Allele-Specific Copy Number Analysis of Tumors
Allele-specific copy number analysis of tumors Peter Van Looa,b,c,1, Silje H. Nordgarda,d,1, Ole Christian Lingjærdee, Hege G. Russnesa,f,g, Inga H. Ryef, Wei Sund,h, Victor J. Weigmand, Peter Marynenc, Anders Zetterbergi, Bjørn Naumej, Charles M. Peroud, Anne-Lise Børresen-Dalea,g,2, and Vessela N. Kristensena,g,k,2,3 aDepartment of Genetics, Institute for Cancer Research, Clinic for Cancer and Surgery, Oslo University Hospital, Montebello, N-0310 Oslo, Norway; bDepartment of Molecular and Developmental Genetics, VIB, B-3000 Leuven, Belgium; cDepartment of Human Genetics, University of Leuven, B-3000 Leuven, Belgium; dDepartment of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7264; eDepartment of Informatics, University of Oslo, Blindern, N-0316 Oslo, Norway; fDepartment of Pathology, Clinic for Cancer and Surgery, Oslo University Hospital, Montebello, N-0310 Oslo, Norway; gInstitute for Clinical Medicine, University of Oslo, Montebello, N-0310 Oslo, Norway; hDepartment of Biostatistics, University of North Carolina, Chapel Hill, NC 27599-7420; iDepartment of Oncology–Pathology, Karolinska Institute, Cancer Center Karolinska, SE-171 77 Stockholm, Sweden; jThe Cancer Clinic, Clinic for Cancer and Surgery, Oslo University Hospital, Montebello, N-0310 Oslo, Norway; and kInstitute for Clinical Epidemiology and Molecular Biology, Akershus University Hospital, Faculty of Medicine, University of Oslo, N-1474 Nordbyhagen, Norway Edited* by David Botstein, Lewis-Sigler Institute, Princeton, NJ, and approved August 23, 2010 (received for review July 9, 2010) We present an allele-specificcopynumberanalysisoftheinvivo count. We obtain accurate genome-wide allele-specific copy- breast cancer genome. We describe a unique bioinformatics ap- number profiles [called “ASCAT (allele-specific copy number proach, ASCAT (allele-specific copy number analysis of tumors), to analysis of tumors) profiles”] for 91 of 112 breast carcinomas fi accurately dissect the allele-specific copy number of solid tumors, assayed.
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