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Respective Prognostic Value of Genomic Grade and Histological Proliferation Markers in Early Stage (pN0) Breast Carcinoma

ABSTRACT: Phenotypic and genomic characterization of Early Stage Breast Carcinoma using Training set (n=109) Validation set (n=105) of SNP6 arrays Affymetrix SNP6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved breast tumoral samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Jaydutt Bhalshankar

PROVIDER: E-GEOD-48064 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genomic instability: a stronger prognostic marker than proliferation for early stage luminal breast carcinomas.

Vincent-Salomon Anne A Benhamo Vanessa V Gravier Eléonore E Rigaill Guillem G Gruel Nadège N Robin Stéphane S de Rycke Yann Y Mariani Odette O Pierron Gaëlle G Gentien David D Reyal Fabien F Cottu Paul P Fourquet Alain A Rouzier Roman R Sastre-Garau Xavier X Delattre Olivier O

PloS one 20131015 10

<h4>Background</h4>The accurate prognosis definition to tailor treatment for early luminal invasive breast carcinoma patients remains challenging.<h4>Materials and methods</h4>Two hundred fourteen early luminal breast carcinomas were genotyped with single nucleotide polymorphisms (SNPs) array to determine the number of chromosomal breakpoints as a marker of genomic instability. Proliferation was assessed by KI67 (immunohistochemistry) and genomic grade index (transcriptomic analysis). IHC3 (IHC4 ...[more]

PMID: 24143191

Similar Datasets

Respective Prognostic Value of Genomic Grade and Histological Proliferation Markers in Early Stage (pN0) Breast Carcinoma

Project description:Phenotypic and genomic characterization of Early Stage Breast Carcinoma using Training set (n=109) Validation set (n=105) of SNP6 arrays

2014-02-18 | GSE48064 | GEO

Respective prognostic value of genomic grade and histological proliferation markers in early stage (pN0) breast carcinoma.

Project description:BackgroundGenomic grade (GG) is a 97-gene signature which improves the accuracy and prognostic value of histological grade (HG) in invasive breast carcinoma. Since most of the genes included in the GG are involved in cell proliferation, we performed a retrospective study to compare the prognostic value of GG, Mitotic Index and Ki67 score.MethodsA series of 163 consecutive breast cancers was retained (pT1-2, pN0, pM0, 10-yr follow-up). GG was computed using MapQuant Dx(R).ResultsGG was low (GG-1) in 48%, high (GG-3) in 31% and equivocal in 21% of cases. For HG-2 tumors, 50% were classified as GG-1, 18% as GG-3 whereas 31% remained equivocal. In a subgroup of 132 ER+/HER2- tumors GG was the most significant prognostic factor in multivariate Cox regression analysis adjusted for age and tumor size (HR = 5.23, p = 0.02).ConclusionsIn a reference comprehensive cancer center setting, compared to histological grade, GG added significant information on cell proliferation in breast cancers. In patients with HG-2 carcinoma, applying the GG to guide the treatment scheme could lead to a reduction in adjuvant therapy prescription. However, based on the results observed and considering (i) the relatively close prognostic values of GG and Ki67, (ii) the reclassification of about 30% of HG-2 tumors as Equivocal GG and (iii) the economical and technical requirements of the MapQuant micro-array GG test, the availability in the near future of a PCR-based Genomic Grade test with improved performances may lead to an introduction in clinical routine of this test for histological grade 2, ER positive, HER2 negative breast carcinoma.

| S-EPMC3329444 | biostudies-literature

Genomic characterization of three acute lymphoblastic leukemia cases and one established cell line REH at the single cell level

Project description:DNA copy number alterations and mutations were characterised by bulk SNP anlaysis and exome sequencing (not sown here) in three acute lymphoblastic leukaemia samples and one establish cell line REH. Further single cell experiments of these cases investigated the mutation and copy number targets previously defined exploring the sub-clonal populations and phylogenic trees within each leukaemia. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples. Copy number analysis of Affymetrix SNP6 arrays or Cytogenetics whole genome 2.7M arrays was performed for three leukaemic samples and one established cell line REH. Remission samples were only available for two of the leukaemia samples (Case A and Case B) and therefore 20 HapMap Caucasien samples were used as controls for the SNP6 array expeeriments.

2013-07-26 | E-GEOD-49215 | biostudies-arrayexpress

SNP6 profiling of metaplastic breast carcinoma

Project description:SNP6 profiling of metaplastic breast carcinoma

2014-10-31 | GSE57548 | GEO

SNP6 profiling of metaplastic breast carcinoma

Project description:SNP6 profiling of metaplastic breast carcinoma Metaplastic breast carcinoma (MBC) is a rare and aggressive histologic type of breast cancer, preferentially displaying a triple-negative phenotype (i.e. lacking estrogen receptor, progesterone receptor and HER2 expression). We sought to define the transcriptomic heterogeneity of MBCs on the basis of current gene expression microarray-based classifiers and to determine whether MBCs display gene copy number profiles consistent with those of BRCA1-associated breast cancers.

2014-10-31 | E-GEOD-57548 | biostudies-arrayexpress

SNP6 profiling of papillary carcinoma of the breast

Project description:SNP6 profiling of papillary carcinoma of the breast

2014-06-20 | GSE55638 | GEO

SNP6 profiling of papillary carcinoma of the breast

Project description:SNP6 profiling of papillary carcinoma of the breast Affymetrix SNP6 arrays were performed according ro manufacturer's directions on DNA extracted from 16 papillary carcinomas of the breast.

2014-06-20 | E-GEOD-55638 | biostudies-arrayexpress

Homo sapiens

Project description:SNP6 profiling of metaplastic breast carcinoma

| PRJNA246689 | ENA

Affymetrix SNP6 array data for ACTH-Independent Macronodular Adrenal Hyperplasia (AIMAH) samples

Project description:AIMAH is an ACTH-independent bilateral enlargement of the adrenal cortex occuring during adulthood. The enlargment is related to the growth of multiple benign nodules. This condition is associated with various degrees of cortisol hypersecretion. The occurence of several nodules in both adrenals, and the existence of familial forms, suggest the existence of a germline genetic predisposition. To find the gene(s), the aim of the project was to look for recurrent chromosomal alterations in the AIMAH nodules. Extensive mapping of somatic gains, losses and copy-neutral loss of heterozygosity (LOH) was performed with Affymetrix SNP6 arrays. A copy neutral LOH of 16p, occuring in 7 of 26 patients, was one of the only recurrent alterations, pointing towards a candidate gene in this region. Of note this condition differs from the congenital adrenal hyperplasias, related to genetic alterations of steroidogenesis (the latter is an ACTH dependent adrenal hyperplasia). Affymetrix SNP6 arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved tumor samples or peripheral blood samples.

2013-11-28 | GSE42171 | GEO

Conserved Role of FOXC1 in TNBC is parallel to FOXA1 in ER+ Breast Cancer

Project description:Triple-negative breast cancer (TNBC) is characterized by lack of receptors, estrogen (ER), progesterone, and Her2, and standard receptor-targeted therapies are ineffective. FOXC1, a transcriptional factor aberrantly overexpressed in many cancers, drives growth, metastasis, and stem-cell-like properties in TNBC. However, the molecular function of FOXC1 is unknown, partly due to heterogeneity of TNBC. Here, we show that although FOXC1 regulates many cancer hallmarks in TNBC, its function is varied in different cell lines, highlighted by the differential response to CDK4/6 inhibitors upon FOXC1 loss. Despite this functional heterogeneity, we show that FOXC1 regulates key oncogenes and tumor suppressors and identify a set of core FOXC1 peaks conserved across TNBC cell lines. We identify the ER-associated and drug-targetable nuclear receptor NR2F2 as a cofactor of FOXC1. Finally, we show that core FOXC1 targets in TNBC are parallelly regulated by the pioneer factor FOXA1 and the nuclear receptor NR2F2 in ER+ breast cancer.

2024-07-03 | PXD053261 | Pride

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