Humanmethylation450 array, by Illumina - Product details

1

Illumina HumanMethylation 450 Array Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Illumina HumanMethylation 450 array, in which the methylation status of more than 485,000 individual CpG sites are examined,^{33 (link)} was used to compare sample groups (progressing NDBE vs nonprogressing NDBE). Once bisulfite converted, 1 ng of DNA was quality-controlled (Illumina FFPE QC kit) with only samples with dCt <5 being taken forward to array analysis. The resulting samples underwent repair suitable for array hybridization using the Illumina FPPE restore kit,³⁴ followed by hybridization to Illumina HumanMethylation450 arrays using manufacturer's protocols and scanned on an Illumina iScan. Normalized intensity files (iDAT) were exported using GenomeStudio for downstream analysis.

Dilworth M.P., Nieto T., Stockton J.D., Whalley C.M., Tee L., James J.D., Noble F., Underwood T.J., Hallissey M.T., Hejmadi R., Trudgill N., Tucker O, & Beggs A.D. (2018). Whole Genome Methylation Analysis of Nondysplastic Barrett Esophagus that Progresses to Invasive Cancer. Annals of Surgery, 269(3), 479-485.

+ Open protocol

+ Expand

2

Epigenetic profiling of NAFLD liver samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

Liver samples were obtained percutaneously for patients undergoing liver biopsy for suspected NAFLD or intraoperatively for assessment of liver histology. Normal control samples were recruited from samples obtained for exclusion of liver malignancy during major oncological surgery. None of the normal control individuals underwent pre-operative chemotherapy and liver histology demonstrated absence of both cirrhosis and malignancy Study design, sampling method and data collection have been described in detail elsewhere.30 (link) For methylation analysis, bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA), and hybridization of the Illumina HumanMethylation450 array (Illumina, SanDiego, CA). mRNA expression analysis was performed using the HuGene 1.1 ST gene (Affymetrix, Santa Clara, Ca, USA) according to the manufacturers protocols. Hybridization signals were analyzed using GenomeStudio software (default settings; GenomeStudio ver. 2011.1, Methylation Analysis Module ver. 1.9.0; Illumina Inc) and internal controls for normalization.

Wahl S., Drong A., Lehne B., Loh M., Scott W.R., Kunze S., Tsai P.C., Ried J.S., Zhang W., Yang Y., Tan S., Fiorito G., Franke L., Guarrera S., Kasela S., Kriebel J., Richmond R.C., Adamo M., Afzal U., Ala-Korpela M., Albetti B., Ammerpohl O., Apperley J.F., Beekman M., Bertazzi P.A., Black S.L., Blancher C., Bonder M.J., Brosch M., Carstensen-Kirberg M., De Craen A.J., de Lusignan S., Dehghan A., Elkalaawy M., Fischer K., Franco O.H., Gaunt T.R., Hampe J., Hashemi M., Isaacs A., Jenkinson A., Jha S., Kato N., Krogh V., Laffan M., Meisinger C., Meitinger T., Mok Z.Y., Motta V., Ng H.K., Nikolakopoulou Z., Nteliopoulos G., Panico S., Pervjakova N., Prokisch H., Rathmann W., Roden M., Rota F., Rozario M.A., Sandling J.K., Schafmayer C., Schramm K., Siebert R., Slagboom P.E., Soininen P., Stolk L., Strauch K., Tai E.S., Tarantini L., Thorand B., Tigchelaar E.F., Tumino R., Uitterlinden A.G., van Duijn C., van Meurs J.B., Vineis P., Wickremasinghe A.R., Wijmenga C., Yang T.P., Yuan W., Zhernakova A., Batterham R.L., Smith G.D., Deloukas P., Heijmans B.T., Herder C., Hofman A., Lindgren C.M., Milani L., van der Harst P., Peters A., Illig T., Relton C.L., Waldenberger M., Järvelin M.R., Bollati V., Soong R., Spector T.D., Scott J., McCarthy M.I., Elliott P., Bell J.T., Matullo G., Gieger C., Kooner J.S., Grallert H, & Chambers J.C. (2016). Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature, 541(7635), 81-86.

+ Open protocol

+ Expand

3

Epigenetic profiling of NAFLD liver samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

Liver samples were obtained percutaneously for patients undergoing liver biopsy for suspected NAFLD or intraoperatively for assessment of liver histology. Normal control samples were recruited from samples obtained for exclusion of liver malignancy during major oncological surgery. None of the normal control individuals underwent pre-operative chemotherapy and liver histology demonstrated absence of both cirrhosis and malignancy Study design, sampling method and data collection have been described in detail elsewhere.30 (link) For methylation analysis, bisulfite conversion was performed using the Zymo EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA), and hybridization of the Illumina HumanMethylation450 array (Illumina, SanDiego, CA). mRNA expression analysis was performed using the HuGene 1.1 ST gene (Affymetrix, Santa Clara, Ca, USA) according to the manufacturers protocols. Hybridization signals were analyzed using GenomeStudio software (default settings; GenomeStudio ver. 2011.1, Methylation Analysis Module ver. 1.9.0; Illumina Inc) and internal controls for normalization.

Wahl S., Drong A., Lehne B., Loh M., Scott W.R., Kunze S., Tsai P.C., Ried J.S., Zhang W., Yang Y., Tan S., Fiorito G., Franke L., Guarrera S., Kasela S., Kriebel J., Richmond R.C., Adamo M., Afzal U., Ala-Korpela M., Albetti B., Ammerpohl O., Apperley J.F., Beekman M., Bertazzi P.A., Black S.L., Blancher C., Bonder M.J., Brosch M., Carstensen-Kirberg M., De Craen A.J., de Lusignan S., Dehghan A., Elkalaawy M., Fischer K., Franco O.H., Gaunt T.R., Hampe J., Hashemi M., Isaacs A., Jenkinson A., Jha S., Kato N., Krogh V., Laffan M., Meisinger C., Meitinger T., Mok Z.Y., Motta V., Ng H.K., Nikolakopoulou Z., Nteliopoulos G., Panico S., Pervjakova N., Prokisch H., Rathmann W., Roden M., Rota F., Rozario M.A., Sandling J.K., Schafmayer C., Schramm K., Siebert R., Slagboom P.E., Soininen P., Stolk L., Strauch K., Tai E.S., Tarantini L., Thorand B., Tigchelaar E.F., Tumino R., Uitterlinden A.G., van Duijn C., van Meurs J.B., Vineis P., Wickremasinghe A.R., Wijmenga C., Yang T.P., Yuan W., Zhernakova A., Batterham R.L., Smith G.D., Deloukas P., Heijmans B.T., Herder C., Hofman A., Lindgren C.M., Milani L., van der Harst P., Peters A., Illig T., Relton C.L., Waldenberger M., Järvelin M.R., Bollati V., Soong R., Spector T.D., Scott J., McCarthy M.I., Elliott P., Bell J.T., Matullo G., Gieger C., Kooner J.S., Grallert H, & Chambers J.C. (2016). Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature, 541(7635), 81-86.

+ Open protocol

+ Expand

4

Targeted Exome Sequencing and Methylation Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

Briefly, patient DNA was extracted from fresh whole blood using manual extraction protocols. In controls obtained from UNSW, the majority (90%) of DNA was extracted from frozen whole blood or lymphocytes using a kit (Qiagen Autopure, Hilden, Germany). Sequencing libraries were prepared using the KAPA HYPER Prep kit (KAPA Biosystems, Wilmington, MA, USA) and followed by targeted exome capture using the Nimblegen SeqCap EZ Exome v3 (64 Mb) kit (Roche, Madison, WI, USA), both according to the manufacturer's instructions. Patient samples were sequenced in a 126‐bp paired end mode using the Illumina HiSeq 2000 platform. Processing and sequence alignment were by standard protocols (GATK pipeline) (McKenna et al. 2010), and variants were annotated using the ANNOVAR software tool (version 2015 Jun17) (Wang et al. 2010). Following variant call and annotation, standard quality control (QC) steps were implemented, that is, common SNPs to remove individuals identified as being discordant for sex, excessive heterozygosity, or relatedness. Genome‐wide methylation data were generated using the Illumina HumanMethylation450 array, which contains probes covering 99% of reference sequences (RefSeq) genes and 96% of CpG islands. A standard QC pipeline was applied to remove probes bound to multiple locations and duplicate individuals (Supporting Information).

Garton F.C., Benyamin B., Zhao Q., Liu Z., Gratten J., Henders A.K., Zhang Z., Edson J., Furlong S., Morgan S., Heggie S., Thorpe K., Pfluger C., Mather K.A., Sachdev P.S., McRae A.F., Robinson M.R., Shah S., Visscher P.M., Mangelsdorf M., Henderson R.D., Wray N.R, & McCombe P.A. (2017). Whole exome sequencing and DNA methylation analysis in a clinical amyotrophic lateral sclerosis cohort. Molecular Genetics & Genomic Medicine, 5(4), 418-428.

+ Open protocol

+ Expand

5

Illumina HumanMethylation450 Array Analysis

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Illumina HumanMethylation450 array was used to quantify DNA methylation in bisulfite converted genomic DNA from whole-blood samples. Each sample consisted of one technical probe. Subjects were excluded based on the following criteria: (1) inconsistency between reported and methylome estimated gender (two subjects excluded); (2) exceeding more than four s.d. from the mean on one of the two first principal components (one subject excluded); (3) inconsistency between actual genotypes and those inferred from methylomic data (none excluded); and (4) subjects with more than 1% of sites with detection p > 0.05 (none detected). An additional subject processed on a single plate was further excluded from analysis. This yielded a total N = 297 samples for analysis. Methylation values were pre-processed using the wateRmelon package^{23 (link)}. First, CpG sites with beadcount <3 in 5% of samples and/or sites with detection p > 0.05 in 1% of study samples were excluded. The β-values were next normalized using the dasen algorithm, logit transformed, adjusted for technical covariates (plate and Sentrix ID) using ComBat^{24 (link)}, and finally adjusted for age, sex, and the six first principal component analysis axes.

Freytag V., Vukojevic V., Wagner-Thelen H., Milnik A., Vogler C., Leber M., Weinhold L., Böhmer A.C., Riedel-Heller S., Maier W., de Quervain D.J., Ramirez A, & Papassotiropoulos A. (2018). Genetic estimators of DNA methylation provide insights into the molecular basis of polygenic traits. Translational Psychiatry, 8, 31.

+ Open protocol

+ Expand

6

Illumina-based DNA Methylation Profiling

Cited 3 times

Check if the same lab product or an alternative is used in the 5 most similar protocols

A detailed description of methylomic profiling protocols can be found in Milnik et al.^{17 (link)}. Briefly, methylomic profiling was performed using the Illumina HumanMethylation450 array. Samples of non-European ancestry were identified using Hapmap references population genotypes and excluded from analysis (n = 35 in BASEL1 sample, yielding N = 533 remaining for analysis; none identified in BASEL2 sample). The β-values were calculated from SWAN normalized intensities^{20 (link)}. Subsequently, β-values were M-transformed and adjusted for processing plate effect (z-transformation), age, sex, and the main sources of technical variations inferred from principal components analysis^{17 (link)}. The β-values with detection p-value > 0.05 were considered as missing. Individual CpG sites were excluded based on the following criteria: non-CpG context, non-autosomal probes, probes with a SNP mapping to the target CpG site or with three or more SNPs within the 50-mer probe (minor allele frequency (MAF )> 0.01) (based on RnBeads package annotation), multi-mapping or polymorphic CpGs (MAF > 0.01 in European population) reported in refs.^{21 (link),22 (link)}, and probes with missing rate ≥5% in final samples. Prior to analysis, missing values were imputed using the R package impute (https://bioconductor.org/packages/release/bioc/html/impute.html) with k = 10.

Freytag V., Vukojevic V., Wagner-Thelen H., Milnik A., Vogler C., Leber M., Weinhold L., Böhmer A.C., Riedel-Heller S., Maier W., de Quervain D.J., Ramirez A, & Papassotiropoulos A. (2018). Genetic estimators of DNA methylation provide insights into the molecular basis of polygenic traits. Translational Psychiatry, 8, 31.

+ Open protocol

+ Expand

7

DNA Methylation Profiling Workflow

Check if the same lab product or an alternative is used in the 5 most similar protocols

The HumanMethylation450 array (Illumina, San Diego, USA) was used to
determine the DNA methylation status of 482,421 CpG sites, following
manufacturer’s instructions as previously reported [29 (link)]. Standard beta-mixture quantile
normalization (BMIQ), background correction, quality control, and rule-based
filtering of samples of probes were implemented using the RnBeads pipeline in
order to calculate final beta values. [30 ]. Beta value is defined as the ratio of fluorescence intensity of the
methylated probe over the overall intensity and was used in all visualization.
Unsupervised hierarchical clustering was done with Euclidean measure for
distance matrix and complete agglomeration method for clustering.

Wu S.P., Cooper B.T., Bu F., Bowman C.J., Killian J.K., Serrano J., Wang S., Jackson T.M., Gorovets D., Shukla N., Meyers P.A., Pisapia D.J., Gorlick R., Ladanyi M., Thomas K., Snuderl M, & Karajannis M.A. (2017). DNA Methylation–Based Classifier for Accurate Molecular Diagnosis of Bone Sarcomas. JCO Precision Oncology, 1, PO.17.00031.

+ Open protocol

+ Expand

8

Illumina HumanMethylation450 Array Processing

Check if the same lab product or an alternative is used in the 5 most similar protocols

The Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA, USA) was used to bisulfite-convert 500 ng of genomic DNA, and 4 μl of bisulfite-converted DNA was measured on the Illumina HumanMethylation450 array using the manufacturer’s protocol (Illumina, San Diego, CA, USA). Preprocessing and normalization of the data were done as described in the DNAmArray workflow (https://molepi.github.io/DNAmArray_workflow/). In brief, IDAT files were read using the minfi [79 (link)], while sample-level quality control (QC) was performed using MethylAid [80 (link)]. Filtering of individual measurements was based on detection P value (P < 0.01), number of beads available (≤ 2), or zero values for signal intensity. Normalization was done using functional normalization [81 ] as implemented in minfi [79 (link)], using five principal components extracted using the control probes for normalization. All samples or probes with more than 5% of their values missing were removed.

Hop P.J., Luijk R., Daxinger L., van Iterson M., Dekkers K.F., Jansen R., van Meurs J.B., ’t Hoen P.A., Ikram M.A., van Greevenbroek M.M., Boomsma D.I., Slagboom P.E., Veldink J.H., van Zwet E.W, & Heijmans B.T. (2020). Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference. Genome Biology, 21, 220.

+ Open protocol

+ Expand

9

DNA Methylation Profiling of Colorectal Cancer

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The set of patients used in the current study consist of a subset of a larger collection of 2,203 samples from 2,101 unique donors (1,103 cases of CRC and 998 controls) that were profiled on the HumanMethylation450 array from Illumina^{15 (link)}. Lymphocyte pellets were extracted from whole blood using Ficoll-Paque PLUS (GE Healthcare). DNA was extracted from lymphocytes using phenol–chloroform or the Qiagen Mini-Amp DNA kit, except for 99 samples (90 cases, 9 controls), for which DNA was extracted from lymphoblastoid cell lines. We used 15 μl of DNA from all samples at concentrations averaging 90 ng/μl (20 ng/μl s.e.). DNA samples were bisulfite-converted using the EZ-96 DNA Methylation-Gold Kit (Zymo Research, Orange, CA); 4 μl of bisulfite-treated DNA was then analysed on the HumanMethylation450 BeadChip from Illumina according to the manufacturer’s protocol.
The OFCCR methylation data was deposited in dbGaP under the accession number phs000779.v1.p1.

Lemire M., Zaidi S.H., Zanke B.W., Gallinger S., Hudson T.J, & Cleary S.P. (2015). The effect of 5-fluorouracil/leucovorin chemotherapy on CpG methylation, or the confounding role of leukocyte heterogeneity: an illustration. Genomics, 106(6), 340-347.

+ Open protocol

+ Expand

10

Epigenetic Markers of Allergic Sensitization

Check if the same lab product or an alternative is used in the 5 most similar protocols

CpGs shown to be associated with allergic sensitization or poly-sensitization in IoW were further tested in an independent cohort, the BAMSE study (sensitization defined as specific IgE > 0.35 kU/L to cat, dog, grass, house dust mite, egg, or peanut).^{26 (link)} As in IoW, DNA was extracted from peripheral whole blood. DNAm was analyzed for 267 subjects at 16 years of age using the Illumina HumanMethylation450 array, and quality control details have been presented elsewhere.^{27 (link)} Robust linear regressions were implemented with similar covariates, gender, and cell type proportions, included in the analyses. Genome-scale gene expressions in peripheral white blood cells of the 267 participants aged 16 years were used to assess biological relevance for the identified CpGs.^{28 (link)}

Zhang H., Kaushal A., Merid S.K., Melén E., Pershagen G., Rezwan F.I., Han L., Ewart S., Arshad S.H., Karmaus W, & Holloway J.W. (2019). DNA methylation and allergic sensitizations: A genome-scale longitudinal study during adolescence. Allergy, 74(6), 1166-1175.

+ Open protocol

+ Expand

Humanmethylation450 array

Lab products found in correlation

Close spelling variants of this product

41 protocols using humanmethylation450 array

Illumina HumanMethylation 450 Array Analysis

Epigenetic profiling of NAFLD liver samples

Epigenetic profiling of NAFLD liver samples

Targeted Exome Sequencing and Methylation Profiling

Illumina HumanMethylation450 Array Analysis

Illumina-based DNA Methylation Profiling

DNA Methylation Profiling Workflow

Illumina HumanMethylation450 Array Processing

DNA Methylation Profiling of Colorectal Cancer

Epigenetic Markers of Allergic Sensitization

About PubCompare

Ready to get started?