publications using FFPE Express technology
Scientist spotlight, MIP technology reveals important copy number changes in pediatric cancers

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

Genome-Wide Human SNP Array 6.0 Genotyping Services
Run your association study with the ARSL. With more than 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 represents more genetic variation on a single array than any other product.

If you'd like to place an order with the Research Services Laboratory, please contact us at Bioinformatics_Services@affymetrix.com.