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Reliable insights to support confident decisions for population studies
Microarrays were developed in the early 90s to study mutations associated with novel genes at the time, such as the p53 gene in cancer, and mutations associated with the HIV epidemic. Their utility quickly transcended into other applications such as gene expression and reproductive health. Their high throughput formats, easy data analysis, and low cost of ownership make them ideal to tackle the next genomics frontiers: biobanking and characterization of large research cohorts, population stratification for polygenic risk score (PRS) development, population-based health screening, and multi-omic research studies.
Find SNPs, indels, and CNVs associated with disease risk
Large-scale genotyping studies aimed at improving understanding of the genetic factors of disease risk and drug response are helping to pave the way toward precision medicine and predictive health. Multi-year cohort studies and research screening initiatives are working to identify genetic effects in many different populations through genotyping analysis and create risk scores, also called “polygenic risk scores,” to quantify susceptibility of that disease in that population. To be successful, these studies require high-density, SNP genotyping arrays that can provide highly accurate imputation, deliver reproducible results, and help ensure there is no loss of SNP markers from lot to lot.
Axiom PangenomiX Array
The Axiom PangenomiX Array is the most comprehensive array within the Axiom microarray catalog for studying disease susceptibility and risk, pharmacogenomics (PGx), and genetic factors underlying wellness and lifestyle in diverse populations. It offers >850,000 markers selected for high genomic coverage from the 1000Genomes Project Phase III and other broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, and PharmaGKB.
Publicly available imputation algorithms enable imputation to the whole genome. For difficult-to-genotype markers, rare variants, or complex gene regions (e.g., CYP2D6), the Axiom PangenomiX Plus Assay enables accurate results through the use of multiplexed PCR to amplify those difficult markers or genes. Genotypes can be plugged into PRS algorithms to produce disease specific risk scores for translational research studies and national and regional health screening initiatives.
Axiom Pan African Cancer Research Array
The Axiom Pan-African Cancer Research Array was developed with the Men of African Descent and Carcinoma of the Prostate (MADCaP) Consortium to enable better association of genetic variants with prostate and other cancers in African populations. Ultimately, it aimed to classify cancer risk in previously understudied ethnic groups (the array was enriched for comprehensive coverage of variants that are polymorphic in African populations, including 18 ethnolinguistic groups from Sub-Saharan Africa [2,3].). It boasts 1.4M markers split between two arrays and is the first of its kind to capture so many markers for the African population.
- Harlemon M et al. (2020) A custom genotyping array reveals population-1 level heterogeneity for the genetic risks of prostate cancer and other cancers in Africa. Cancer Res 80(13):2956–2966.
- Gurdasani D et al. (2015) The African Genome Variation Project shapes medical genetics in Africa. Nature 517(7534):327–332.
- Blog Post: The First Large Pan-African GWAS Tackling Cancer Health Disparities in African Populations
Axiom Transplant Genotyping Array
The Axiom Transplant Genotyping Array was designed with the International Genetics & Translational Research in Transplantation Network (iGeneTRAiN), a network established to further research in solid-organ transplantation (specifically heart, kidney, liver, and lung transplants) by utilizing genetic information to improve transplant success and tailoring treatments for patient-specific recommended therapeutics. iGeneTRAiN’s ultimate goal is to translate this information into clinical practice and to minimize graft rejection and complications of rejection.
Biobank research and discovery
Biobank studies are at the forefront of novel variant research and discovery in a variety of disease fields. The resulting data is made available to researchers worldwide, providing a large
reference data sets that can be useful in assessing potential case associations of rare variants identified in studies of other populations. For more information, check out this brochure.
Many of the world’s largest population genetic epidemiology projects, such as the UK Biobank’s original 500,000 cohort, have chosen Axiom products for their genotyping studies.
The UK Biobank Array was designed by leading researchers in the fields of epidemiology, human disease, and population genetics for use by the UK Biobank in one of the largest genotyping studies to date. The UK Biobank’s prospective genotyping study of 500,000 individuals is aimed at uncovering the complex interactions between genes, lifestyle, and environment (marker–phenotype interactions).
The UK Biobank Array was designed by leading researchers in the fields of epidemiology, human disease, and population genetics for use by the UK Biobank in one of the largest genotyping studies to date. The UK Biobank’s prospective genotyping study of 500,000 individuals is aimed at uncovering the complex interactions between genes, lifestyle, and environment (marker–phenotype interactions).
| Category | Axiom PangenomiX Array | Asia Precision Medicine Research Array | UK Biobank |
|---|---|---|---|
| Total markers | >900,000 | >750,000 | >800,000 |
| GWAS | >800,000 | >540,000 | >600,000 |
| NHGRI EBI GWAS Catalog | >25,000 | >23,400 | >8,000 |
| ACMG 73 | >16,000 | >9,200 | >9,000 |
| ClinVar variants | >23,000 | >43,000 | >7,500 |
| High value markers from inherited disorders | >5,300 | >2,000 | >75 |
| Pharmacogenomic | 92,639 | 69,988 | 67,197 |
| Blood typing | >2,700 | >140 | >650 |
| HLA typing | >14,000 | >10,400 | >8,200 |
| COVID-19 and host response | >53,000 | - | - |
| Cancer risk variants | >6,000 | >8,000 | >6,500 |
| Loss of function | >3,600 | >43,000 | >30,000 |
| Expression quantitative trait loci | >17,000 | >15,000 | >17,000 |
| Neuropsychiatric conditions and lung function; CNV regions for developmental delay | >6,000 | >910 | >2,300 |
| Fingerprinting and sample tracking | >300 | >300 | >300 |
| Lifestyle and wellness genetic testing | >1,400 | >1,200 | >250 |
| Y chromosome markers | >440 | >400 | >800 |
| Mitochondrial markers | >1,100 | >500 | >350 |
Data set of total markers versus arrays and biobanks
These biobank and research genomic data sets are being combined with other data sets to create “multi-omic” profiles on individuals for more comprehensive, multi-modal, understanding of human disease. Multi-omic studies can include data sets from genomics, transcriptomics or gene expression, proteomics, metabalomics, methylomics or epigenome, and microbiome, and even physical data (height, weight, etc).
Population-specific arrays
Ethnically diverse genotyping studies and reference data sets are critical and propelling predictive genomics forward. Different markers have different allelic frequencies in different populations and understanding these differences will enable better disease risk prediction and better therapeutic selection. Axiom Population-Optimized arrays are genotyping panels that offer genetic coverage of rare and common variants for efficient genome-wide disease association studies. The arrays include markers that are specific to HapMap populations with high coverage of rare and common variants. The use of imputation enables a highly cost-effective, budget-conscious alternative to other commercially available arrays.
Optimized pre-designed arrays offer increased study power in diverse populations and applications.
| Target populations | Common variant studies | Common and rare variant studies | Replicatin and epidemiology |
|---|---|---|---|
| Northern Europe | Axiom CEU | Axiom EUR | |
| Asian | Axiom CHB | Axiom ASI | Axiom EAS |
| African | Axiom PanAFR | Axiom AFR | |
| Southern European and Latin American | Axiom LAT | ||
| MAF>5% | MAC>2.5% | MAF>1% |
Custom designed arrays
Research projects and populations are unique, and your array can be too. Thermo Fisher has over 40 bioinformaticians with years of custom design and genotyping analysis expertise that can work with you to bring to life a custom designed array. The Axiom Genomic Database has over 26 million SNPs and insertion-deletions that have been verified and can be added to your array.
Axiom myDesign arrays offer outstanding scale and flexibility to design the most optimal array for your disease and population studies involving genome-wide association, replication, fine mapping, and candidate gene studies. Include markers of your choosing or select markers from the Axiom Genomic Database, which contains over 11 million high-performance genotype-tested (biologically and technically validated) annotated common and rare variants. Proprietary imputation-based SNP selection algorithms can be used to design population-optimized GWAS marker modules that deliver high genomic coverage and accuracy.
To order a human custom design, talk to your sales representative today or email bioinformaticsservices@thermofisher.com.
Research laboratory 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.
If you would like to place a genotyping order with MRSL, please contact us via email at bioinformaticsservices@thermofisher.com.
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