GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data.
Lyng H,
Lando M,
Brøvig RS,
Svendsrud DH,
Johansen M,
Galteland E,
Brustugun OT,
Meza-Zepeda LA,
Myklebost O,
Kristensen GB,
Hovig E,
Stokke T.
Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway. heidi.lyng@rr-research.no
Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.
PMID: 18500990 [PubMed - indexed for MEDLINE]
PMCID: PMC2441472