Ukb axiom array

Manufactured by Thermo Fisher Scientific

Sourced in United States

The UKB Axiom Array is a high-throughput genotyping platform developed by Thermo Fisher Scientific. It is designed to perform comprehensive genome-wide genotyping analysis. The array features a dense set of genetic markers covering the human genome.

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Axiom array (59 citations)

22 protocols using ukb axiom array

Genotyping and Quality Control of UKB Data

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The 487,409 UKB subjects were genotyped using the UKB Axiom Array and United Kingdom BiLEVE Axiom Array from Affymetrix^{50 (link)}. Genotypes were imputed using the Haplotype Reference Consortium (HRC) and the UK10K haplotype resource^{51 (link)}. Next, we performed quality control of SNPs using PLINK v.1.90^{27 (link)} based on the following exclusion criteria: SNPs with missing genotype call rates >0.05, minor allele frequency <0.01, Hardy-Weinberg equilibrium P < 1.00 × 10⁻⁶, insertion-deletion. Finally, 1,141,242 SNPs were extracted for further analyses after referring to the HapMap 3 SNPs and strand-ambiguous SNPs (i.e., SNPs with alleles A/T or C/G)^{52 (link),53 (link)}.

Jung H., Jung H.U., Baek E.J., Kwon S.Y., Kang J.O., Lim J.E, & Oh B. (2024). Integration of risk factor polygenic risk score with disease polygenic risk score for disease prediction. Communications Biology, 7, 180.

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Genotyping and Sequencing of Icelandic and British Cohorts

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In the Icelandic data set, those with ICV measurements and with others phenotypes/traits participated in the number of projects at deCODE genetics. The preparation, chip-genotyping and or whole-genome sequencing of these samples was carried out at deCODE genetics.^{30 (link),31 (link)} Using Graphtyper^{32 (link)} on WGS (using GAIIx, HiSeq, HiSeqX and NovaSeq Illumina technology to a mean depth of at least ×17.8), data of 61 205 Icelanders, 42.9 million high quality sequence variants were identified. Along with WGS set, deCODE genetics has also chip-genotyped 155 250 Icelanders using one of the Illumina genotyping arrays. The genotype calls (including SNP and insertions/deletions) based on WGS set were imputed into chip-genotyped subjects and long-range phased by using haplotype sharing and genealogical information.^{33 (link)}In the UKB, the samples were genotyped on two Affymetrix arrays. Initial set of 50 000 samples was chip-genotyped using the Affymetrix UK BiLEVE Axiom array.^{34 (link)} The additional set of 450 000 samples were chip-genotyped for 850 000 sequence variants using the Affymetrix UKB Axiom® array.^{34 (link)} Both arrays target 95% of same variants.^{34 (link)} The chip-genotypes were used to impute for additional markers by using 1000 Genomes phase 3,^{35 (link)} UK10K^{36 (link)} and HRC reference panels.

Nawaz M.S., Einarsson G., Bustamante M., Gisladottir R.S., Walters G.B., Jonsdottir G.A., Skuladottir A.T., Bjornsdottir G., Magnusson S.H., Asbjornsdottir B., Unnsteinsdottir U., Sigurdsson E., Jonsson P.V., Palmadottir V.K., Gudjonsson S.A., Halldorsson G.H., Ferkingstad E., Jonsdottir I., Thorleifsson G., Holm H., Thorsteinsdottir U., Sulem P., Gudbjartsson D.F., Stefansson H., Thorgeirsson T.E., Ulfarsson M.O, & Stefansson K. (2022). Thirty novel sequence variants impacting human intracranial volume. Brain Communications, 4(6), fcac271.

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UK Biobank Genetic Data Quality Control

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Genotypes of the UKB data set were analyzed with the Affymetrix (Santa Clara, CA, USA) UKB Axiom Array and the UK BiLEVE Axiom Array. Further information about quality control procedures, imputation, and principal components analysis can be found in Bycroft et al. [7 (link)]. Participants were removed from the present study based on the following characteristics: non-British ancestry, high missingness, relatedness, quality control failure, and gender mismatch.

Zhu C., Zhao Q., He J., Böckerman P., Luo S, & Chen Q. (2023). Genetic basis of STEM occupational choice and regional economic performance: a UK biobank genome-wide association study. Human Genomics, 17, 40.

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UK Biobank Genetic Imputation Protocol

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At baseline, imputation data of 93, 095, 623 SNPs were available for 487,409 participants using the UKB Axiom Array and the United Kingdom BiLEVE Axiom Array from Affymetrix (Santa Clara, CA, United States ) (Sudlow et al., 2015 (link)). Genotyping imputation was performed using the United Kingdom10K Project and 1,000 Genome Project Phase 3 reference panels (Consortium et al., 2015 (link); Genomes Project et al., 2015 (link)). Quality control was performed based on the following exclusion criteria using PLINK v.1.90: SNPs with missing genotype call rates >0.05, minor allele frequency < 0.01, and P for Hardy-Weinberg equilibrium test <1.00 × 10^–6). A total of 5,664,578 SNPs was retained for further analysis.

Baek E.J., Jung H.U., Ha T.W., Kim D.J., Lim J.E., Kim H.K., Kang J.O, & Oh B. (2022). Genome-Wide Interaction Study of Late-Onset Asthma With Seven Environmental Factors Using a Structured Linear Mixed Model in Europeans. Frontiers in Genetics, 13, 765502.

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UK Biobank Genotyping and Quality Control

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The 487,409 UK Biobank (UKB) participants were genotyped using the UKB Axiom Array and the United Kingdom BiLEVE Axiom Array from Affymetrix (Sudlow et al., 2015 (link); Bycroft et al., 2018 (link)). Genotypes were imputed using the Haplotype Reference Consortium (HRC) and UK10K haplotype resource (McCarthy et al., 2016 (link)). Next, we performed quality control of SNPs using PLINK v.1.90 (Purcell et al., 2007 (link)) based on the following exclusion criteria: SNPs with missing genotype call rates >0.05, minor allele frequency <0.01, Hardy-Weinberg equilibrium p-value < 1.00 × 10⁻⁶, insertion-deletion 780000. Finally, 1,149,057 SNPs were extracted for further analyses after referring to HapMap 3 SNPs and strand-ambiguous SNPs (that is, SNPs with the allele A/T or C/G) (International HapMap Consortium, 2003 (link); International HapMap Consortium, 2005 (link); Agrawal et al., 2022 (link)).

Jung H., Jung H.U., Baek E.J., Chung J.Y., Kwon S.Y., Kang J.O., Lim J.E, & Oh B. (2023). Investigation of heteroscedasticity in polygenic risk scores across 15 quantitative traits. Frontiers in Genetics, 14, 1150889.

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UK Biobank Pregnancy History and Cardiovascular Disease

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The present study included data from the UKB, of which details have been described previously.11 (link) Briefly, the UKB is a large-scale prospective study in the general population of the UK, in which over 500 000 individuals aged 40–69 years were recruited between 2006 and 2010.11 (link)
For the MR analysis, we used individual-level imputed data on genetic variants. Genotyping was performed using the Affymetrix UK BiLEVE Axiom array and the Affymetrix UKB Axiom array.12 13 (link) Genotype imputation was based on the Haplotype Reference Consortium and the UK10K haplotype reference panel.14 (link)
Of the 502 412 UKB participants, we excluded 43 because they withdrew from the study, 15 207 because they had missing genetic data and 1476 women without data on history of pregnancy. Consequently, 485 686 individuals (221 155 ever pregnant women, 41 506 never pregnant women and 223 025 men) contributed to the present analysis.
Specific definitions of HDPs, CVD events and additional variables, and a power analysis are provided in the online supplemental methods.

Tschiderer L., van der Schouw Y.T., Burgess S., Bloemenkamp K.W., Seekircher L., Willeit P., Onland-Moret C, & Peters S.A. (2023). Hypertensive disorders of pregnancy and cardiovascular disease risk: a Mendelian randomisation study. Heart, 110(10), 710-717.

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UK Biobank Pregnancy and Cardiovascular Disease

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The present study included data from the UKB, of which details have been described previously.^{12 (link)} Briefly, the UKB is a large-scale prospective study in the general population of the UK, in which over 500,000 individuals aged 40-69 years were recruited between 2006 and 2010.^{12 (link)} The study was approved by the North-West Multi-Centre Research Ethics Committee (16/NW/0274) and all participants provided written informed consent.
For the MR analysis, we used individual-level imputed data on genetic variants. Genotyping was performed using the Affymetrix UK BiLEVE Axiom array and the Affymetrix UKB Axiom Array.^{13 (link),14 (link)} Genotype imputation was based on the Haplotype Reference Consortium and the UK10K haplotype reference panel.^{15 (link)}Of the 502,412 UKB participants, we excluded 43 because they withdrew from the study, 15,207 because they had missing genetic data, and 1,476 women without data on history of pregnancy. Consequently, 485,686 individuals (221,155 ever pregnant women, 41,506 never pregnant women, and 223,025 men) contributed to the present analysis.
Specific definitions of HDPs, CVD events, and additional variables, and a power analysis are provided in the Supplementary Methods.

Tschiderer L., van der Schouw Y.T., Burgess S., Bloemenkamp K.W., Seekircher L., Willeit P., Onland-Moret N.C, & Peters S.A. (2023). Hypertensive disorders of pregnancy and cardiovascular disease risk: A Mendelian Randomisation study. European heart journal, 44(Suppl 2), 655.2726.

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Genome-wide Genotyping and Imputation in UK Biobank

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Genome-wide genotyping was performed in UKB individuals using either the Affymetrix UKB Axiom array or Affymetrix UK BiLEVE Axiom, which included 812,428 SNPs. Imputation was conducted using IMPUTE2 with the reference panel of the UK10K projects, Haplotype Reference Consortium, and 1000 Genomes^{23 (link)}. For quality control on the genotype data, the UKB excluded the SNPs with INFO < 0.9, Hardy–Weinberg equilibrium (HWE) testing p values < 0.0001, minor allele frequencies (MAF) < 0.01 and genotyping call rate <95%. A total of 488,377 individuals and 805,426 SNPs were kept after applying quality control (QC). After removing individuals who reported inconsistencies between self-reported sex and genetic sex, as well as those with missing covariate information, 376,807 individuals of white British ancestry subset (UK Biobank field ID: 21000)^{23 (link)} were retained for further analysis^{23 (link)}.

Cheng B., Bai Y., Liu L., Meng P., Cheng S., Yang X., Pan C., Wei W., Liu H., Jia Y., Wen Y, & Zhang F. (2024). Mendelian randomization study of the relationship between blood and urine biomarkers and schizophrenia in the UK Biobank cohort. Communications Medicine, 4, 40.

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UKB Genotyping and Quality Control

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The UKB genotyped 487,409 participants using the UKB Axiom array and the United Kingom BiLEVE Axiom array from Affymetrix (Santa Clara, CA, United States) (Sudlow et al., 2015 (link); Bycroft et al., 2018 (link)). Genotyping was performed using the United Kingom10 K Project and 1,000 Genome Project Phase 3 reference panels (Huang et al., 2015 (link)). SNP quality control procedures were applied to 93,095 623 imputed SNPs based on the following exclusion criteria: SNPs with missing genotype call rates >0.05, minor allele frequency <0.01, and p-value for Hardy-Weinberg equilibrium test <1.00 × 10^–6. In total, 5,664 578 SNPs were retained for further analysis.

Chung J.Y., Jung H.U., Kim D.J., Baek E.J., Kim H.K., Kang J.O., Lim J.E, & Oh B. (2022). Identification of five genetic variants with differential effects on obesity-related traits based on age. Frontiers in Genetics, 13, 970657.

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UKB Genotyping Imputation and Quality Control

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At baseline, imputation data for 93,095,623 SNPs were available for 487,409 participants using the UKB Axiom Array and the UK BiLEVE Axiom Array from Affymetrix (Sudlow et al., 2015 (link)). Genotyping imputation was performed using the UK10K Project and 1,000 Genome Project Phase 3 reference panels (UK10K Consortium et al., 2015 (link)). Quality control was performed based on the following exclusion criteria using PLINK v.1.90: SNPs with missing genotype call rates >0.05; minor allele frequency (MAF) < 0.01; and p-value for Hardy-Weinberg equilibrium test <1.00 × 10⁻⁶ (Purcell et al., 2007 (link)). A total of 5,664,578 SNPs were retained for further analysis.

Baek E.J., Jung H.U., Chung J.Y., Jung H.I., Kwon S.Y., Lim J.E., Kim H.K., Kang J.O, & Oh B. (2022). The effect of heteroscedasticity on the prediction efficiency of genome-wide polygenic score for body mass index. Frontiers in Genetics, 13, 1025568.

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