Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic alterations in MPT patients with multiple primary tumors

ABSTRACT: Multiple primary tumors (MPT) usually develop in MPT patients with hereditary cancer syndromes. Nonetheless, the genetic etiology of a large proportion of MPT cases remains unclear. In this study, germline copy number variations (CNVs) and cnLOH (copy-neutral loss of heterozygosity) were investigated in 22 MPT MPT patients having no mutations in the main cancer predisposition genes. Our main goal was to uncover new genes potentially related to a high risk of developing MPT. Twenty MPT patients have family history of cancer and 12 met criteria for hereditary cancer syndromes. Seventeen rare germline CNVs covering 40 genes were identified in 11 MPT patients, including an EPCAM/MSH2 deletion in one Lynch Syndrome MPT patient. An enrichment analysis with the genes mapped in the rare CNVs revealed a significant number of genes associated with carcinogenesis and/or related to functions implicated with tumor development, such as proliferation and cell survival. A network analysis emphasized the relevance of TP53 pathway in carcinogenesis. A high number of germline cnLOH was detected in nine MPT patients, especially in two cases. Eighteen genes were covered both by rare CNVs and cnLOH, seven of them (ABCC1, KDM4C, KIAA0430, MYH11, NDE1, PIWIL2 and ULK2) were directly related to cellular growth and proliferation. These genes may represent interesting candidates for further studies in MPT risk.

ORGANISM(S): Homo sapiens

PROVIDER: GSE85586 | GEO | 2017/08/14

SECONDARY ACCESSION(S): PRJNA338889

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Affymetrix]

Project description:Only a small proportion of cases suspected to have Lynch Syndrome (LS) can be explained by mutation in the mismatch repair (MMR) genes. This study aimed to identify rare CNVs that may contribute to an increased risk for hereditary colorectal cancer in patients with MMR proficiency.

2015-11-30 | GSE72667 | GEO

Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes [Agilent]

2015-11-30 | GSE72665 | GEO

Rare germline copy number variations and disease susceptibility in familial melanoma

Project description:Mounting evidence suggests that copy number variations (CNVs) can contribute to cancer susceptibility. The main goal of this study was to evaluate the role of germline CNVs in melanoma predisposition in high-risk melanoma families. We used genome-wide tiling comparative genomic hybridization and SNP arrays to characterize CNVs in 335 individuals (240 melanoma cases) from American melanoma-prone families (22 with germline CDKN2A or CDK4 mutations). We found that the global burden of overall CNVs (or deletions or duplications separately) was not significantly associated with case-control or CDKN2A/CDK4 mutation status after accounting for the familial dependence. However, we identified several rare CNVs that either involved known melanoma genes (e.g. PARP1, CDKN2A) or co-segregated with melanoma (duplication on 10q23.23, 3p12.2 and deletions on 8q424.3, 2q22.1) in families without mutations in known melanoma high-risk genes. Some of these CNVs were correlated with expression changes in disrupted genes based on RNASeq data from a subset of melanoma cases included in the CNV study. These results suggest that rare co-segregating CNVs may influence melanoma susceptibility in some melanoma-prone families and genes found in our study warrant further evaluation in future genetic analyses of melanoma.

2016-12-01 | GSE85010 | GEO

Identification of candidate predisposing copy number variants in familial and early-onset colorectal cancer patients

Project description:In the majority of colorectal cancers (CRC) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. In order to identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP-based array CGH on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in 6 patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition. Copy number detection was performed using CNAG2.0 software for 250k SNP arrays and using the Affymetrix Genotyping Console v2.1 software for SNP 6.0 arrays, Reference genomes are included in this data set. Germline genomic DNA from 41 patients with early-onset microsatellite stable colorectal cancer was hybridized on Affymetrix Nsp/6.0 SNP-based arrays according to manufacturer's procedures.

2010-11-01 | E-GEOD-13429 | biostudies-arrayexpress

Gene expression comparison of colorectal cancer samples from patients diagnosed at a young and elderly age

Project description:Colorectal cancer (CRC) incidence increases with age and early onset of the disease is an indication of genetic predisposition, estimated to cause up to 30 % of all CRC cases. To identify genes associated with an increased risk for CRC, genome-wide gene expression levels of CRCs from patients diagnosed at an early age and CRCs from patients diagnosed at higher age were investigated. Patients with known hereditary predisposition syndromes were excluded from the study. Twenty four patients were diagnosed at a young age (mean, 43 years; range, 28-53 years), referred to as the early onset group. They were excluded from the HNPCC and FAP syndromes by clinical criteria and no other cancer syndromes were recorded for these patients. The second group consisted of 17 patients with primary diagnosis at old age (mean, 79 years; range, 69-87 years), referred to as the late onset group. The samples from the late onset group were selected to reflect the composition of the early onset group with respect to gender, tumor localization and tumor stage according to The International Union Against Cancer (UICC)/American Joint Committee on Cancer (AJCC). Microsatellite instability (MSI) status was previously analyzed in all samples to eliminate the potential risk of including patients with inherited DNA repair deficiencies.

2011-09-06 | E-GEOD-25071 | biostudies-arrayexpress

Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

Project description:Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

| PRJNA593313 | ENA

Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

Project description:Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

| PRJNA593311 | ENA

Gene expression comparison of colorectal cancer samples from patients diagnosed at a young and elderly age

2011-09-07 | GSE25071 | GEO

Project description:Rare CNVs in Lynch Syndrome patients negative for mutations in mismatch repair genes

| PRJNA294618 | ENA

Large genomic alteration of 7q in two patients with multiple primary cancers, including triple negative breast cancer, and family history of malignant neoplasms

Project description:A great percentage of patients with multiple primary cancers (MPCs) and family history of cancer are suspected to have a hereditary cancer predisposition syndrome. However, only a small proportion of these cases are explained by mutations in high-penetrance genes, suggesting the involvement of undiscovered genes in cancer predisposition. In this study, we report the molecular and clinical characterization of two unrelated patients with MPCs, a positive family history of cancer, no germline pathogenic mutations in BRCA1, BRCA2 and TP53 genes and large genomic rearrangements mapped on chromosome 7q.

2016-02-15 | GSE77138 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data