title: Illumina HumanMethylation450 BeadChip (v1.2, extended annotation)
status: Public on Nov 26 2014
contact.city: Rotterdam
contact.first: Martin
contact.middle: Anne
contact.last: Rijlaarsdam
contact.email: m.a.rijlaarsdam@gmail.com
contact.address: Wytemaweg 80
contact.department: Pathology
contact.country: Netherlands
contact.institute: Erasmus MC
contact.phone: 0031645408508
organism: Homo sapiens
description: The Illumina annotation manifest (v1.2) for 450K array was extended. Briefly, probes close to small nuclear RNAs and microRNAs from snoRNABase and miRBase were identified, as were probes within repeats as defined by RepeatMasker (source: UCSC). Probes close to the transcription start site (TSS) of imprinted genes were also identified (geneimprint.com / igc.otago.ac.nz). Known imprinting control regions (ICR) were retrieved from WAMIDEX and igc.otago.ac.nz. Imprinting is indicated using the expressed allele. Illumina probe classes were extended with a number of merged categories. Where applicable the upstream (-) and downstream (+) margins reported in this manuscript are analogous to the Illumina annotation (-1500+0; -200+0). All results are based on the GRch37/hg19 assembly. also, Cross hybridizing probes and probes with a SNP at or within 10 bp of the target CpG (allele frequency >= 0.05) are indicated according to [1]. Please see the attached supplementary information for more details (start from pdf).
  1. Chen, Y.A., et al., Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics, 2013. 8(2): p. 203-9.
manufacture_protocol: See manufacturer's website