Infinium Methylation450K manifest column headings

Detailed descriptions of the Infinium HumanMethylation450K manifest file column headings are listed.

IlmnID: Unique identifier from the Illumina CG database. (The probe ID).

Name: The IlmnID.

Infinium_Design_Type: Infinium I (2 probes/locus) or Infinium II (1 probe/locus).

Next_Base: For Infinium I probes, the nucleotide immediately following the CpG. Blank for Infinium II.

Color_Channel: For Infinium I probes, the color channel of the “Next_Base” signal.

Forward_Sequence: Plus (+) strand (HapMap) sequence (5'-3') flanking the CG.

Genome_Build: Genome Build referenced by the manifest.

CHR: Chromosome containing the CpG (Build 37).

MAPINFO: Chromosomal coordinates of the CpG (Build 37).

SourceSeq: The original, genomic sequence used for probe design before bisulfite conversion.

Chromosome_36: Chromosome containing the CpG (Build 36).

Coordinate_36: Chromosomal coordinates of the CpG (Build 36).

Strand: The Forward (F) or Reverse (R) designation of the Design Strand.

• *Note: in methylation manifest files, the Forward Strand = the genomic Plus (+) Strand and the Reverse Strand = the genomic Minus (-) Strand. In this context, Forward and Reverse ARE NOT EQUIVALENT to the Forward and Reverse Strand designations originating from dbSNP or as given in Infinium Genotyping manifests.

Probe_SNPs: rsid(s) of SNP(s) located 10­-50 bases from the target CpG.

Probe_SNPs_10: rsid(s) of SNP(s) located ≤ 10 bases from the target CpG.

Random_Loci: CpG loci chosen randomly by consortium members during the design process are marked “True”.

Methyl27_Loci: CpG’s carried over from the HumanMethylation27 array (95% carryover) are marked “True”.

UCSC_RefGene_Name: Target gene name(s), from the UCSC database. *Note: multiple listings of the same gene name indicate splice variants.

UCSC_RefGene_Accession: The UCSC accession number(s) of the target transcript(s). Accession numbers are given in the same order as the target gene transcripts.

UCSC_RefGene_Group: Gene region feature category describing the CpG position, from UCSC. Features listed in the same order as the target gene transcripts.

• TSS200 = 0-200 bases upstream of the transcriptional start site (TSS). TSS1500 = 200-1500 bases upstream of the TSS. 5'UTR = Within the 5' untranslated region, between the TSS and the ATG start site. Body = Between the ATG and stop codon; irrespective of the presence of introns, exons, TSS, or promoters. 3'UTR = Between the stop codon and poly A signal.

UCSC_CpG_Islands_Name: Chromosomal coordinates of the CpG Island from UCSC.

Relation_to_UCSC_CpG_Island: The location of the CpG relative to the CpG island.

• Shore = 0-2 kb from island. Shelf = 2-4 kb from island. N = upstream (5’) of CpG island. S = downstream (3’) of CpG island.

Phantom: Classifications from the FANTOM (Functional Annotation of the Mammalian Genome) consortium as a low- or high-CpG density region associated with FANTOM 4 promoters.

DMR: Differentially methylated regions (experimentally determined).

• DMR = Differentially Methylated Region. CDMR = Cancer-specific Differentially Methylated Region. RDMR = Reprogramming-specific Differentially Methylated Region.

Enhancer: Predicted enhancer elements (determined by the ENCODE Consortium using informatics) are marked “True”.

HMM_Island:Hidden Markov Model Islands. Chromosomal map coordinates of computationally predicted CpG islands.

Regulatory_Feature_Name: Chromosomal map coordinates of the regulatory feature (determined by the ENCODE Consortium using informatics).

Regulatory_Feature_Group: Description of the regulatory feature referenced in “Regulatory_Feature_Name” as provided by the Methylation Consortium.

• Gene_Associated Gene_Associated_Cell_type_specific NonGene_Associated Promoter_Associated Promoter_Associated_Cell_type_specific Unclassified Unclassified_Cell_type_specific

DHS: DNase I Hypersensitivity Site (experimentally determined by the ENCODE project).

Information in the methylation manifest references Genome Build 37 (HG19) unless otherwise stated.

For any feedback or questions regarding this article (Illumina Knowledge Article #1567), contact Illumina Technical Support [e-mail].