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Humanmethylation450 450k

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The HumanMethylation450 (450k) is a microarray-based DNA methylation analysis platform. It is designed to detect DNA methylation levels across the human genome at over 450,000 CpG sites. The platform provides a comprehensive and unbiased assessment of DNA methylation patterns.

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Epic 850 k, by Illumina (2 mentions)

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Infinium HumanMethylation450 BeadChip (450K array) (33 citations) Infinium HumanMethylation450 (450K) BeadChip (26 citations) HumanMethylation450 BeadChip (450K) (10 citations) HumanMethylation450 BeadChip (450k) array (9 citations) Infinium HumanMethylation450 BeadChip array (450k array) (4 citations) HumanMethylation450 (“450k”) microarray, (4 citations) Infinium HumanMethylation450 (450k) array (3 citations) HumanMethylation450 (“450k”) microarray platform (2 citations) Illumina Infinium HumanMethylation450 BeadChip (450K BeadChip; (2 citations)

7 protocols using humanmethylation450 450k

1

Methylation Analysis with Illumina 450K

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The Illumina HumanMethylation450 (450K) was used to process DNAm levels. The 450K array covers over 450,000 CpG sites across the genome. Details of the methylome analysis is described in a previous study (Ratanatharathorn et al., 2017 (link)). Briefly, a quality control protocol, the Psychiatric Genomics Consortium (PGC) pipeline, was used. In the PGC pipeline, samples and probes were filtered out as previously described (Ratanatharathorn et al., 2017 (link)).
Saito T., Braun P.R., Daniel S., Jellison S.S., Hellman M., Shinozaki E., Lee S., Cho H.R., Yoshino A., Toda H, & Shinozaki G. (2020). The relationship between DNA methylation in neurotrophic genes and age as evidenced from three independent cohorts: Differences by delirium status. Neurobiology of aging, 94, 227-235.
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2

Comprehensive Molecular Profiling of Gliomas

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Routine neuropathologic diagnostics were performed in concordance with the 5th version of the WHO classification from 2021 [4 (link)]. The following molecular data were obtained as part of daily routine diagnostics: the IDH mutation status was available for all patients of the discovery and validation cohort and was obtained via immunohistochemistry or direct sequencing of the mutation hotspot region [26 (link),27 (link)]; 1p/19q codeletion status was available for 66 patients (92%) of the discovery cohort and for all patients of the validation cohort; genome-wide methylation analyses with copy number analyses were available for 89% of the discovery cohort (n = 64) and 95% of the validation cohort (n = 38) and were generated using the Illumina HumanMethylation450 (450k) or Methylation EPIC (850k) array platforms as previously described [28 (link)]. For all IDHmut glioma, the CDKN2A/B homozygous deletion status was derived from methylation profiling to identify malignant IDHmut WHO grade 4 astrocytomas that would have otherwise been undergraded.
Dao Trong P., Kilian S., Jesser J., Reuss D., Aras F.K., Von Deimling A., Herold-Mende C., Unterberg A, & Jungk C. (2023). Risk Estimation in Non-Enhancing Glioma: Introducing a Clinical Score. Cancers, 15(9), 2503.
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3

Newborn to Childhood DNA Methylation Profiling

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Cohorts collected samples of newborn blood from umbilical cord blood at birth (Table 1) and child blood using venepuncture at 4–13 years of age (Additional file 1: Table S1). DNAm was assessed with the Illumina® HumanMethylation450 (450 k) or the HumanMethylationEPIC (EPIC) BeadChip assay at Illumina or cohort-specific laboratories. Cohorts performed sample processing, quality control and normalization as described in Additional file 2: Methods.
We used normalized, untransformed DNAm beta values, ranging from 0 (completely unmethylated) to 1 (completely methylated), after trimming extreme outliers (3 × interquartile range from the quartile limit). Certain individuals were removed due to trimming of extreme values, resulting in different sample sizes across probes and cohorts. We excluded probes mapped to X or Y chromosomes, polymorphic CpGs which overlap with known single-nucleotide polymorphisms, probes with cohort-level call rate < 90%, control probes and cross-reactive probes (targeting repetitive sequences/co-hybridizing to alternate sequences) [20 (link), 21 (link)].
Sammallahti S., Koopman-Verhoeff M.E., Binter A.C., Mulder R.H., Cabré-Riera A., Kvist T., Malmberg A.L., Pesce G., Plancoulaine S., Heiss J.A., Rifas-Shiman S.L., Röder S.W., Starling A.P., Wilson R., Guerlich K., Haftorn K.L., Page C.M., Luik A.I., Tiemeier H., Felix J.F., Raikkonen K., Lahti J., Relton C.L., Sharp G.C., Waldenberger M., Grote V., Heude B., Annesi-Maesano I., Hivert M.F., Zenclussen A.C., Herberth G., Dabelea D., Grazuleviciene R., Vafeiadi M., Håberg S.E., London S.J., Guxens M., Richmond R.C, & Cecil C.A. (2022). Longitudinal associations of DNA methylation and sleep in children: a meta-analysis. Clinical Epigenetics, 14, 83.
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4

Methylation Array Protocol for Genome-wide Analysis

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For methylation arrays the Illumina HumanMethylation450 (450k) or MethylationEPIC (EPIC) kits were used to obtain the DNA methylation status at >450 000 and >850 000 CpG sites, respectively, according to the manufacturer’s instructions at the Genomics and Proteomics Core Facility of the German Cancer Research Center in Heidelberg, Germany and at the Department of Neuropathology as described previously.19 (link)
Kessler T., Berberich A., Casalini B., Drüschler K., Ostermann H., Dormann A., Walter S., Hai L., Schlesner M., Herold-Mende C., Jungk C., Unterberg A., Bendszus M., Sahm K., von Deimling A., Winkler F., Platten M., Wick W., Sahm F, & Wick A. (2020). Molecular profiling-based decision for targeted therapies in IDH wild-type glioblastoma. Neuro-oncology Advances, 2(1), vdz060.
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5

Newborn Umbilical Cord Blood DNA Methylation

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Newborn umbilical cord blood DNAm was assessed with the Illumina® HumanMethylation450 (450k) or HumanMethylationEPIC (EPIC) BeadChip assay at Illumina or cohort-specific laboratories. Cohorts performed sample processing, quality control and normalization as described in Supplementary methods.
We used normalized, untransformed beta values, ranging from 0 (completely unmethylated) to 1 (completely methylated), after trimming extreme outliers (3×interquartile range from the quartile limit).
We excluded probes mapped to X/Y chromosomes, polymorphic CpGs (overlapping with known single-nucleotide-polymorphisms [SNPs]),29 (link) control or cross-reactive probes (targeting repetitive sequences/co-hybridizing to alternate sequences).30 (link),31 (link)Function-related information was derived from GeneCards and GWAS Catalog (https://www.genecards.org; https://www.ebi.ac.uk/gwas, accessed August 17th, 2020).
Sammallahti S., Hidalgo A.P., Tuominen S., Malmberg A., Mulder R.H., Brunst K.J., Alemany S., McBride N.S., Yousefi P., Heiss J.A., McRae N., Page C.M., Jin J., Pesce G., Caramaschi D., Rifas-Shiman S.L., Koen N., Adams C.D., Magnus M.C., Baïz N., Ratanatharathorn A., Czamara D., Håberg S.E., Colicino E., Baccarelli A.A., Cardenas A., DeMeo D.L., Lawlor D.A., Relton C.L., Felix J.F., van IJzendoorn M.H., Bakermans-Kranenburg M.J., Kajantie E., Räikkönen K., Sunyer J., Sharp G.C., Houtepen L.C., Nohr E.A., Sørensen T.I., Téllez-Rojo M.M., Wright R.O., Annesi-Maesano I., Wright J., Hivert M.F., Wright R.J., Zar H.J., Stein D.J., London S.J., Cecil C.A., Tiemeier H, & Lahti J. (2021). Maternal anxiety during pregnancy and newborn epigenome-wide DNA methylation. Molecular psychiatry, 26(6), 1832-1845.
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6

Integrated Molecular Profiling for Neuropathologic Diagnostics

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Neuropathologic diagnostics was performed in concordance with the WHO classification from 2016 [9 (link)]. The following molecular data were obtained as part of daily routine: IDH mutation status was obtained by immunohistochemistry or direct sequencing of the mutation hotspot region for all patients [16 (link)]. 1p/19q codeletion status was available for all patients. Genome wide methylation analysis with copy number analysis was available for 171 patients (83%) and was generated using the Illumina HumanMethylation450 (450 k) or Methylation EPIC (850 k) array platforms as described [17 (link)].
Dao Trong P., Gluszak M., Reuss D., von Deimling A., Wick A., König L., Debus J., Herold-Mende C., Unterberg A, & Jungk C. (2023). Isocitrate-dehydrogenase-mutant lower grade glioma in elderly patients: treatment and outcome in a molecularly characterized contemporary cohort. Journal of Neuro-Oncology, 161(3), 605-615.
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7

Umbilical Cord Blood DNA Methylation Analysis

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Cohorts collected umbilical cord blood at birth. DNA methylation was assessed with the Illumina® HumanMethylation450 (450k) or the HumanMethylationEPIC (EPIC) BeadChip assay at Illumina or cohort-speci c laboratories. Cohorts performed sample processing, quality control, and normalization as described in the Supplementary Methods. We used normalized, untransformed DNA methylation beta values, ranging from 0 (completely unmethylated) to 1 (completely methylated), after trimming extreme outliers (3 × interquartile range from the 25 th and 75 th quartile limits). We excluded probes on the sex chromosomes, polymorphic CpGs which overlap with known single-nucleotide-polymorphisms, probes with cohort-level call-rate <95%, control probes, and cross-reactive probes (targeting repetitive sequences/co-hybridizing to alternate sequences) 39, (link)40 (link) .
Kotsakis Ruehlmann A., Sammallahti S., Cortés Hidalgo A.P., Bakulski K.M., Binder E.B., Campbell M.L., Caramaschi D., Cecil C.A.M., Colicino E., Cruceanu C., Czamara D., Dieckmann L., Dou J., Felix J.F., Frank J., Håberg S.E., Herberth G., Hoang T.T., Houtepen L.C., Hüls A., Koen N., London S.J., Magnus M.C., Mancano G., Mulder R.H., Page C.M., Räikkönen K., Röder S., Schmidt R.J., Send T.S., Sharp G., Stein D.J., Streit F., Tuhkanen J., Witt S.H., Zar H.J., Zenclussen A.C., Zhang Y., Zillich L., Wright R., Lahti J, & Brunst K.J. (2023). Epigenome-wide meta-analysis of prenatal maternal stressful life events and newborn DNA methylation. Molecular psychiatry, 28(12).
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