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Sample GSM517071 Query DataSets for GSM517071
Status Public on May 27, 2010
Title HF-23896-(1), Affymetrix SNP6.0 array
Sample type genomic
Source name HF-23896-(1)
Organism Homo sapiens
Characteristics organ: Lung Cancer
Extracted molecule genomic DNA
Extraction protocol Qiagen AllPrep extraction kit was used according to the manufacturer's instructions
Label biotin
Label protocol Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0
Hybridization protocol Affymetrix Genome-Wide SNP Nsp/Sty Assay Kit 5.0/6.0
Scan protocol Affymetrix user manual (GeneChip scanner 3000)
Description none
Data processing Raw intensity data from the Affymetrix SNP 6.0 array was obtained for the tumor sample and matched normal. These data were normalized using a method first described for Illumina genotyping arrays. Specifically, we followed an adaptation of the Illumina method adapted for Affymetrix arrays normalization protocol implemented in the PennCNV package ( to obtain normalized B-allele Frequency (BAF) and LogR Ratio (LRR) values for each probeset. BAF represents the raw proportion of signal coming from allele B (Theta) normalized using Theta values from a pool of normal samples with pre-determined AA, AB, or BB genotypes at that probe position. LRR represents the log of the ration of the total signal from A and B alleles for a sample divided by expected total signal from a pool of normal samples given the same value of Theta. In brief, the raw intensity values (CEL files) were processed to obtain normalized allele-specific values for each probe using the Affymetrix Power Tools version 1.10 ( tools apt-probeset-genotype and apt-probeset-summarize. A reference probe-intensity distribution obtained from the HapMap project samples was used for the quantile normalization step. BAF and LRR values were calculated with the script “” from the PennCVN-Affy package. This script additionally implements a correction for GC-content bias in the LRR values. Data from the HapMap project were used for the reference clusters of AA, AB, and BB genotype signal intensity values. LRR values for somatic CNVs were calculated as the difference of the Tumor and Normal LRR values.
Submission date Mar 02, 2010
Last update date May 24, 2010
Contact name Peter Haverty
Organization name Genentech, Inc.
Department Bioinformatics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
Platform ID GPL6801
Series (2)
GSE20584 Affymetrix SNP6.0 array for comparison of lung tumor and adjacent normal to high-throughput sequencing data
GSE20585 The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Data table header descriptions
VALUE B-Allele Frequency (BAF)
LRR Log-R Ratio (LRR) values

Data table
CN_473963 2 -0.4676
CN_473964 2 -0.2932
CN_473965 2 -0.2291
CN_477984 2 -0.3708
CN_473981 2 0.0918
CN_473982 2 -0.1778
CN_497980 2 -0.1202
CN_497981 2 0.112
CN_513369 2 -0.6327
CN_513370 2 0.4577
CN_517762 2 0.1859
CN_517763 2 -0.0497
CN_502615 2 -0.372
CN_502613 2 0.6872
CN_502614 2 -0.094
CN_502616 2 -0.7861
CN_502842 2 0.5892
CN_502843 2 0.3757
CN_466171 2 0.3915
CN_466172 2 0.1346

Total number of rows: 1851567

Table truncated, full table size 42188 Kbytes.

Supplementary file Size Download File type/resource
GSM517071.CEL.gz 48.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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