Axiom PangenomiX Array

The Applied Biosystems Axiom PangenomiX Array is a human genotyping research array designed for whole-genome imputation with diverse and global population coverage. It is a valuable research tool for human genomics, including applications such as genome-wide association studies (GWAS), population health initiatives, polygenic risk score research and development, and clinical research for trials in drug discovery. The Axiom PangenomiX Array can scan the whole genome from as little as 100 ng genomic DNA. It can enable target single nucleotide polymorphism (SNP) identification, copy number variant analysis, human leukocyte antigen (HLA) typing and more in a single, cost-effective assay with ready-to-use data analysis.

Ethnic diversity at your fingertips—the largest population coverage on a high throughput array

More than 800,000 markers were selected for high genomic coverage from the 1000 Genomes Project phase 3, yielding coverage for European, African, admixed American, East Asian, and South Asian populations. This means variants prevalent in different populations can be accurately represented and accounted for, leading to more inclusive research outcomes.

In addition to markers selected specifically to maximize imputation power and ethnic diversity, additional markers were chosen from broadly referenced public databases, including ACMG 73, ClinVar, NHGRI-EBI GWAS catalog, CPIC, PharmGKB, and PharmaADME, and can be directly genotyped for each sample.

The Axiom PangenomiX Array also offers CNV analysis for fixed genomic regions and de novo copy number discovery to detect copy number changes across the whole genome. The Axiom PangenomiX Plus Array enables genotyping of markers of important genes in difficult-to-genotype regions, such as pharmacogene CYP2D6, and comes with Pharmacogenomic Translation Reports with general metabolizer status.

Comprehensive array content for your research

Genome-wide association study (GWAS) imputation module with ~800,000 markers across all ancestral populations
Evidence-based markers for relevant variants including ClinVar variants for comprehensive coverage of ACMG 73 genes
Pharmacogenomics (PGx) variants cited in Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines and Pharmacogenomics Knowledge Base (PharmGKB) disease-related variants (Alzheimer’s disease, cancer, cardiovascular and cardiometabolic diseases, diabetes, and neurological disorders)
Blood phenotyping variants for blood typing of common and rare blood groups, bleeding disorders, and blood conditions such as sickle cell anemia
HLA typing of 11 major histocompatibility complex (MHC) Class I and Class II loci
COVID-19, host response, and immune-related markers

Axiom PangenomiX Array data sheet

For additional information on specifications, workflow, and application-specific content

Download data sheet

Imputation to enhance accuracy and coverage

The Axiom PangenomiX Array includes over 800,000 markers in the GWAS module. Common variants are intelligently selected via a proprietary imputation-based marker selection strategy for genome-wide coverage in the five major ancestral populations. This process allows access to a vast number of low frequency markers (minor allele frequency [MAF] >1%) and common markers (MAF >5%) for any given population, through imputation. The intelligent, imputation-aware design helps ensure that the selection of markers offers high imputation accuracy across all ancestral populations. The autosomal markers in the GWAS grid are valuable in ascertaining the ethnic breakdown of individuals genotyped with the Axiom PangenomiX Array. Combined with the mitochondrial and Y chromosome markers, the Axiom PangenomiX Array is a powerful array for determining ancestry and migration patterns in genetic testing.

Number of imputed markers with r²≥0.8 and MAF >1%.
Number of imputed variants		Imputation accuracy
Population	MAF > 1%	MAF > 1%	MAF > 5%
African (AFR)	15.2 M	0.90	0.92
Admixed American (AMR)	10.3 M	0.92	0.94
East Asian (EAS)	7.5 M	0.88	0.93
European (EUR)	8.8 M	0.91	0.95
South Asian (SAS)	9.01 M	0.90	0.94

Superior coverage and accuracy

How do we stack up against population-scale disease testing products on the market today? The Axiom PangenomiX Array was designed with your disease and pharmacogenomic research studies in mind, based on years of expertise developing and testing arrays used in landmark population disease testing like the Precision Medicine Diversity Research Array (PMDA) and UKBiobank arrays. Allow us to walk you through the Axiom difference by requesting contact with one of our knowledgeable predictive genomics experts.

Coverage

Accuracy

Axiom PangenomiX Array markers for research applications* For more detailed content information access the datasheet
Cancer risk variants	>13,000
Mental, behavioral, neurological, and neurodevelopmental risk variants	>4,300
Inherited eye disease risk variants	>3,700
Autoimmune and inflammatory disease risk variants	>1,150
Loss of function variants, autosomal inheritance	>3,600
Cardiovascular disease risk variants	>8,500
Respiration disorder risk variants	>500
Diabetes risk variants	>1,500
Musculoskeletal disease risk variants	>5,900

* Disease categories as classified by NHGRI, OMIM, and ClinVar

Customization to meet you where you are—Axiom MyDesign arrays

Not seeing the content you’re looking for? Thermo Fisher Scientific has over 40 bioinformaticians with years of custom design and genotyping analysis expertise who can work with you to bring a custom designed array to life in as little as six weeks. Include markers of your choosing or select markers from the Axiom Genomic Database, which contains over 11 million high-performance genotype.

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Genotyping services

Our Microarray Research Services Laboratory (MRSL) is a high-throughput facility that offers affordable and fast genotyping services for large-scale, microarray-based studies. With one of the largest microarray capacities in the world, MRSL generates high-quality data and enables academic and research institutions to complete their large-scale PoP studies quickly. Our short turnaround times allow our customers to conduct their data analysis rapidly, improving their time to publication and grant submission.

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To order a human custom design or place an MRSL order, request to speak to representative or email bioinformaticsservices@thermofisher.com.