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SNP (Single Nucleotide Polymorphism) array-based data are results from the Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina's assays: Human1M-Duo Bead Chip and HumanHap550.  These platforms are used for inferring genotype, copy number variation and loss of heterozygosity.

Data Overview

TCGA includes three platforms for array-based detection of Single Nucleotide Polymorphisms (SNPs).  Each platform allows analysis of SNP genotype and copy number variation.  Level 1 data represents the degree of hybridization between the sample and a probe for the SNP or CNV probe.  Level 2 data converts the measured values to biologically relevant data such as genotype and allele frequency.  Level 3 data describes regions of the genome that seem to have segmental duplications or deletions in the tumor compared to the normal sample for the patient (copy number variation; CNV) and loss of heterozygosity (LOH).  Currently, the mapped genome position is in reference to NCBI's Build 36 (hg18), although the Broad is planning to eventually also include coordinates using NCBI's Build 37 (hg19).

Available Platforms

Platform Code

Platform Alias

Platform Name

Available

Example

FTP Display

genome_wide_snp_6

genome_wide_snp_6

Affymetrix Genome-Wide Human SNP Array 6.0

yes

example icon

tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
<disease_study>/cgcc/<center>
/genome_wide_snp_6/snp

human1mduo

human1mduo

Illumina Human1M-Duo Bead Chip

yes

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/anonymous/tumor/
ov/cgcc/hudsonalpha.org/human1mduo/snp/

humanhap550

humanhap550

Illumina HumanHap550

yes

example icon

/tcgafiles/ftp_auth/
distro_ftpusers/tcga4yeo/tumor/
<disease_study>/cgcc/<center>/
humanhap550/snp/

The Affymetrix platform has been submitted by The Broad (broad.mit.edu) and WashU (genome.wustl.edu), while the Illumina platforms have been submitted by Hudson Alpha (hudsonalpha.org).

Data File Descriptions

Level 1 Data

Platform Code

File Type

Description

Example

genome_wide_snp_6

binary
.CEL

file of measured probe cel intensities, readable using apt-cel-extract from Affymetrix Tool Kit
tab delimited file of:
probe_id
x = microarray's x grid  position of probe
y = microarray's y grid position of probe
MEAN =mean of intensities over a number of analyzed pixels in the grid cel
STDDEV = standard deviation of the intensities of the analyzed pixels in the grid cel
NPIXELS = number of pixels analyzed for the cel

example icon

human1mduo
humanhap550

binary
_Red.idat

binary Illumina file. Data available as text in the .XandYintensity.txt file

example icon

 

binary
_Grn.idat

binary Illumina file. Data available as text in the .XandYintensity.txt file

example icon

 

tab delimited
.XandYintensity.txt

Composite Element RER
Chr
Pos
X
Y

example icon

Level 2 Data

Platform Code (center)

File Type

Description

Example

genome_wide_snp_6 (broad.mit.edu)

tab delimited
.ismpolish.data.txt

Hybridization REF (probe ID)
Signal

example icon

 

tab delimited
.raw.copynumber.data.txt

mapping using NCBI Reference Assembly 36:
Composite Element REF
Chromosome
Physical Position
Signal

example icon

 

tab delimited
.no_outlier.copynumber.data.txt

Composite Element REF
Chromosome
PhysicalPosition
Signal

example icon

 

tab delimited
.byallele.copynumber.data.txt

Composite Element REF
Chromosome
PhysicalPosition
Signal_A
Signal_B

example icon

 

tab delimited
.after_5NN.copynumber.data.txt

Composite Element REF
Chromosome
PhysicalPosition
Signal

example icon

genome_wide_snp_6 (genome.wustl.edu)

tab delimited
.genotype.dat

Composite Element REF
Chromosome
PhysicalPosition
Genotype

example icon


tab delimited
.intensities.dat

Composite Element REF
Chromosome
PhysicalPosition
Signal

example icon


tab delimited
.pairedcn.dat

Composite Element REF
Chromosome
PhysicalPosition
Value

example icon

human1mduo
humanhap550 

tab delimited
.B_Allele_freq.txt

Composite Element REF
Chr
per sample
B Allele
Freq

example icon

 

tab delimited
.Delta_B_Allele_freq.txt

Composite Element REF
Chr
per sample:
Delta Allele
Freq

example icon

 

tab delimited
.Genotypes.txt

Composite Element REF
Chr
per sample:
genotype

example icon

 

tab delimited
.Normal_LogR.txt

Composite Element REF
Chr
per sample:
Log2(Rnorm/Rref)

example icon

 

tab delimited
.Paired_LogR.txt

Composite Element REF
Chr
Pos
Log2(Rtum/Rnorm)

example icon

 

tab delimited
.Unpaired_LogR.txt

Composite Element REF
Chr
Pos
Log2(Rtum/Rref)

example icon

Level 3 Data

Platform Code

File Type

Description

Example

genome_wide_snp_6

tab delimited
.seg.data.txt

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

example icon

human1mduo
humanhap550

tab delimited
.seg.txt

Normalization Name
chrom
loc.start
loc.end
mean

example icon

 

tab delimited
seq.normal.txt

Normalization Name(barcode)
chrom
loc.start
loc.end
mean

example icon

 

tab delimited
.loh.txt


Normalization Name
chrom
loc.start
loc.end
mean

example icon

Data Validation

Specific Validations

Apart from the standard GCC validation set listed below, SNP has no data type-specific validations.

Standard Validations

SNP archives undergo standard validation sets shown in the Standard Archive Validation chart for GCC archives:

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