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GRCh38 / hg38

• Manifest with mapping information (MSA, EPICv2, EPIC+, EPIC, HM450)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

  Previous versions: (EPIC, HM450, HM27, header description)
  
• Mask information (MSA, EPICv2, EPIC+)
  Column header: (header description), see M_general column for the recommended masking
  

  Probe_ID

  mask

  maskUniq

  M_general

  Previous versions: (EPIC, HM450, HM27, header description)
  Previous population-specific SNP masking: (EPIC, HM450, HM27, header description)
• Trait associations (MSA)
  Column header:

  Probe_ID

  Trait_Associations

  Header description:
  (2) Trait_Associations: a comma-delimited string of trait associations. EWAS hits has the following format: EWAS_hit:[trait]:[PMID]:[q-value of association]. NA is used when the info is missing.
• Gene annotation (GENCODEv41) and promoters (MSA, EPICv2)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probe_strand

  Probe_ID

  genesUniq

  geneNames

  transcriptTypes

  transcriptIDs

  distToTSS

  Previous versions:
  GENCODEv36 (EPICv2, EPIC, HM450, HM27)
  GENCODEv22 (EPIC, HM450, HM27)
  
• Functional annotations (CGI, enhancer, TF binding, chromatin state, ...) (MSA, EPICv2, EPIC, HM450, HM27)
  Column header: (header description)

  Probe_ID

  Knowledgebase

• SNP annotations (MSA, EPICv2, HM450)
  Column header: (header description)

  chrm

  beg

  end

  strand

  rs

  designType

  U

  REF

  ALT

  Probe_ID

  This is for converting probes to genotype VCFs.
  Previous version: rs probes (EPIC, header description)
  Previous version: channel-switching Infinium-I probes (EPIC, header description)
• Bisulfite non-uniqueness of 3'-subsequence of 10-50 bases in length (EPIC, HM450, HM27)
  Column header: (header description)

  probeID

  copy_10

  copy_11

  copy_12

  copy_13

  ...

  copy_49

  copy_50

GRCh37 / hg19

(Links to all archived platforms)

Other Genomes

(Click here if you are using arrays on non-target species.)

GRCm38 / mm10

• Manifest with mapping information (MM285)
Column header: (header description)

CpG_chrm

CpG_beg

CpG_end

address_A

address_B

target

nextBase

channel

Probe_ID

mapFlag_A

mapChrm_A

mapPos_A

mapQ_A

mapCigar_A

AlleleA_ProbeSeq

mapNM_A

mapAS_A

mapYD_A

mapFlag_B

mapChrm_B

mapPos_B

mapQ_B

mapCigar_B

AlleleB_ProbeSeq

mapNM_B

mapAS_B

mapYD_B

type

Note: This annotation is based on the design paper (N=296,070). It described a slightly different set that corrects the Illumina A2 manifest (N=287,692).
See Manifest comparison for details. Sesame default preprocessing is based on the 296070 version.
Previous versions:
Illumina A2 manifest (MM285) (N=287,692)
LEGX manifest (MM285, header description)

• Mouse array design groups (MM285)
  Column header:

  Probe_ID

  design

  Header description:
  (2) design: contains the annotation of the probes. For the syntenic EPIC probe mapping, search for EPIC prefix in the design column.
• Mask information (MM285)
  Column header: (header description), see M_general column for the recommended masking
  

  Probe_ID

  mask

  maskUniq

  M_general

  Header description:
  (2) mask: a boolean indication of whether probes are recommended to be masked in data preprocessing. Probes masked by default includes control probes, multi-mapping probes (mapQ < 30 for either allele A or B) and non-informative probes (uk probes) Previous versions:
  Illumina A2 manifest (MM285),
  LEGX manifest (MM285)
  
• Gene annotation (GENCODEvM25) and promoters (MM285)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probe_strand

  probeID

  genesUniq

  geneNames

  transcriptTypes

  transcriptIDs

  distToTSS

Previous versions:
Illumina A2 manifest (MM285)

• Functional annotations (CGI, enhancer, TF binding, chromatin state, ...) (MM285)
  Column header: (header description)

  Probe_ID

  Knowledgebase

Note: This annotation is based on the design paper (N=296,070). It described a slightly different set that corrects the Illumina A2 manifest (N=287,692).
See Manifest comparison for details. Sesame default preprocessing is based on the 296070 version.

• The Illustration of the new array ID system
  The mouse array employs an improved ID system on top of the traditional "cg" numbers. The new ID system uniquely specifies the design details. The new ID is designed to accomodate more flexible probe design such as replicates and opposite-strand design.
• ChromHMM annotation of 66 samples (MM285)
  Column header: (header description)

  chrm

  beg

  end

  probeID

  ENCFF005IEW_forebrain_embryonic_12.5

  ENCFF014LBF_hindbrain_postnatal_0

  ENCFF023ETX_liver_embryonic_14.5

  ENCFF065PNO_midbrain_embryonic_16.5

  ENCFF072LNA_liver_embryonic_11.5

  ...

• Imprinting ICR/DMR annotation (MM285, also see ICR annotation, and a comparison of different ICR/DMR evidences).
• PhastCons Evolutionary Conservation (MM285)

  Probe_ID

  score

• PhyloP Evolutionary Conservation (MM285)

  Probe_ID

  score

GRCm39 / mm39

• Manifest with mapping information (MM285)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

Other genomes

• 310 species manifest from Ensemble v101 (MM285)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

GRCh38 / hg38

• Manifest with mapping information (Mammal40)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

  Previous versions: Old manifest (Mammal40, header description)
  
• KnowYourCG annotations (CGI, enhancer, TF binding, chromatin state, ...) (Mammal40)
  Column header: (header description)

Other genomes

• 310 species manifest from Ensemble v101 (Mammal40)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

Update Mar-06-2024:

• Added Methylation Screening Array (MSA) manifest and annotations
Update Apr-27-2023:

• Added KYCG annotation files links
Update Nov-10-2022:

• Added EPICv2 manifest and annotations
Update Sep-03-2022:

• update to Ensembl manifests, mouse manifests and human anotation
• update to the documentation of column headers
Update Jun-15-2021:

• updated gene annotation to GENCODE v36 to be consistent with GDC. CGI column is updated to contain CGI only when CGIposition is not NA.
• updated mouse array gene model
Update Apr-14-2021:

• updated gene annotation to GENCODE v37
Update Jul-4-2020:

• More detailed annotation to SNP and channel-switching probes
Release Sep-9-2018:

• Added gene_HGNC column for gene symbols corrected for HGNC compatibility
• Updated SNP masking with dbSNP build 151
• All maskings were redone on hg19. Previously hg19 manifest file was "borrowing" hg38 maskings.
• CCS probes have shrunk in numbers based on AF filtering (>1%).
• See Updates Summary for more details.
Release Aug-8-2018:

• Fix to MASK_mapping, some mapping with NM>0 are now masked as well
• Addition of NM columns and gene annotation to the manifest file.
• Previously, masking of mapping issues were merged from hg19 and hg38. Now masking on hg19 and hg38 was re-built entirely independently. There is some small decrease in the number of masking due to this change and a small increase due to the added NM-based masking (included in MASK_mapping).
• See Updates Summary for more details.
Release Mar-4-2018

• Fix to hg19 decoy mapping inconsistency.
Release Jan-4-2018

• Updated strand information.
Release Nov-23-2017

• Changed to RDS from RData following R's recommendation.
• Update to missing value representation.
• Update to table headers.
• Added gene annotation in short forms.
• Added mapping to genome both including and excluding alt-chromosomes.
• Made consistent naming of columns with underscores.
Release Mar-13-2017
• fix to relative position in SNP masking of type-I probes.
  

Human MSA - Goldberg et al. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies, bioRxiv 2024
mLiftOver - Chen and Zhou. mLiftOver: Harmonizing Data Across Infinium DNA Methylation Platforms, Bioinformatics 2024
Human EPICv2 - Kaur and Lee et al. Comprehensive evaluation of the Infinium human MethylationEPIC v2 BeadChip, Epigenetics Communications 2023
Mammalian and nonhuman species - Ding et al. Comparative epigenome analysis using Infinium DNA methylation BeadChips, Briefing in Bioinformatics 2023
Mouse MM285 - Zhou W et al. DNA methylation dynamics and dysregulation delinated by high-throughput profiling in the mouse, Cell Genomics 2022
Human EPIC, HM450 - Zhou W, Laird PW and Shen H, Comprehensive characterization, annotation and innovative use of Infinium DNA Methylation BeadChip probes, Nucleic Acids Research 2017

Questions regarding this annotation can be addressed to wanding.zhou@pennmedicine.upenn.edu.