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E-GEOD-22133 GSE22133 transcription profiling by array, com... Homo sapiens

Genomic Subtypes of Breast Cancer Identified by Array Comparative Genomic Hybridization

·发布 2010年6月23日 ·更新 2014年5月2日

1436

样本数

718

实验数

芯片平台

实验描述

Breast cancer is a profoundly heterogeneous disease with respect to biological and clinical behavior. Gene expression profiling has been used to dissect this complexity and stratify tumors into intrinsic gene expression subtypes associated with distinct biology, patient outcome and different genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes. We applied global DNA copy number and gene expression profiling in 359 breast tumors. All tumors were classified according to intrinsic gene expression subtypes and included cases from genetically predisposed women. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to identify significant DNA copy number aberrations and genomic subgroups of breast cancer. We identified 31 genomic regions that were highly amplified in >1% of the 359 breast tumors. Several amplicons were found to co-occur, the 8p12 and 11q13.3 regions being the most frequent combination besides amplicons on the same chromosomal arm. Unsupervised hierarchical clustering with 133 significant GISTIC regions (66 and 67 with DNA copy number gain and loss, respectively) revealed six genomic subtypes, termed: 17q12, basal-complex, luminal-simple, luminal-complex, amplifier and mixed subtype. Four of them had striking similarity to intrinsic gene expression subtypes and showed association to conventional tumor biomarkers and clinical outcome. However, luminal A-classified tumors were distributed in two main genomic subtypes, luminal-simple and luminal-complex, the former group having better prognosis while the latter group included also luminal B and the majority of BRCA2-mutated tumors. The basal-complex subtype displayed extensive genomic homogeneity and harbored the majority of BRCA1-mutated tumors. The 17q12 subtype comprised mostly HER2-amplified and HER2-enriched subtype tumors and had the worst prognosis. The amplifier and mixed subtypes contained tumors from all gene expression subtypes, the former being enriched for 8p12-amplified cases while the mixed subtype included many tumors with predominantly DNA copy number losses and poor prognosis. Genomic profiling of 359 breast tumors using tiling BAC aCGH. A number of cases were hybridized as replicates or replicate as dye-swaps. Gene expression profiling of 359 breast tumors using 55K oligonucleotide microarrays.

芯片平台

A-GEOD-4723

SWEGENE_BAC_32K_Full（356 例）

A-GEOD-5345

SWEGENE H_v2.1.1 55K（359 例）

A-GEOD-7247

SWEGENE_BAC_33K_Full（3 例）

样本属性

er_neg, er_pos, NA

familial status

brca1, brca2, familial, sporadic

genomic subtype

17q12, amplifier, Basal-complex, Luminal-complex, Luminal-simple, mixed

grade

1, 2, 3, NA

hu subtype

basal, ERBB2, LumA, LumB, nonClassified, normal

Organism

Homo sapiens

organism part

Breast tumor

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osbin

1, NA

pgr

NA, pgr_neg, pgr_pos

primary

reference

promega male reference, Stratagene Universal reference RNA

实验信息

登记号

E-GEOD-22133

GEO 编号

GSE22133

实验类型

transcription profiling by array, comparative genomic hybridization by array

物种

Homo sapiens

发布日期

2010年6月23日

更新日期

2014年5月2日

提交者

Lena Luts、 Niklas Loman、 Håkan Olsson、 Päivi Heikkilä、 Outi Kilpivaara、 Kristiina Aittomäki、 Heli Nevanlinna、 Rainer Fagerholm、 Ake Borg、 Oskar Johannsson、 Bjarni A Agnarsson、 Adalgeir Arason、 Carl Blomqvist、 Rosa B Barkardottir、 Carina Strand、 Per Malmström

外部链接

ArrayExpress 原始页 NCBI GEO：GSE22133

分析服务

Genomic Subtypes of Breast Cancer Identified by Array Comparative Genomic Hybridization

联系地址

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