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A platform (within the scope of TCGA) is a vendor-specific technology for assaying or sequencing that could possibly be customized by a GSC or GCC.

Identifying Platforms

In TCGA data and applications, platforms are identified by name, code or alias.

See the platform code report to view a complete list of available platform names, codes and aliases used in TCGA.

Platform Names

Platform names are composed of two components: the vendor name followed by the official platform name from the vendor.

 

 

Platform name example:

Agilent Human miRNA Microarray

For a customized platform, the platform name is the vendor name followed by the official platform name that includes the word 'Custom'.

Custom platform name example:

Agilent Human Genome CGH Custom Microarray 2x415K

For a complete list of platform names, see the platforms code report.

Platform Codes

A platform code is assigned by centers that produce data for that platform. This code is an abbreviation of the platform name and reflects the code that is used internally by the center.

For a complete list of platform codes, see the column "Platform Alias" in the platforms code report.

 

Platform Aliases

Platform aliases are assigned by the DCC to shorten or simplify the platform name. On the whole, aliases are identical to their corresponding platform codes.

For a complete list of platform aliases, see the platforms code report.

Platforms and Associated Reference Genome Assemblies

The results from the various platforms of the TCGA project are generally reported in relation to a reference human genome assembly or in relation to reference sets of probes representing genes, miRNA or proteins. The reference sets are indicated in the Level_2 and Level_3 data files for the platform (for example the maf and vcf files), the platform's associated annotation files, and in the DESCRIPTION.txt or idf files for the data submission. The table below summarizes the various platforms with their data reference and source of that reference.

Platform Abbreviation

Platform Reference Standards

Disease Study and Center

Determination of Reference Standard

agilentg4502a_07_1

genes

unc.edu

DCC manual curation

agilentg4502a_07_2

genes

unc.edu

DCC manual curation

agilentg4502a_07_3

genes

unc.edu

DCC manual curation

bio

NA(bio)

intgen.org
genome.wustl.edu
nationwidechildrens.org

DCC manual curation

cgh-1x1m_g4447a

36.1

mskcc.org

DCC manual curation

diagnostic_images

NA(images)

intgen.org
nationwidechildrens.org

DCC manual curation

genome_wide_snp_6

36

broad.mit.edu
genome.wustl.edu

DCC manual curation

h-mirna_8x15k

miRNAID

unc.edu

DCC manual curation

h-mirna_8x15kv2

miRNAID

unc.edu

DCC manual curation

hg-cgh-244a

36

hms.harvard.edu
mskcc.org

DCC manual curation

hg-cgh-415k_g4124a

36

hms.harvard.edu

DCC manual curation

hg-u133_plus_2

ProbeID

genome.wustl.edu

DCC manual curation

ht_hg-u133a

ProbeID

broad.mit.edu

DCC manual curation

huex-1_0-st-v2

ProbeID

lbl.gov

DCC manual curation

human1mduo

36

hudsonalpha.org

DCC manual curation

humanhap550

36

hudsonalpha.org

DCC manual curation

humanmethylation27

hg18

jhu-usc.edu

DCC manual curation

humanmethylation450

hg18

jhu-usc.edu

DCC manual curation

illuminadnamethylation_oma002_cpi

36.1

jhu-usc.edu

DCC manual curation

illuminadnamethylation_oma003_cpi

36.1

jhu-usc.edu

DCC manual curation

illuminaga_dnaseq

36

brca(genome.wustl.edu)
coad(hgsc.bcm.edu)
laml(genome.wustl.edu)
ov(broad.mit.edu,genome.wustl.edu)
read(hgsc.bcm.edu)

TSV,MAF

illuminaga_dnaseq

37

blca(broad.mit.edu)
brca(genome.wustl.edu)
cesc(broad.mit.edu)
kirc(broad.mit.edu)
luad(broad.mit.edu)
lusc(broad.mit.edu)

MAF

illuminaga_dnaseq

ncbi-human-build36

coad(ucsc.edu)
read(ucsc.edu)

VCF

illuminaga_dnaseq

grch37-lite

brca(ucsc.edu)

VCF

illuminaga_dnaseq

hg18

read(broad.mit.edu)

VCF

illuminaga_mirnaseq

GRCh37-lite

brca(bcgsc.ca)
hnsc(bcgsc.ca)
kirc(bcgsc.ca)
kirp(bcgsc.ca)
luad(bcgsc.ca)
lusc(bcgsc.ca)
stad(bcgsc.ca)
ucec(bcg
sc.ca)

SDRF

illuminaga_mirnaseq

NCBI36.1

coad(bcgsc.ca)
laml(bcgsc.ca)
read(bcgsc.ca)

SDRF

illuminaga_rnaseq

hg19(GRCh37)

coad(unc.edu)
laml(bcgsc.ca)
read(unc.edu)
ucec(unc.edu)

SDRF,DCC manual curation

illuminaga_rnaseq

GRCh37-lite

stad(bcgsc.ca)

SDRF

illuminahiseq_dnaseqc

hg18(GRCh36)

hms.harvard.edu

SDRF

illuminahiseq_mirnaseq

GRCh37-lite

bcgsc.ca

SDRF

illuminahiseq_rnaseq

hg19(GRCh37)

unc.edu

SDRF

mda_rppa_core

protein

mdanderson.org

DCC manual curation

microsat_i

NA(usat)

nationwidechildrens.org

DCC manual curation

pathology_reports

NA(reports)

intgen.org
nationwidechildrens.org

DCC manual curation

solid_dnaseq

36

coad(hgsc.bcm.edu)
ov(hgsc.bcm.edu)
read(hgsc.bcm.edu)

MAF

solid_dnaseq

hg18

read(broad.mit.edu)

VCF

solid_dnaseq

hg36.1

coad(ucsc.edu)
read(ucsc.edu)

VCF

mixed_dnaseq37kirc(hgsc.bcm.edu)MAF

tissue_images

NA(images)

intgen.org
nationwidechildrens.org

DCC manual curation

Platforms and Associated Level_2 and Level_3 data files

Each platform as analyzed by a TCGA center, has its own associated Level_2 and Level_3 data files.  Below is a table summarizing the tab delimited text files in submitted data archives and the fileheader, which summarizes the columns of the files.  Some data files have two headerlines, with the second line being the column header.  These cases are indicated in the table by including a "Header2" designation in the column for FileHeader.

Platform

Center

Data Level

Filename Template

Study Abbreviation

File Header

agilentg4502a_07_1

unc.edu

Level_2

level2.data.txt

gbm

Reporter REF log2 lowess normalized(cy5/cy3)

agilentg4502a_07_1

unc.edu

Level_3

txt_lmean.out.logratio.gene.tcga_level3.data.txt

gbm

Composite Element REF log2 lowess normalized (cy5/cy3) collapsed by gene symbol

agilentg4502a_07_2

unc.edu

Level_2

level2.data.txt

ov, gbm

Reporter REF log2 lowess normalized(cy5/cy3)

agilentg4502a_07_2

unc.edu

Level_3

txt_lmean.out.logratio.gene.tcga_level3.data.txt

ov, gbm

Composite Element REF log2 lowess normalized (cy5/cy3) collapsed by gene symbol

agilentg4502a_07_3

unc.edu

Level_2

level2.data.txt

lusc, ov, kirp, coad, ucec, luad, kirc, lgg, read, brca

Reporter REF log2 lowess normalized(cy5/cy3)

agilentg4502a_07_3

unc.edu

Level_3

txt_lmean.out.logratio.gene.tcga_level3.data.txt

lusc, kirp, ov, coad, ucec, luad, lgg, read, kirc, brca

Composite Element REF log2 lowess normalized (cy5/cy3) collapsed by gene symbol

cgh-1x1m_g4447a

mskcc.org

Level_2

_GCN_V3.mat

lusc, ov

Composite Element REF normalizedLog2Ratio

cgh-1x1m_g4447a

mskcc.org

Level_3

_CBS_out.txt

lusc, ov

sample chrom loc.start loc.end num.mark num.informative seg.mean pval l.lcl l.ucl r.pval r.lcl r.ucl

genome_wide_snp_6

broad.mit.edu

Level_2

after_5NN.copynumber.data.txt

lusc, read

Composite Element REF Chromosome PhysicalPosition Signal

genome_wide_snp_6

broad.mit.edu

Level_2

birdseed.data.txt

lusc, thca, kirp, blca, cesc, lgg, read, stad, hnsc, dlbc, brca, ov, coad, paad, ucec, luad, lihc, skcm, prad, kirc, gbm

Composite Element REF Call Confidence

genome_wide_snp_6

broad.mit.edu

Level_2

byallele.copynumber.data.txt

lusc, read

Composite Element REF Chromosome PhysicalPosition Signal_A Signal_B

genome_wide_snp_6

broad.mit.edu

Level_2

byallele.copynumber.data.txt

lusc, thca, kirp, blca, cesc, lgg, read, stad, hnsc, dlbc, brca, ov, coad, paad, ucec, luad, lihc, skcm, prad, kirc, gbm

Composite Element REF Signal_A Signal_B

genome_wide_snp_6

broad.mit.edu

Level_2

ismpolish.data.txt

lusc, thca, kirp, blca, cesc, lgg, read, stad, hnsc, dlbc, brca, ov, coad, paad, ucec, luad, lihc, skcm, prad, kirc, gbm

Composite Element REF Signal

genome_wide_snp_6

broad.mit.edu

Level_2

no_outlier.copynumber.data.txt

lusc, read

Composite Element REF Chromosome PhysicalPosition Signal

genome_wide_snp_6

broad.mit.edu

Level_2

raw.copynumber.data.txt

lusc, read

Composite Element REF Chromosome PhysicalPosition Signal

genome_wide_snp_6

broad.mit.edu

Level_2

raw.copynumber.data.txt

lusc, thca, kirp, blca, cesc, lgg, read, stad, hnsc, dlbc, brca, ov, coad, paad, ucec, luad, lihc, skcm, prad, kirc, gbm

Composite Element REF Signal

genome_wide_snp_6

broad.mit.edu

Level_2

tangent.copynumber.data.txt

lusc, thca, kirp, blca, cesc, lgg, read, stad, hnsc, dlbc, brca, ov, coad, paad, ucec, luad, lihc, skcm, prad, kirc, gbm

Composite Element REF Signal

genome_wide_snp_6

broad.mit.edu

Level_3

hg18.seg.txt

thca, lusc, kirp, blca, cesc, stad, lgg, read, hnsc, dlbc, brca, ov, coad, ucec, paad, luad, lihc, skcm, prad, kirc, gbm

Sample Chromosome Start End Num_Probes Segment_Mean

genome_wide_snp_6

broad.mit.edu

Level_3

hg19.seg.txt

thca, lusc, kirp, blca, cesc, stad, lgg, read, hnsc, dlbc, brca, ov, coad, ucec, paad, luad, lihc, skcm, prad, kirc, gbm

Sample Chromosome Start End Num_Probes Segment_Mean

genome_wide_snp_6

broad.mit.edu

Level_3

nocnv_hg18.seg.txt

thca, lusc, kirp, blca, cesc, stad, lgg, read, hnsc, dlbc, brca, ov, coad, ucec, paad, luad, lihc, skcm, prad, kirc, gbm

Sample Chromosome Start End Num_Probes Segment_Mean

genome_wide_snp_6

broad.mit.edu

Level_3

nocnv_hg19.seg.txt

thca, lusc, kirp, blca, cesc, stad, lgg, read, hnsc, dlbc, brca, ov, coad, ucec, paad, luad, lihc, skcm, prad, kirc, gbm

Sample Chromosome Start End Num_Probes Segment_Mean

genome_wide_snp_6

broad.mit.edu

Level_3

seg.data.txt

lusc, read

ID chrom loc.start loc.end num.mark seg.mean

genome_wide_snp_6

genome.wustl.edu

Level_2

alleleSpecificCN.dat

laml

Composite Element REF Chromosome PhysicalPosition SignalMax SignalMin

genome_wide_snp_6

genome.wustl.edu

Level_2

genotype.dat

laml

Composite Element REF Chromosome PhysicalPosition Genotype

genome_wide_snp_6

genome.wustl.edu

Level_2

intensities.dat

laml

Composite Element REF Chromosome PhysicalPosition Signal

genome_wide_snp_6

genome.wustl.edu

Level_2

pairedcn.dat

laml

Composite Element REF Chromosome PhysicalPosition Value

genome_wide_snp_6

genome.wustl.edu

Level_3

segmented.dat

laml

chromosome start end numberProbes log2CopyNumber Sample ID

hg-cgh-244a

hms.harvard.edu

Level_2

_lowess_normalized.tsv

ov, gbm

CompositeElement REF normalizedLog2Ratio

hg-cgh-244a

hms.harvard.edu

Level_3

_Segment.tsv

ov, gbm

Chromosome Start End Probe_Number Segment_Mean

hg-cgh-244a

mskcc.org

Level_2

_GCN_V3.mat

gbm

Composite Element REF normalizedLog2Ratio

hg-cgh-244a

mskcc.org

Level_3

_CBS_out.txt

gbm

sample chrom loc.start loc.end num.mark num.informative seg.mean pval l.lcl l.ucl r.pval r.lcl r.ucl

hg-cgh-415k_g4124a

hms.harvard.edu

Level_2

_lowess_normalized.tsv

gbm

CompositeElement REF normalizedLog2Ratio

hg-cgh-415k_g4124a

hms.harvard.edu

Level_2

_lowess_normalized.tsv

lusc, ov, gbm

Composite Element REF normalizedLog2Ratio

hg-cgh-415k_g4124a

hms.harvard.edu

Level_2

_lowess_normalized.tsv

ov

Composite Element REF

hg-cgh-415k_g4124a

hms.harvard.edu

Level_3

_Segment.tsv

lusc, ov, gbm

Chromosome Start End Probe_Number Segment_Mean

hg-u133_plus_2

genome.wustl.edu

Level_2

MAS5.txt

laml

Composite Element REF Signal

h-mirna_8x15k

unc.edu

Level_2

level2.data.txt

gbm

Reporter REF Quantile_Normalized

h-mirna_8x15k

unc.edu

Level_3

gene.tcga_level3.data.txt

gbm

Composite Element REF unc_DWD_Batch_adjusted

h-mirna_8x15kv2

unc.edu

Level_2

level2.data.txt

ov

Reporter REF Quantile_Normalized

h-mirna_8x15kv2

unc.edu

Level_3

gene.tcga_level3.data.txt

ov

Composite Element REF unc_DWD_Batch_adjusted

ht_hg-u133a

broad.mit.edu

Level_2

level2.data.txt

lusc, ov, gbm

Composite Element REF Signal

ht_hg-u133a

broad.mit.edu

Level_3

level3.data.txt

lusc, ov, gbm

Composite Element REF Signal

huex-1_0-st-v2

lbl.gov

Level_2

HuEx-1_0-st-v2.revision.exon

lusc, ov, gbm

Composite Element REF Signal

huex-1_0-st-v2

lbl.gov

Level_3

FIRMA.txt

lusc, ov, gbm

Composite Element REF Score

huex-1_0-st-v2

lbl.gov

Level_3

gene.txt

lusc, ov, gbm

Composite Element REF Signal

human1mduo

hudsonalpha.org

Level_2

B_Allele_Freq.txt

lusc, ov

Composite Element REF Chr Pos B Allele Freq

human1mduo

hudsonalpha.org

Level_2

Delta_B_Allele_Freq.txt

lusc, ov

Composite Element REF Chr Pos Delta Allele Freq

human1mduo

hudsonalpha.org

Level_2

Genotypes.txt

lusc, ov

Composite Element REF Chr Pos genotype

human1mduo

hudsonalpha.org

Level_2

Normal_LogR.txt

lusc, ov

Composite Element REF Chr Pos Log2(Rnorm/Rref)

human1mduo

hudsonalpha.org

Level_2

Paired_LogR.txt

lusc, ov

Composite Element REF Chr Pos Log2(Rtum/Rnorm)

human1mduo

hudsonalpha.org

Level_2

Unpaired_LogR.txt

ov

Composite Element REF Chr Pos Log2(Rtum/Rref)

human1mduo

hudsonalpha.org

Level_3

Human1MDuo.revision.seg.txt

lusc, ov

Normalization Name chrom loc.start loc.end mean

human1mduo

hudsonalpha.org

Level_3

loh.txt

lusc, ov

Normalization Name chrom loc.start loc.end mean

human1mduo

hudsonalpha.org

Level_3

segnormal.txt

lusc, ov

Normalization Name chrom loc.start loc.end mean

humanhap550

hudsonalpha.org

Level_2

B_Allele_Freq.txt

gbm

Composite Element REF Chr Pos B Allele Freq

humanhap550

hudsonalpha.org

Level_2

Delta_B_Allele_Freq.txt

gbm

Composite Element REF Chr Pos Delta Allele Freq

humanhap550

hudsonalpha.org

Level_2

Genotypes.txt

gbm

Composite Element REF Chr Pos genotype

humanhap550

hudsonalpha.org

Level_2

Normal_LogR.txt

gbm

Composite Element REF Chr Pos Log2(Rnorm/Rref)

humanhap550

hudsonalpha.org

Level_2

Paired_LogR.txt

gbm

Composite Element REF Chr Pos Log2(Rtum/Rnorm)

humanhap550

hudsonalpha.org

Level_2

Unpaired_LogR.txt

gbm

Composite Element REF Chr Pos Log2(Rtum/Rref)

humanhap550

hudsonalpha.org

Level_3

HumanHap550.revision.seg.txt

gbm

Normalization Name chrom loc.start loc.end mean

humanhap550

hudsonalpha.org

Level_3

loh.txt

gbm

Normalization Name chrom loc.start loc.end mean

humanhap550

hudsonalpha.org

Level_3

segnormal.txt

gbm

Normalization Name chrom loc.start loc.end mean

humanmethylation27

jhu-usc.edu

Level_2

HumanMethylation27.revision.lvl-2

laml, kirc

Composite Element REF Methylated_Intensity Unmethylated_Intensity Detection_P_value

humanmethylation27

jhu-usc.edu

Level_2

HumanMethylation27.revision.lvl-2

lusc, kirp, ov, coad, ucec, luad, gbm, stad, read, brca

Composite Element REF Beta_Value Methylated_Signal_Intensity (M) Un-Methylated_Signal_Intensity (U)

humanmethylation27

jhu-usc.edu

Level_3

HumanMethylation27.revision.lvl-3

laml, kirc

Composite Element REF Beta_value Gene_Symbol Chromosome Genomic_Coordinate

humanmethylation27

jhu-usc.edu

Level_3

HumanMethylation27.revision.lvl-3

lusc, kirp, ov, coad, ucec, luad, gbm, read, stad, brca

Composite Element REF Beta_Value Gene_Symbol Chromosome Genomic_Coordinate

humanmethylation450

jhu-usc.edu

Level_2

HumanMethylation450.revision.lvl-2

laml, thca, lusc, kirp, blca, read, stad, hnsc, brca, coad, ucec, paad, luad, skcm, prad, kirc

Composite Element REF Methylated_Intensity Unmethylated_Intensity Detection_P_value

humanmethylation450

jhu-usc.edu

Level_2

HumanMethylation450.revision.lvl-2

lgg, gbm

Composite Element REF Beta_Value Detection_P_value

humanmethylation450

jhu-usc.edu

Level_3

HumanMethylation450.revision.lvl-3

laml, lusc, thca, kirp, blca, stad, read, hnsc, brca, coad, ucec, paad, luad, skcm, prad, kirc

Composite Element REF Beta_value Gene_Symbol Chromosome Genomic_Coordinate

illuminadnamethylation_oma002_cpi

jhu-usc.edu

Level_2

IlluminaDNAMethylation_OMA002_CPI.revision.lvl-2

gbm

Composite Element REF Beta Value

illuminadnamethylation_oma003_cpi

jhu-usc.edu

Level_2

IlluminaDNAMethylation_OMA003_CPI.revision.lvl-2

gbm

Composite Element REF Beta Value

illuminaga_mirnaseq

bcgsc.ca

Level_3

isoform.quantification.txt

laml, lusc, coad, kirp, ucec, luad, stad, read, kirc, hnsc, brca

miRNA_ID isoform_coords read_count reads_per_million_miRNA_mapped cross-mapped miRNA_region

illuminaga_mirnaseq

bcgsc.ca

Level_3

mirna.quantification.txt

laml, lusc, coad, kirp, ucec, luad, stad, read, kirc, hnsc, brca

miRNA_ID read_count reads_per_million_miRNA_mapped cross-mapped

illuminaga_rnaseq

bcgsc.ca

Level_3

exon.quantification.txt

laml, stad

exon raw_counts median_length_normalized RPKM

illuminaga_rnaseq

bcgsc.ca

Level_3

gene.quantification.txt

laml, stad

gene raw_counts median_length_normalized RPKM

illuminaga_rnaseq

bcgsc.ca

Level_3

spljxn.quantification.txt

laml, stad

junction raw_counts

illuminaga_rnaseq

unc.edu

Level_3

exon.quantification.txt

coad, ucec, read

exon raw_counts median_length_normalized RPKM

illuminaga_rnaseq

unc.edu

Level_3

gene.quantification.txt

coad, ucec, read

gene raw_counts median_length_normalized RPKM

illuminaga_rnaseq

unc.edu

Level_3

spljxn.quantification.txt

coad, ucec, read

junction raw_counts

illuminahiseq_dnaseqc

hms.harvard.edu

Level_3

_Segment.tsv

coad, read

Chromosome Start End Tumor_Count Normal_Count Segment_Mean

illuminahiseq_mirnaseq

bcgsc.ca

Level_3

isoform.quantification.txt

lusc, thca, ov, ucec, luad, lihc, blca, cesc, prad, stad, lgg, kirc, hnsc, brca

miRNA_ID isoform_coords read_count reads_per_million_miRNA_mapped cross-mapped miRNA_region

illuminahiseq_mirnaseq

bcgsc.ca

Level_3

mirna.quantification.txt

lusc, thca, ov, ucec, luad, lihc, blca, cesc, prad, stad, lgg, kirc, hnsc, brca

miRNA_ID read_count reads_per_million_miRNA_mapped cross-mapped

illuminahiseq_rnaseq

unc.edu

Level_3

exon.quantification.txt

lusc, kirp, luad, kirc, hnsc, lihc, brca, blca

exon raw_counts median_length_normalized RPKM

illuminahiseq_rnaseq

unc.edu

Level_3

gene.quantification.txt

lusc, kirp, luad, kirc, hnsc, lihc, brca, blca

gene raw_counts median_length_normalized RPKM

illuminahiseq_rnaseq

unc.edu

Level_3

spljxn.quantification.txt

lusc, kirp, luad, kirc, hnsc, lihc, brca, blca

junction raw_counts

illuminahiseq_rnaseqv2

unc.edu

Level_3

exon.quantification.txt

lusc, kirp, luad, hnsc, lihc, blca, brca

exon raw_counts median_length_normalized RPKM

illuminahiseq_rnaseqv2

unc.edu

Level_3

unc.edu.uuid..junction_quantification.txt

lusc, kirp, luad, hnsc, lihc, blca, brca

junction raw_counts

illuminahiseq_rnaseqv2

unc.edu

Level_3

unc.edu.uuid..rsem.genes.normalized_results

lusc, kirp, luad, hnsc, lihc, blca, brca

gene_id normalized_count

illuminahiseq_rnaseqv2

unc.edu

Level_3

unc.edu.uuid..rsem.genes.results

lusc, kirp, luad, hnsc, lihc, blca, brca

gene_id raw_count scaled_estimate transcript_id

illuminahiseq_rnaseqv2

unc.edu

Level_3

unc.edu.uuid..rsem.isoforms.normalized_results

lusc, kirp, luad, hnsc, lihc, blca, brca

isoform_id normalized_count

illuminahiseq_rnaseqv2

unc.edu

Level_3

unc.edu.uuid..rsem.isoforms.results

lusc, kirp, luad, hnsc, lihc, blca, brca

isoform_id raw_count scaled_estimate

mda_rppa_core

mdanderson.org

Level_2

MDA_RPPA_Core.SuperCurve.Level_2

brca

Sample REF Order

mda_rppa_core

mdanderson.org

Level_2

MDA_RPPA_Core.SuperCurve.Level_2

coad, ov, ucec, gbm, read, kirc

"Sample REF" "Order"

mda_rppa_core

mdanderson.org

Level_3

MDA_RPPA_Core.protein_expression.Level_3

brca

Composite Element REF Protein.Expression

mda_rppa_core

mdanderson.org

Level_3

MDA_RPPA_Core.protein_expression.Level_3

ov, coad, ucec, kirc, gbm, read

Composite Element REF Protein Expression

To obtain detailed information for platform design, visit the TCGA Data Portal for links to vendor websites. FASTA sequence files and their corresponding Array Description Format files are also available here.

The DCC does not collect or track vendor annotations. If you have trouble finding supporting materials, you should contact the vendor directly.

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