Genome‐wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients

• DOI: 10.1002/gcc.20569
• Publication Date: 2008-04-08T15:24:09Z
• Authors: Silje H. Nordgard; Fredrik E. Johansen; Grethe I. G. Alnæs; Elmar Bucher; Ann‐Christine Syv...; Bjørn Naume; Anne‐Lise Børrese...; Vessela N. Kriste...
• Keywords: carcinomas; Cell Survival; Genome, Human; Gene Expression Profiling; Chromosome Mapping; Breast Neoplasms; Polymorphism, Single Nucleotide; Neoplasm Proteins; 3. Good health; Gene Expression Regulation, Neoplastic; 03 medical and health sciences; breast cancer; 0302 clinical medicine; SDG 3 - Good Health and Well-being; Haplotypes; CNAs; gene expression; Humans; Female; RNA, Messenger; Chromosome Deletion; Chromosomes, Human, Pair 16; Germ-Line Mutation

Abstract Breast carcinomas are characterized by DNA copy number alterations (CNAs) with biological and clinical significance. This explorative study integrated CNA, expression, germline genotype data of 112 early‐stage breast cancer patients. Recurrent CNAs differed substantially between tumor subtypes classified according to expression pattern. Deletion 16q was overrepresented in Luminal A, a predictor good prognosis, both overall for the nonluminal A subgroups. The deleted region most significantly associated survival mapped 16q22.2, harboring genes TXNL4B DXH38 , whose strongly correlated deletion. area frequently resided on 16q23.1, 3.5 MB downstream survival, included suppressor gene ADAMTS18 cell recognition CNTNAP4 . Whole‐genome association analysis identified single nucleotide polymorphisms (SNPs) their corresponding haplotypes, residing several different chromosomes, be deletion 16q. where these SNPs reside encode proteins involved extracellular matrix ( CHST3 SPOCK2 ), regulation cycle JMY PTPRN2 Cwf19L2 ) chromosome stability KPNB1 ). © 2008 Wiley‐Liss, Inc.