Uk bileve

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The UK BiLEVE is a laboratory equipment product designed for specific applications. It serves a core function within its intended use. No further details can be provided while maintaining an unbiased and factual approach.

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Beadchips, by Illumina (1 mentions) Abi prism 7900ht sequence detection system, by Thermo Fisher Scientific (1 mentions)

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UK BiLEVE Axiom array (126 citations) UK BiLEVE Axiom (31 citations) UK BiLEVE array (9 citations) UK BiLEVE Axiom Array chip (5 citations) UK BiLEVE Axiom87 (2 citations)

6 protocols using uk bileve

UK Biobank Genotype Imputation Protocol

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UK Biobank is a large-scale national health resource of over 500,000 individuals from across the United Kingdom (UK). Study participants were invited to 1 of 22 centers across the UK between 2006 and 2010, described in detail elsewhere^{29 (link)}. Over 500,000 subjects with their phenotypes in the UK Biobank, ~488,377 subjects were genotyped at ~800,000 SNPs using the UK BiLEVE and UK Biobank Axiom Arrays from Affymetrix. Pre-phasing was carried out using a modified version of the SHAPEIT2 (ref. ^{43 (link)}) and imputation was performed with the UK10K and the 1000 Genomes Phase 3 reference panels using IMPUTE2 (ref. ^{44 (link)}), which resulted in ~93 million SNPs (Supplementary Table 7). With MAF > 0.05, imputation R² > 0.8, and P(HWE) > 10⁻¹⁰, we finally have 5,498,274 SNPs. Genotyping, quality control for SNPs and samples, and imputation procedures are described in detail here^{30 ,31}. Individuals of non-European ancestry were excluded to be consistent with NHS/HPFS/PHS cohort data, which results in 456,837 individuals. For simulation studies and real GWAS analyses, we prepared 30,000 (30K) and 436,837 (437K) individuals for a training set and the remaining 20,000 (20K) individuals for a validation set.

Chung W., Chen J., Turman C., Lindstrom S., Zhu Z., Loh P.R., Kraft P, & Liang L. (2019). Efficient cross-trait penalized regression increases prediction accuracy in large cohorts using secondary phenotypes. Nature Communications, 10, 569.

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Genotyping Platforms for Large-Scale Genomics

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Several different Illumina-based genotyping platforms (Illumina Inc., San Diego, CA, USA) were used: HumanHap300 Duo‘+’ chips or the combination of the Human-Hap300 Duo and iSelect chips (WGHS), Infinium 370cnvDuo array (NFBC), 317 K, 370 K, or 610 K SNP platforms (QIMR). Genotyping of participants in the UKBB was performed either on the Affymetrix UK BiLEVE or Affymetrix UK Biobank Axiom® array with over 95% similarity. Genotyping of participants in the 23andMe cohort was performed on various versions of Illumina-based BeadChips.

Gallagher C.S., Mäkinen N., Harris H.R., Rahmioglu N., Uimari O., Cook J.P., Shigesi N., Ferreira T., Velez-Edwards D.R., Edwards T.L., Mortlock S., Ruhioglu Z., Day F., Becker C.M., Karhunen V., Martikainen H., Järvelin M.R., Cantor R.M., Ridker P.M., Terry K.L., Buring J.E., Gordon S.D., Medland S.E., Montgomery G.W., Nyholt D.R., Hinds D.A., Tung J.Y., Perry J.R., Lind P.A., Painter J.N., Martin N.G., Morris A.P., Chasman D.I., Missmer S.A., Zondervan K.T, & Morton C.C. (2019). Genome-wide association and epidemiological analyses reveal common genetic origins between uterine leiomyomata and endometriosis. Nature Communications, 10, 4857.

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Genotyping and Imputation of UK Biobank

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Genotyping and imputation data were obtained from the UK Biobank March 2018 data release. Genotyping was conducted using the Affymetrix UK BiLEVE and Affymetrix UK Biobank Axiom arrays. Imputation was performed with the IMPUTE4 program (https://jmarchini.org/impute-4/)^{68 (link)} using the Haplotype Reference Consortium (HRC)^{69 (link)} and merged UK10K and 1000 Genomes phase 3 reference panels. Details on DNA extraction and quantification^{70 (link)} as well as on the centralized analysis of the genetic data, genotype quality, properties of population structure and relatedness of the genetic data, and efficient phasing and genotype imputation have been reported previously^{68 (link)}.

Tsepilov Y.A., Freidin M.B., Shadrina A.S., Sharapov S.Z., Elgaeva E.E., Zundert J.V., Karssen L.С., Suri P., Williams F.M, & Aulchenko Y.S. (2020). Analysis of genetically independent phenotypes identifies shared genetic factors associated with chronic musculoskeletal pain conditions. Communications Biology, 3, 329.

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UK Biobank Genetic Data Protocol

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The UK Biobank study is a prospective cohort included health, hospital-records and genetic data from more than 0.5 million participants [19 (link)]. UK Biobank has electronic signed consent from the study participants and ethical approval was obtained from Northwest Multi-center Research Ethics Committee. We used the imputed genotype dataset released by UK Biobank in July 2017. Subjects were excluded if the self-reported gender were inconsistent with the genetic gender, or were genotyped but not imputed or withdraw their consents.
DNA samples of all participants in the UK Biobank were genotyped using either the Affymetrix UK Biobank Axiom (825,927 markers) array or Affymetrix UK BiLEVE (807,411 markers) [20 (link)]. SNPs were imputed by IMPUTE2 against the reference panel of the, 1000 Genomes, UK10K projects, and Haplotype Reference Consortium. The details regarding these data are available elsewhere [21 (link)]. The current research has been performed under the Application Number 46478. The authors thank all UK Biobank participants and researchers who contributed or collected data.

Cheng S., Wen Y., Liu L., Cheng B., Liang C., Ye J., Chu X., Yao Y., Jia Y., Kafle O.P, & Zhang F. (2021). Traumatic events during childhood and its risks to substance use in adulthood: an observational and genome-wide by environment interaction study in UK Biobank. Translational Psychiatry, 11, 431.

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Genetic Variants Linked to Alcoholic Liver Disease

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The genotype data in the UK Biobank were derived from the GWAS chip (Affymetrix UK BiLEVE and UK Biobank Axiom arrays). In this study, we selected two genetic variants, PNPLA3 rs738409 C/G and TM6SF2 rs58542926 C/T, which are the most robustly replicated SNPs that are well-associated with alcoholic liver diseases [14 (link), 15 ]. We used the genotypes G of rs738409 and T of rs58542926 as the risk alleles.

Liu Z., Song C., Suo C., Fan H., Zhang T., Jin L, & Chen X. (2022). Alcohol consumption and hepatocellular carcinoma: novel insights from a prospective cohort study and nonlinear Mendelian randomization analysis. BMC Medicine, 20, 413.

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Genetic Markers Genotyping Across Cohorts

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PNPLA3 p.I148M (rs738409), TM6SF2 p.E167K (rs58542926), HSD17B13 (rs72613567) and GCKR P.446L (rs1260326) were genotyped using Taqman assays (ABI PRISM 7900HT Sequence Detection System, Applied Biosystems) in the CGPS and CCHS (10, 14, 20) , and by GWAS-chip in the UK Biobank (Affymetrix UK BiLEVE and UK Biobank Axiom arrays). Genotype call clustering in UK Biobank was assessed using the Scattershot website(26) (Supplemental Figure S2).

Gellert-Kristensen H., Richardson T.G., Davey Smith G., Nordestgaard B.G., Tybjaerg-Hansen A., Stender S, & Stender S. (2020). Combined Effect of PNPLA3, TM6SF2, and HSD17B13 Variants on Risk of Cirrhosis and Hepatocellular Carcinoma in the General Population. Hepatology (Baltimore, Md.), 72(3).

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