Infinium humanmethylation450 beadchip array 450k array, by Illumina - Product details

1

DNA Methylation Profiling for Genomic Analysis

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DNA methylation profiling was performed as described previously^{6 (link),7 (link)}. DNA was extracted in the same manner as described for WGS using 500ng as input material for fresh frozen tissue and 250ng input material for FFPE tissue. Array data was created using the Infinium HumanMethylation450 BeadChip array (450k array) according to the manufacturer’s instructions (Illumina, San Diego, USA) at the DKFZ Genomics and Proteomics Core Facility (Heidelberg, Germany). For a subset of samples (described in Supplementary Table 1) Methylation BeadChip (EPIC) arrays were used. CpG probes that were used for the analysis were filtered based on presence of a common SNP within five bases of the probe, reads not mapping uniquely to the reference genome, probes mapping to the X and Y chromosome and reads not overlapping between 450K arrays and EPIC arrays.
Clustering was performed after correction of samples for the origin of the DNA (FFPE or Fresh frozen) using Surrogate Variable Analysis (sva)^{40 (link)} and only the 10000 most variable probes based on the full dataset after correction were selected for clustering. Distance was calculated using 1-Pearson correlation and linkage was calculated using average as measure. Subsequently, t-stochastic neighbourhood embedding (t-SNE) analysis using RTSNE (v0.13) was applied to generate the figures⁴¹.

Lambo S., Gröbner S.N., Rausch T., Waszak S.M., Schmidt C., Gorthi A., Romero C., Mauermann M., Brabetz S., Krausert S., Buchhalter I., Koster J., Zwijnenburg D.A., Sill M., Hübner J.M., Mack N., Schwalm B., Ryzhova M., Hovestadt V., Papillon-Cavanagh S., Chan J.A., Landgraf P., Ho B., Milde T., Witt O., Ecker J., Sahm F., Sumerauer D., Ellison D.W., Orr B.A., Darabi A., Haberler C., Figarella-Branger D., Wesseling P., Schittenhelm J., Remke M., Taylor M.D., Gil-da-Costa M.J., Łastowska M., Grajkowska W., Hasselblatt M., Hauser P., Pietsch T., Uro-Coste E., Bourdeaut F., Masliah-Planchon J., Rigau V., Alexandrescu S., Wolf S., Li X.N., Schüller U., Snuderl M., Karajannis M.A., Giangaspero F., Jabado N., von Deimling A., Jones D.T., Korbel J.O., von Hoff K., Lichter P., Huang A., Bishop A., Pfister S.M., Korshunov A, & Kool M. (2019). The Molecular Landscape of ETMR at Diagnosis and Relapse. Nature, 576(7786), 274-280.

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DNA Methylation Profiling for Genomic Analysis

Cited 2 times

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

DNA methylation profiling was performed as described previously^{6 (link),7 (link)}. DNA was extracted in the same manner as described for WGS using 500ng as input material for fresh frozen tissue and 250ng input material for FFPE tissue. Array data was created using the Infinium HumanMethylation450 BeadChip array (450k array) according to the manufacturer’s instructions (Illumina, San Diego, USA) at the DKFZ Genomics and Proteomics Core Facility (Heidelberg, Germany). For a subset of samples (described in Supplementary Table 1) Methylation BeadChip (EPIC) arrays were used. CpG probes that were used for the analysis were filtered based on presence of a common SNP within five bases of the probe, reads not mapping uniquely to the reference genome, probes mapping to the X and Y chromosome and reads not overlapping between 450K arrays and EPIC arrays.
Clustering was performed after correction of samples for the origin of the DNA (FFPE or Fresh frozen) using Surrogate Variable Analysis (sva)^{40 (link)} and only the 10000 most variable probes based on the full dataset after correction were selected for clustering. Distance was calculated using 1-Pearson correlation and linkage was calculated using average as measure. Subsequently, t-stochastic neighbourhood embedding (t-SNE) analysis using RTSNE (v0.13) was applied to generate the figures⁴¹.

Lambo S., Gröbner S.N., Rausch T., Waszak S.M., Schmidt C., Gorthi A., Romero C., Mauermann M., Brabetz S., Krausert S., Buchhalter I., Koster J., Zwijnenburg D.A., Sill M., Hübner J.M., Mack N., Schwalm B., Ryzhova M., Hovestadt V., Papillon-Cavanagh S., Chan J.A., Landgraf P., Ho B., Milde T., Witt O., Ecker J., Sahm F., Sumerauer D., Ellison D.W., Orr B.A., Darabi A., Haberler C., Figarella-Branger D., Wesseling P., Schittenhelm J., Remke M., Taylor M.D., Gil-da-Costa M.J., Łastowska M., Grajkowska W., Hasselblatt M., Hauser P., Pietsch T., Uro-Coste E., Bourdeaut F., Masliah-Planchon J., Rigau V., Alexandrescu S., Wolf S., Li X.N., Schüller U., Snuderl M., Karajannis M.A., Giangaspero F., Jabado N., von Deimling A., Jones D.T., Korbel J.O., von Hoff K., Lichter P., Huang A., Bishop A., Pfister S.M., Korshunov A, & Kool M. (2019). The Molecular Landscape of ETMR at Diagnosis and Relapse. Nature, 576(7786), 274-280.

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DNA Methylation Analysis of Whole Blood

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DNA was extracted from whole blood for all cases and controls using standard techniques. Extracted DNA was sodium bisulfite converted using the Qiagen EZ DNA Methylation kit (Qiagen, Valencia, CA), according to the manufacturer’s protocol. All DNA samples were processed according to the manufacturer’s protocol for DNAm analysis using either the Illumina Infinium HumanMethylation450 BeadChip array (450K array) or the Illumina MethylationEPIC (EPIC array; an additional set of CHD8 test case sequence variants only) at The Centre for Applied Genomics (SickKids). The distribution of the samples on the arrays was randomized for all cases and controls and for age and sex variables. The 450K array covers > 485,000 individual CpG sites, whereas the EPIC array covers > 850,000 individual CpG sites genome-wide at single-nucleotide resolution, encompassing > 99% of RefSeq genes and > 96% of annotated CpG islands.

Siu M.T., Butcher D.T., Turinsky A.L., Cytrynbaum C., Stavropoulos D.J., Walker S., Caluseriu O., Carter M., Lou Y., Nicolson R., Georgiades S., Szatmari P., Anagnostou E., Scherer S.W., Choufani S., Brudno M, & Weksberg R. (2019). Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants. Clinical Epigenetics, 11, 103.

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DNA Methylation and Transcriptome Analysis of Airway Biopsies

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DNA methylation levels were measured in bronchial biopsies using the Infinium HumanMethylation450 BeadChip array (450 k array) (Illumina, San Diego, CA, USA). Raw intensity data were processed using the minfi package [19] . Samples and probes failing quality control were removed and raw β values normalised using the dasen method as implemented in the wateRmelon package [20] . DNA methylation levels at each CpG-site were expressed as β-values, ranging from zero (no methylation) to one (complete methylation). A detailed description can be found in the supplementary methods. An overview of the sample dropout during quality control is shown in supplementary figure S1a.
RNA sequencing RNA samples from airway wall biopsies were processed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). The cDNA fragment libraries were loaded unto an Illumina HiSeq2500 sequencer for paired-end sequencing (2×100 bp). Trimmed fastQ files where aligned to build b37 of the human reference genome using HISAT (version 0.1.5) and gene level quantification was performed by HTSeq (version 0.6.1p1) using Ensembl version 75 as gene annotation database [21] . A detailed description can be found in the supplementary methods. An overview of the sample dropout during quality control is shown in supplementary figure S1b.

Vermeulen C.J., Xu C.J., Vonk J.M., Ten Hacken N.H.T., Timens W., Heijink I.H., Nawijn M.C., Boekhoudt J., van Oosterhout A.J., Affleck K., Weckmann M., Koppelman G.H, & van den Berge M. (2020). Differential DNA methylation in bronchial biopsies between persistent asthma and asthma in remission. The European respiratory journal, 55(2).

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Infinium humanmethylation450 beadchip array 450k array

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4 protocols using infinium humanmethylation450 beadchip array 450k array

DNA Methylation Profiling for Genomic Analysis

DNA Methylation Profiling for Genomic Analysis

DNA Methylation Analysis of Whole Blood

DNA Methylation and Transcriptome Analysis of Airway Biopsies

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