The Affymetrix Axiom platform is a hybridization-based genotyping array that offers a flexible choice of predesigned modules and customizable contents. Its utility has been shown in large cohorts, such as the UK Biobank26 (link) and Million Veteran Program,29 (link) multirace/ethnic cohorts,30 (link) and in focused research areas such as transplant research.24 (link) There are approximately 1.38 million features available. Some SNPs and copy number polymorphisms (CNPs) take more than one feature to be genotyped with high quality. As a result, the TM-Array contains approximately 879,000 SNPs and CNPs.
Axiom platform
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Axiom platform is a high-throughput genotyping solution designed for genetic research and clinical applications. The platform utilizes microarray technology to analyze thousands of genetic markers simultaneously, providing a comprehensive view of an individual's genetic profile.
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7 protocols using axiom platform
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Affymetrix Axiom Genotyping Platform
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Genome-Wide SNP Data Analysis in KORA Cohort
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For all KORA individuals, genome-wide SNP data were already available. [10 (link), 11 (link), 13 (link), 14 (link)] KORA S4/F4 samples were genotyped on the Affymetrix® Axiom platform. Genotypes were called with the Affymetrix® software and annotated to NCBI build 37. We excluded SNPs with call rates <98%, HWE p-values <5x10-6, and minor allele frequency <1%. SHAPEIT v2 was used for pre-phasing, imputation performed with IMPUTE v2.3.0 using the 1000G phase1 reference panel. In total,18,185,628 SNPs genotyped on the Affymetrix® Axiom platform were available for analysis.
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Multiomics Analysis of Infection Response
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Broad molecular analyses are an important focus of PROGRESS. All study participants will be genotyped using the CAP2 array, a customized array based on the Axiom platform (Affymetrix). The CAP2 array comprises the standard genome-wide content of the Axiom CEU array and about 60,000 custom SNPs. This custom content consists of SNPs selected from existing literature evidence, eQTL data bases, GWAS data bases, and data bases of functionally relevant mutations. Genetic data from the CAP2 array are suitable for imputation of genotype data with common genomic references. Genome-wide gene-expression measurements using the HumanHT-12v4 Expression BeadChip (Illumina) comprise 47.000 transcript features in RNA from stabilized whole blood (PAXgene Blood RNA System, PreAnalytiX). Proteome analyses involve gel-free LC-MS/MS focused measurements in EDTA plasma samples stabilized by protease inhibitors (BD P100 Blood Collection System for plasma protein preservation, Becton Dickinson) and depleted for highly abundant proteins. Collected biospecimen also allow measurements of other serum and plasma parameters as well as cytokines. As patient samples are available from consecutive study time points, time series data can be established which are amenable to temporal analysis of molecular response to infection.
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High-throughput SNP genotyping for sea lice
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A custom SNP genotyping array containing 201,279 assays for L. salmonis was developed for use on the Affymetrix Axiom platform. Purified DNA extracted from 1629 individuals was quantified, normalized and genotyped according to the manufacturer's protocol. Individual sample performance was assessed using the Affymetrix Best Practice workflow, which lead to the exclusion of 42 samples, leaving 1587. Each SNP assay was subsequently classified into one of six categories reflecting assay performance; only the genotypes from "PolyHighResolution" SNP assays were used for mapping (n = 101,622 SNPs). Information on the polymorphic SNP markers scored in this study can be found in Supplementary File 2 of Messmer et al. (2018) (link).
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Developing a South Asian Genotyping Array
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We partnered with Thermo Fisher Scientific to develop a custom genotyping array using their Axiom platform. The SARGAM (South Asian Research Genotyping Array for Medicine) assays a total of 639,029 SNPs, including 515,921 variants chosen to optimize imputation accuracy as well as 102,752 putatively functional variants that had a minor allele frequency of >0.1% in our medical cohorts. The imputation-based SNPs were chosen using an algorithm similar to the one described by Hoffmann et al.41 (link), based on the South Asian medical cohort phased reference panel described above. The initial list of putative functional variants was obtained from a variety of sources, including this project, gnomAD19 (link), the UK Biobank42 (link) and properly consented MedGenome internal data.
We initially started with a larger list of 924,667 SNPs that were assayed on two custom test arrays that were then used to genotype 960 individuals from the GAsP2 study for quality control purposes. We removed SNPs that could not be genotyped accurately as well as low-priority variants to arrive at the final SARGAM array design.
We initially started with a larger list of 924,667 SNPs that were assayed on two custom test arrays that were then used to genotype 960 individuals from the GAsP2 study for quality control purposes. We removed SNPs that could not be genotyped accurately as well as low-priority variants to arrive at the final SARGAM array design.
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High-Throughput Genotyping of Radiata Pine
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From the 6 protected replicates, needle samples were collected from all individuals (n = 390) and stored at −80°C before DNA extraction. Total genomic DNA was extracted using a commercial NucleoSpin Plant II kit (Machery-Nagel, Duren, Germany) with modifications (Telfer et al. 2013 ). DNA purity and concentration were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA) and quantified using the Agilent 5200 fragment analyzer (Palo Alto, CA, USA). The samples were genotyped using the 36K axiom SNP chip for radiata pine (NZPRAD02) developed on the Axiom platform (Thermo Fisher Scientific, Waltham, MA, USA) (Graham et al. 2022 ). Currently, this is the densest SNP array for radiata pine, capable of assaying 36,285 SNPs. A total of 390 individuals were included in the final genotype data with a total of 27,000 SNPs. These genotype data were filtered to include only SNPs with a mean allele frequency >0.05 and maximum missing data of 0.4% using the rrBLUP package (Endelman 2011 ). This filtering resulted in the retention of 15,624 SNPs for analysis. The genotyping reproducibility rate was high (99.9%), as estimated from 10 samples that were replicated during DNA extraction.
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Replication of Genetic Association Study
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For our replication study, we used the pre-imputed dataset released by the TMM32 (link),33 (link). Within this dataset, we used the subsets genotyped using Omni2.5 SNP array (Illumina Inc., San Diego, CA, USA) as well as the customized genotyping array designed by the TMM based on the Axiom platform (Thermo Fisher Scientific, Waltham, MA USA), denoted as Japonica array version 2 (JPAv2). The genotyped data were pre-phased using SHAPEIT version 2 r837 and imputed using IMPUTE2 version 2.2.2 and 2KJPN with an allele frequency panel of ~ 2000 Japanese individuals34 (link)–36 (link). After conducting the same quality control with the main dataset, 4,935,024 and 5,686,147 variants in the JPAv2 and Omni2.5 datasets, respectively, were selected for further analysis.
Replication analysis was conducted using the same exclusion criteria as those for the main analysis. Additionally, we excluded the Miyagi population in the subjects genotyped by JPAv2, because of small sample size (n = 678). The all subjects in the dataset genotyped by Omni2.5 belonged in the Miyagi population. Ultimately, 2791 and 1597 individuals for the JPAv2 and Omni2.5 dataset, respectively, were selected for replication analysis.
Replication analysis was conducted using the same exclusion criteria as those for the main analysis. Additionally, we excluded the Miyagi population in the subjects genotyped by JPAv2, because of small sample size (n = 678). The all subjects in the dataset genotyped by Omni2.5 belonged in the Miyagi population. Ultimately, 2791 and 1597 individuals for the JPAv2 and Omni2.5 dataset, respectively, were selected for replication analysis.
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