scholarly journals Copy number variations primed lncRNAs deregulation contribute to poor prognosis in colorectal cancer

Aging ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 6089-6108 ◽  
Author(s):  
Huimin Liu ◽  
Xiaoyu Gu ◽  
Guihua Wang ◽  
Ying Huang ◽  
Shaoqing Ju ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Poor Prognosis ◽  
Copy Number Variations

scholarly journals Genetic characterization of colorectal cancer using a next generation sequencing approach to identify a specific pattern of somatic alterations in tumors arising from different anatomic sites

2016 ◽  
Author(s):  
Carmelo Laudanna ◽  
Gianluca Santamaria ◽  
Simona Migliozzi ◽  
Duarte Mendes Oliveira ◽  
Donatella Malanga ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Treatment Options ◽  
Copy Number Variations ◽  
Specific Pattern ◽  
Surgical Approaches ◽  
Anatomical Location ◽  
Molecular Alterations ◽  
Somatic Alterations ◽  
Novel Biomarkers

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide, with nearly 1.4 million new cases diagnosed in 2012. CRC results from the accumulation of multiple genetic and epigenetic aberrations. Tumor localization in the large intestine tract determines different surgical approaches and treatment options. Considering the heterogeneous nature of these tumors we hypothesized that different patterns of molecular alterations could be associated with a specific anatomical location. To identify distinct genomic alterations (e.g, copy number variations and mutations) associated to different CRC anatomical sites we sequenced 32 CRCs samples from different location (right-sided, left-sided etc.) using the Ion AmpliSeq™ Comprehensive Cancer Panel that covered the whole coding sequence of 409 tumor suppressor genes and oncogenes frequently altered in cancer. Interestingly left-sided tumors were generally more altered respect to right-sided ones. Cluster analysis of all samples allowed the identification of 21-gene core that were significantly mutated in all sample groups. As expected, KRAS and APC mutations were frequently in the tumors resected from different anatomical localizations. Unsupervised analysis of copy number variations reveals a core of 160-gene significantly altered. In addition to the expected SRC, MYC and CEBPA, we found interestingly genes in validation status. Despite missing a significant number of cases, gene panel provides a solid alternative approach to WES in order to characterize a signature of alterations correlated with CRC tumor and the identification of novel biomarkers in colorectal carcinoma that could be used as potential clinical target.

scholarly journals Cytogenomic Changes in Sporadic Colorectal Cancer and Surrounding Nonneoplastic Tissues: The Relevance of Subtelomeric Copy Number Variations

2021 ◽  
Author(s):  
Mariana Rocha ◽  
Evelin Aline Zanardo ◽  
Alexandre Torchio Dias ◽  
Fabrícia Andréia Rosa Madia ◽  
Thaís Virgínia Moura Machado Costa ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Copy Number Variations ◽  
Sporadic Colorectal Cancer ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pathogenic Cnvs ◽  
Mechanism Of Carcinogenesis ◽  
Tumor Genome ◽  
Dependent Probe

Abstract The purpose of this study was to investigate the relevance of subtelomeric cytogenomic changes in patients with sporadic colorectal cancer (CRC) using multiplex ligation-dependent probe amplification (MLPA) and single nucleotide polymorphism arrays. The results revealed pathogenic genomic alterations in the TNFRS18 (1p), CHL1 (3p), TRIML2 (4q), FBXO25 (8p), NKX3-1 (8p), RECQL4 (8q), DOCK8 (9p), ZMYND11 (10p), KDM5A (12p), PSPC1 (13q), ADPRTL2 (14q), MTA1 (14q), DECR2 (16p), GAS8 (16q), THOC1 (18p), CTDP1 (18q), SOX12 (20p), ADRM1 (20q), UCKL1 (20q), OPRL1 (20q), IL17RA (22q), and SYBL1 (Xq) genes. We detected copy number variations (CNVs) with frequencies greater than 40% in the probes located in 20q, which contains very important genes in the study of tumors. These findings showed instability in the tumor genome and altered regions associated with cell migration, transcription activation, apoptosis, and immune system deregulation. Unexpectedly, we detected concomitant pathogenic CNVs in tumors and surrounding tissues. Our data suggest that characterizing the genomic CRC profile is an important contribution to better understanding instability as a mechanism of carcinogenesis in CRC patients.

Circulating tumor DNA-based mutational landscape of advanced colorectal cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e15034-e15034
Author(s):  
Fang Yan ◽  
Wei Gao ◽  
Lifei Zhu ◽  
Wenzhuan Xie ◽  
Chan Gao ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Circulating Tumor Dna ◽  
Copy Number Variations ◽  
The Cancer Genome Atlas ◽  
Genomic Alteration ◽  
Driver Genes ◽  
Tissue Samples ◽  
Mutational Landscape ◽  
Tumor Dna

e15034 Background: Alterations in oncogenic driver genes are extensively tested to guide anticancer treatment in colorectal cancer (CRC). As the repertoire of therapeutic targets continue to grow, we are interested to interrogate the possibility of resorting to circulating tumor DNA (ctDNA) where tissue samples are not readily available. Methods: Targeted next generation sequencing (NGS) was performed on ctDNA obtained from patients with advanced CRC using a 150-gene panel. Mutational profiles of ctDNA were compared with those detected in tissue samples from the 3D Medicine database as well as The Cancer Genome Atlas (TCGA) database. Genomic aberrations such as single nucleotide variations (SNVs), insertions/deletions, copy number variations, gene rearrangement and fusions were analyzed. Results: Notably, 244 of 256 samples (95.3%) were ctDNA-positive, as indicated by a maximum somatic allele frequency (MSAF) of > 0%. At least one reportable genomic alteration was detected in 96.5% of all cases, with an average of 8.12 mutations per case. The most frequently mutated genes were TP53 (47%), APC (42%), KRAS (32%) in ctDNA. A similar trend was also observed for SNVs, where TP53 (46.9% vs. 77.6% vs. 53.8%), APC (41.8% vs. 66.0% vs. 73.0%), and KRAS (30.5% vs. 48.4% vs. 43.5%) had the highest mutation frequencies across three data sets (ctDNA, tissues and the TCGA database). The SNV profiles of therapeutically relevant genes for CRC were also largely consistent between ctDNA and the tissue samples included in the 3D Medicine database: BRAF (7.0% vs. 8.7%), KRAS (30.5% vs. 48.4%), NRAS (2.7 vs. 3.1%), ERBB2 (5.1% vs. 5.2%), MLH1 (0.8% vs. 2.9%), MSH2 (2.7% vs. 3.1%), and MSH6 (3.1% vs. 3.7%). Patients harboring copy number gains had a significantly higher level of MSAF than those free of gene amplifications (p < 0.0001). Conclusions: Mutational landscape of ctDNA in general correlated with that detected in prior tissue samples as well as the TCGA database, supporting a role for ctDNA testing as a complementary approach to tissue testing in CRC.

scholarly journals Cell-free DNA copy number variations in plasma from colorectal cancer patients

2017 ◽  
Vol 11 (8) ◽  
pp. 1099-1111 ◽  
Author(s):  
Jian Li ◽  
Rachel L. Dittmar ◽  
Shu Xia ◽  
Huijuan Zhang ◽  
Meijun Du ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Copy Number Variations ◽  
Dna Copy Number ◽  
Dna Copy Number Variations ◽  
Cell Free Dna ◽  
Free Dna ◽  
Colorectal Cancer Patients
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