title: Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data.
abstract: Intra-tumor heterogeneity concerns the existence of genetically different subclones within the same tumor. Single sample quantification of heterogeneity relies on precise determination of chromosomal copy numbers throughout the genome, and an assessment of whether identified mutation variant allele fractions match clonal or subclonal copy numbers. We discuss these issues using data from SNP arrays, whole exome sequencing and pathologist purity estimates on several breast cancers characterized by ERBB2 amplification. We show that chromosomal copy numbers can only be estimated from SNP array signals or sequencing depths for subclonal tumor samples with simple subclonal architectures under certain assumptions.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Lönnstedt
authors.forename: Franco
authors.initials: F
authors.lastname: Caramia
authors.forename: Jason
authors.initials: J
authors.lastname: Li
authors.forename: Debora
authors.initials: D
authors.lastname: Fumagalli
authors.forename: Roberto
authors.initials: R
authors.lastname: Salgado
authors.forename: Andrew
authors.initials: A
authors.lastname: Rowan
authors.forename: Max
authors.initials: M
authors.lastname: Salm
authors.forename: Nnennaya
authors.initials: N
authors.lastname: Kanu
authors.forename: Peter
authors.initials: P
authors.lastname: Savas
authors.forename: Stuart
authors.initials: S
authors.lastname: Horswell
authors.forename: Stephan
authors.initials: S
authors.lastname: Gade
authors.forename: Sibylle
authors.initials: S
authors.lastname: Loibl
authors.forename: Patrick
authors.initials: P
authors.lastname: Neven
authors.forename: Christos
authors.initials: C
authors.lastname: Sotiriou
authors.forename: Charles
authors.initials: C
authors.lastname: Swanton
authors.forename: Sherene
authors.initials: S
authors.lastname: Loi
authors.forename: Terence P
authors.initials: TP
authors.lastname: Speed
mesh_terms: D000782:Aneuploidy; D001943:Breast Neoplasms / Q000235:genetics*; D005260:Female; D018628:Gene Dosage; D005787:Gene Frequency; D018740:Genetic Heterogeneity; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA