Description of suffixes in the cg probes ID in Infinium MethylationEPIC v2.0

This article describes the new naming features in the Infinium MethylationEPIC v2.0 Arrays and the description of the suffixes in the cg probes ID.

IlmnID is a composite of multiple information fields:

Name of the probe

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.

Common locus target identifiers

• cg - CG probe

• ca - CAH probe

• cc - CCH probe

• ct - CTH probe

• cl - Control probe

• rs - SNP probe

Strand_TB

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.

• T - Top strand

• B - Bottom strand

Strand_CO

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.

Converted/unconverted designations

• C - Converted strand

• O - Opposite strand

Infinium Probe Design Type

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.

Infinium design type designations

• 1 - Infinium Type I design

• 2 - Infinium Type II design

Specific synthetic oligonucleotide probe replicate

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".

Example IlmnID: cg12345678_TC13

Name: This probe would be a CG probe with an eight-digit code that relates to the probe sequence.

Strand_TB: The following "T" indicates that the probe targets the top strand.

Strand_CO: The adjacent "C" indicates that the probe targets the strand that is initially bisulfite converted.

Infinium Design Type: The "1" indicates that the probe has a Type I Infinium design.

Specific synthetic oligonucleotide probe replicate: The "3" indicates that the probe was synthesized three times for representation on the array.

Reference:

Infinium MethylationEPIC v2.0 Manifest File Release Notes

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