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Title: Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer [SET 15]      
keywords:
Variation
ID:
PRJNA295308
description:
Sporadic breast cancer (SBC) is a common and heterogeneous disease. There is no reliable way of early prediction of risk for SBC in the general population. We studied 282 females with SBC concentrating on copy number aberrations in tumor-free breast tissue (uninvolved margin, UM) outside the area of primary tumor (PT). Totally 1162 UMs (1-14 per breast) were studied. PT and blood/skin as control was also analyzed. Comparative analysis between genetic profiles for UM(s), PT(s) and blood/skin from the same patient is the core of study design. We identified 108 patients with at least one aberrant UM specimen, representing 38.3% of all cases. Gains were the dominating mutations in microscopically normal breast cells and gain of ERBB2, with overexpression of HER2 protein, was the most common aberration in normal cells. Five additional receptor genes (EGFR, FGFR1, IGF1R, LIFR and NGFR) also showed gains, and these were occasionally present in combination with the gain of ERBB2. Up to 67.6% of patients showed gain of one or more of these genes in normal cells. The aberrations found in normal cells from UMs were previously described in cancer literature, which suggest their causative, driving role in this disease. We demonstrate that analysis of normal cells from cancer-bearing patients leads to identification of genetic signatures that may predispose to SBC. Early detection of signals suggesting a predisposition towards development of SBC, long before detectable tumors are formed, is a key to the anticipated shift into a preventive paradigm of personalized medicine of breast cancer. Overall design: We studied 282 female breast cancer patients that were assessed as affected by sporadic disease at the time of diagnosis and all underwent mastectomy. In total, 1162 UMs (uninvolved margin tissues), ranging from 1 to 14 UMs per patient, taken outside the location of clinically characterized index primary tumor, were analyzed on Illumina arrays. For each subject, DNA from at least one control tissue was also analyzed, which was predominantly blood DNA, alternatively skin-derived DNA. We also studied primary tumor (PT), or up to 3 primary tumor foci from patients with diagnosis of multifocal disease. This GEO project contains the genotyping profiles (processed and normalized data including Log R Ratio and B allele frequency) for these 1162 UMs used in the study. Information on phenotypes (age at diagnosis, tumor focality, tumor grade, tumor molecular phenotype) is also provided, whenever available. This subSeries represents 133 tumor samples (genotype data from primary tumor tissue) from subject showing at least one UM sample with aberration. [29_PrimaryTumors_GPL6984.txt] 29 tumors samples genotyped on the platform GPL6984 (Human1M-Duov3_B) [2_PrimaryTumors_GPL13135.txt] 2 tumors samples genotyped on the platform GPL13135 (HumanOmniExpress BeadChip). [4_PrimaryTumors_GPL18636.txt] 4 tumors samples genotyped on the platform GPL18636 (Illumina Human660W-Quad v1.0). Please note that GPL18636 on GEO has chromosome coordinates in genome buid 36. In the matrix table I'm maintaining the same IDs as on GEO, but the chromosomal positions (“Position_hg19”) is reported in chromosomal build 37. I did this to provide with experiments which can be directly compared with all the others, which are run on platforms that already support chromosome build 37. [98_PrimaryTumors_GPL18224.txt] 98 tumors samples genotyped on the platform GPL18224 (Infinium HumanOmniExpressExome).
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA295308
authentication:
none
authorization:
none
ID:
pmid:26430163
name:
Homo sapiens
ncbiID:
ncbitax:9606
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject