GSE13372_HCC1143 {acnr}

Annotated copy-number regions from the GEO GSE13372 data set.

Description

The GEO GSE13372 data set is from the Affymetrix GenomeWideSNP_6 chip type. We have extracted one tumor/normal pair corresponding to the breast cancer cell line HCC1143. For consistency with the other data sets in the package the tumor and normal samples are labeled according to their tumor cellularity, that is, 100

Format

A data frame with 205842 observations of 7 variables:

c

total copy number (not log-scaled)

b

allelic ratios in the diluted tumor sample (after TumorBoost)

genotype

germline genotypes

bT

allelic ratios in the diluted tumor sample (before TumorBoost)

bN

allelic ratios in the matched normal sample

region

a character value, annotation label for the region. Should be encoded as "(C1,C2)", where C1 denotes the minor copy number and C2 denotes the major copy number. For example,

(1,1)

Normal

(0,1)

Hemizygous deletion

(0,0)

Homozygous deletion

(1,2)

Single copy gain

(0,2)

Copy-neutral LOH

(2,2)

Balanced two-copy gain

(1,3)

Unbalanced two-copy gain

(0,3)

Single-copy gain with LOH

genotype

the (germline) genotype of SNPs. By definition, rows with missing genotypes are interpreted as non-polymorphic loci (a.k.a. copy number probes).

cellularity

A numeric value between 0 and 1, the percentage of tumor cells in the sample.

Details

These data have been processed from the files available from GEO using scripts that are included in the 'inst/preprocessing/GSE13372' directory of this package. This processing includes normalization of the raw CEL files using the CRMAv2 method implemented in the aroma.affymetrix package.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13372

References

Chiang DY, Getz G, Jaffe DB, O'Kelly MJ et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 2009 Jan;6(1):99-103. PMID: 19043412

Bengtsson, H., Wirapati , P. & Speed, T.P. (2009). A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6, Bioinformatics 25(17), pp. 2149-56.

Bengtsson H., Neuvial, P. and Speed, T. P. (2010) TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC bioinformatics 11 (2010), p. 245.

Examples

dat <- loadCnRegionData("GSE13372_HCC1143")
unique(dat$region)