Method
GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
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* Corresponding author: Heidi Lyng heidi.lyng@rr-research.no
1 Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway
2 Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway
3 Department of Oncology, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway
4 Norwegian Microarray Consortium, Department of Molecular Bioscience, University of Oslo, NO-0316 Oslo, Norway
5 Department of Gynecologic Oncology, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway
6 Department of Medical Informatics, University of Oslo, NP-0316 Oslo, Norway
7 Institute of Informatics, University of Oslo, NO-0316 Oslo, Norway
Genome Biology 2008, 9:R86 doi:10.1186/gb-2008-9-5-r86
Published: 23 May 2008Additional files
Additional data file 1:
Calculation steps in GeneCount.
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Additional data file 2:
An example of FISH probe locations.
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Additional data file 3:
Comparison of FISH DNA copy numbers and smoothed aCGH ratio levels in non-Hodgkin's lymphomas.
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Additional data file 4:
Discrepancies between GeneCount and FISH DNA copy numbers.
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Additional data file 5:
Comparison of tumor cell fractions derived by histological examination and by GeneCount estimation in cervical cancers.
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Additional data file 6:
Standard deviation (noise) of the log-transformed aCGH ratios.
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Additional data file 7:
Comparison of results from ratio level and GeneCount analyses in cervical cancers.
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Additional data file 8:
Regions with DNA copy number heterogeneity in non-Hodgkin's lymphomas.
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Additional data file 9:
Regions with DNA copy number heterogeneity in cervical cancers.
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Additional data file 10:
Tumor cell fraction required for detection of heterogeneous copy number changes.
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Additional data file 11:
Analysis of the evolutionary sequence of subpopulations in heterogeneous tumors.
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Additional data file 12:
The minimum tumor cell fraction that can be calculated in GeneCount.
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Additional data file 13:
The tumor cell fraction required for detection of homogeneous copy number changes.
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