title: Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients.
abstract: Breast carcinomas are characterized by DNA copy number alterations (CNAs) with biological and clinical significance. This explorative study integrated CNA, expression, and germline genotype data of 112 early-stage breast cancer patients. Recurrent CNAs differed substantially between tumor subtypes classified according to expression pattern. Deletion of 16q was overrepresented in Luminal A, and a predictor of good prognosis, both overall and for the nonluminal A subgroups. The deleted region most significantly associated with survival mapped to 16q22.2, harboring the genes TXNL4B and DXH38, whose expression was strongly correlated with the deletion. The area most frequently deleted resided on 16q23.1, 3.5 MB downstream of the area most significantly associated with survival, and included the tumor suppressor gene ADAMTS18 and the cell recognition gene CNTNAP4. Whole-genome association analysis identified germline single nucleotide polymorphisms (SNPs) and their corresponding haplotypes, residing on several different chromosomes, to be associated with deletion of 16q. The genes where these SNPs reside encode proteins involved in the extracellular matrix (CHST3 and SPOCK2), in regulation of the cell cycle (JMY, PTPRN2, and Cwf19L2) and chromosome stability (KPNB1).
authors.affiliation: Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway.
authors.forename: Silje H
authors.initials: SH
authors.lastname: Nordgard
authors.forename: Fredrik E
authors.initials: FE
authors.lastname: Johansen
authors.forename: Grethe I G
authors.initials: GI
authors.lastname: Alnaes
authors.forename: Elmar
authors.initials: E
authors.lastname: Bucher
authors.forename: Ann-Christine
authors.initials: AC
authors.lastname: Syvänen
authors.forename: Bjørn
authors.initials: B
authors.lastname: Naume
authors.forename: Anne-Lise
authors.initials: AL
authors.lastname: Børresen-Dale
authors.forename: Vessela N
authors.initials: VN
authors.lastname: Kristensen
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D002470:Cell Survival; D002872:Chromosome Deletion; D002874:Chromosome Mapping; D002885:Chromosomes, Human, Pair 16 / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D018095:Germ-Line Mutation; D006239:Haplotypes; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger
chemical_list: D009363:Neoplasm Proteins; D012333:RNA, Messenger