Infinium Methylation Screening Array Manifest Column Headings

The Infinium Methylation Screening Array Manifest Column Headings PDF file is available for download from the Infinium Methylation Screening Array Manifest Files page. Below are the detailed descriptions of the Infinium Methylation Screening Array Manifest file columns.

IlmnID: Unique identifier extended with the following design strand designations: Illumina strand (T/B), Assay Strand (C / O), Infinium Design Type (1/2), Rep_Num. A more detailed explanation can be found on the table below. Name: Unique identifier from the Illumina CG database AddressA_ID: For Infinium I beadtypes this is the Address ID for the probe specific for the A allele. For Infinium II beadtypes this is the Address ID for the probe used for both A and B alleles (in this case AddressB_ID and AlleleB_ProbeSeq columns will be empty) AlleleA_ProbeSeq: The sequence of the probe identified in the AddressA_ID column. AddressB_ID: For Infinium I beadtypes this is the Address ID for the probe specific for the B allele AlleleB_ProbeSeq: For Infinium I beadtypes the sequence of the probe identified in the AddressB_ID column 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 (Red/Green) col: Color_Channel: For Infinium I probes the color channel of the Next_Base signal (R/G). Used for Bioconductor methylation array analysis software tools Probe_Type: Probe type: cg=CpG, rs=dbSNP rsID, ch=Cp Strand_FR: The Forward (F) or Reverse (R) designation of the Design Strand. F is equal to reference, + strand Strand_TB: The Illumina Top (T) or Bottom (B) designation of the Design strand Strand_CO: The assay Converted (C) or Opposite (O) designation of the Design strand Infinium_Design: Infinium Design (1) - 2 probes or (2)- 1 probe. Used for Bioconductor methylation array analysis software tools Infinium_Design_Type: Infinium I (2 probes/locus) or Infinium II (1 probe/locus) Rep_Num: Reflects the replicate number if the Name has replicate designs CHR: Chromosome containing the CpG (GRCh38) MAPINFO: Chromosomal coordinates of the CpG (GRCh38) Species: Species which the assays were designed for (Homo sapiens) Genome_Build: Genome Build referenced for this manifest Source_Seq: The original genomic sequence used for probe design prior to bisulfite conversion Forward_Sequence: Plus (+) strand sequence (5'-3') flanking the CG Top_Sequence: Top strand sequence (5'-3') flanking the CG UCSC_RefGene_Group: NCBI RefSeq Gene region: 5UTR=5' untranslated region between the TSS and ATG start site, 3UTR=3' untranslated region between stop codon and poly A signal, exon_#, TSS200=1-200 bp 5' the TSS, TS1500=200-1500 bp 5' of the TSS. Intronic regions included UCSC_RefGene_Name: NCBI RefSeq Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants UCSC_RefGene_Accession: NCBI RefSeq Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts UCSC_CpG_Islands_Name: Chromosomal coordinates of the CpG Island from UCSC. Relation_to_UCSC_CpG_Island: Island=within boundaries of a CpG Island, N_Shore=0-2kb 5' of Island, N_Shelf=2kb-4kb 5' of Island, S_Shore=0-2kb 3' of Island, S_Shelf=2kb-4kb 3' of Island GencodeV41_Group: Gencode v41 Gene region: 5UTR=5' untranslated region between the TSS and ATG start site, 3UTR=3' untranslated region between stop codon and poly A signal, exon_#, TSS200=1-200 bp 5' the TSS, TS1500=200-1500 bp 5' of the TSS. Intronic regions included GencodeV41_Name: Gencode v41 Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants GencodeV41_Accession: Gencode v41 Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts Phantom5_Enhancers: Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with FANTOM5 promoters HMM_Island: Hidden Markov Model Islands. Chromosomal map coordinates of computationally predicted CpG islands Regulatory_Feature_Name: Chromosomal map coordinates of the regulatory feature (informatically determined by the original ENCODE Consortium) Regulatory_Feature_Group: Description of the regulatory feature referenced in Regulatory_Feature_Name as provided by the original ENCODE Consortium - Gene_Associated, Gene_Associated _Cell_type_specific, nonGene_Associated, Promoter_Associated_Cell_type_specific, Unclassified, Unclassified_Cell_type_specific DNase_Hypersensitivity_NAME: Name of the DNase Hypersensitivity site as defined in ENCODE v5 Encode_CisReg_Site: Name and classification of the CisRegulatory Region as defined in ENCODE v5 Encode_CisReg_Site_Evid: Evidence for each CisReg Region/Classification based on 87 studies in ENCODE v5 based on AllData-Full classification OpenChromatin_NAME: Classification of Open Chromatin sites based on 1600+ studies in ENCODE v5 OpenChromatin_Evidence_Count: Evidence for each Open Chromatin site classification based on 1600+ studies in ENCODE v5 EPICv2_Locus_Match: Locus Name (IlmnID) in Infinium MethylationEPICv2.0 Manifest EPICv1_Locus_Match: Locus Name (IlmnID) in Infinium MethylationEPICv1.0 Manifest Methyl450_Locus_Match: Locus Name (IlmnID) in Infinium Methylation450K Manifest EPICv2_ProbeSeq_Match: Indicates if the AlleleA_ProbeSeq matches for EPIC v2 EPICv1_ProbeSeq_Match: Indicates if the AlleleA_ProbeSeq matches for EPIC v1 Methyl450_ProbeSeq_Match: Indicates if the AlleleA_ProbeSeq matches for Methylation450K SNP_ID: rsIDs of SNPs located in the probe. Multiple listings of SNP rsIDs are allowed. dbSNP v155 used as reference SNP_DISTANCE: Distance of SNPs from query base of the probe. Multiple listings of the distance values are associated with rsid. dbSNP v155 used as reference SNP_MinorAlleleFrequency: Minor allele frequency of SNPs. Multiple listings of the minor allele frequencies are associated with rsid. dbSNP v155 used as reference CHR_GRCh37: Chromosome containing the CpG (GRCh37) MAPINFO_GRCh37: Chromosomal coordinates of the CpG (GRCh37)

The logic for how the IlmnID is determined is shown below in the leftmost table column and other relevant information on how the IlmnID is generated is given in the remaining columns:

IlmnID	Name	Strand_TB	Strand_CO	Infinium_Design_Type	The specific synthetic oligonucleotide probe replicate
The IlmnID is a composite of multiple information fields: the name of the probe, whether the probe targets the top or bottom strand, whether the probe targets the bisulfite converted strand or complementary strand after amplification, the Infinium probe design type, and the number of times the probe was synthesized for array representation. Example of IlmnID: cg12345678_TC13 This probe would be a CG probe with an eight digit code that relates to the probe sequence. The following "T" indicates that the probe targets the top strand. The adjacent "C" indicates that the probe targets the strand that is initially bisulfite converted. The "1" indicates that the probe has a Type I Infinium design. The "3" indicates that the probe was synthesized three times for representation on the array The multiple fields that comprise the IlmnID are provided in the table columns to the right.	The name of the probe is determined by combining the locus target identifier, which designates the function of a given probe, with an eight digit code that relates to the probe sequence. In situations where the eight digit code has not yet been generated, standard genomic coordinates are used. Example of probe name: cg12345678 Examples of locus target identifiers: cg= CpG interrogating ch= CpH interrogating rs = SNP interrogating	Strand_TB relates to whether the probe is designed to target the top or bottom strands of a given locus as defined by Illumina's standard designation for ambiguous SNP probes. Examples of top/bottom strand designations: Top strand = T Bottom strand = B	Strand_CO refers to whether the probe is designed to target the originally bisulfite converted DNA strand, or the strand resulting from amplification of the originally converted DNA strand. Examples of converted/unconverted designations: Converted strand = C Opposite strand = O	Infinium_Design_ Type refers to whether the probe utilizes a Type I design that uses two attempted bead types to probe a single locus, or a Type II design that uses one attempted bead type to probe a single locus. Examples of Infinium design type designations: Infinium Type I design = 1 Infinium Type II design = 2	This value depends on how many times a probe was synthesized for representation on the array. For instance, if the probe was synthesized three separate times, the probe generated by the first synthesis would be denoted as "1", while the probe generated from the second synthesis would be denoted as "2", and the probe generated from the third synthesis would be denoted as "3".

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