GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data.
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.
Lyng
Heidi
H
Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway. heidi.lyng@rr-research.no
Lando
Malin
M
Brøvig
Runar S
RS
Svendsrud
Debbie H
DH
Johansen
Morten
M
Galteland
Eivind
E
Brustugun
Odd T
OT
Meza-Zepeda
Leonardo A
LA
Myklebost
Ola
O
Kristensen
Gunnar B
GB
Hovig
Eivind
E
Stokke
Trond
T
D002294:Carcinoma, Squamous Cell / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D018628:Gene Dosage; D006801:Humans; D008228:Lymphoma, Non-Hodgkin / Q000235:genetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D014178:Translocation, Genetic; D002583:Uterine Cervical Neoplasms / Q000235:genetics
D004273:DNA, Neoplasm