Transcriptomics

Dataset Information

64

Fine-scale mapping of copy-number alterations with massively parallel sequencing


ABSTRACT: In order to benchmark the reproducibility of Affymetrix 238K Sty arrays for detecting copy-number alterations. We performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by array pre-processing with the GISTIC algorithm (PMID: 18077431). For each SNP probeset, we calculated the median copy number across replicate arrays. The median copy number profile for each tumor cell line was segmented with the GLAD algorithm (PMID: 15381628) to partition the genome into regions of constant copy number. We compared the copy-number alterations detected by GLAD segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246. Keywords: disease state analysis 77 replicates of HCC1143 (breast ductal carcinoma), 69 replicates of HCC1143BL (matched normal), 42 replicates of HCC1954 (breast ductal carcinoma), 36 replicates of HCC1954BL (matched normal), 1 replicate of NCI-H2347 (lung adenocarcinoma)

ORGANISM(S): Homo sapiens  

SUBMITTER: Carsten Russ   Chad Nusbaum  Scott L Carter  Gad Getz  David Jaffe  Derek Y Chiang  Matthew Meyerson  Eric S Lander  Derek Chiang  Xiaojun Zhao 

PROVIDER: E-GEOD-12019 | ArrayExpress | 2008-11-13

SECONDARY ACCESSION(S): GSE12019PRJNA114305

REPOSITORIES: GEO, ArrayExpress

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Publications

High-resolution mapping of copy-number alterations with massively parallel sequencing.

Chiang Derek Y DY   Getz Gad G   Jaffe David B DB   O'Kelly Michael J T MJ   Zhao Xiaojun X   Carter Scott L SL   Russ Carsten C   Nusbaum Chad C   Meyerson Matthew M   Lander Eric S ES  

Nature methods 20081130 1


Cancer results from somatic alterations in key genes, including point mutations, copy-number alterations and structural rearrangements. A powerful way to discover cancer-causing genes is to identify genomic regions that show recurrent copy-number alterations (gains and losses) in tumor genomes. Recent advances in sequencing technologies suggest that massively parallel sequencing may provide a feasible alternative to DNA microarrays for detecting copy-number alterations. Here we present: (i) a st  ...[more]

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