Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis

2016 ◽  
Vol 46 (5) ◽  
pp. 371-376 ◽  
Author(s):  
Marina Gonçalves Diniz ◽  
Alessandra Pires Duarte ◽  
Rolando A. Villacis ◽  
Bruna V. A. Guimarães ◽  
Luiz Cláudio Pires Duarte ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Microarray Analysis ◽  
Copy Number ◽  
Neutral Loss ◽  
High Density ◽  
Whole Genome ◽  
Copy Number Alterations ◽  
Whole Genome Microarray

scholarly journals Copy number alterations and epithelial-mesenchymal transition genes in diffuse and intestinal gastric cancers in Mexican patients

2021 ◽  
Author(s):  
Violeta Larios-Serrato ◽  
José Darío Martínez-Ezquerro ◽  
Hilda-Alicia Valdez-Salazar ◽  
Javier Torres ◽  
Margarita Camorlinga-Ponce ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Copy Number ◽  
Epithelial Mesenchymal Transition ◽  
High Density ◽  
Whole Genome ◽  
Copy Number Alterations ◽  
Hallmarks Of Cancer ◽  
Mesenchymal Transition ◽  
Molecular Functions ◽  
Mexican Patients

Gastric cancer (GC) is a malignancy with the highest mortality among diseases of the digestive system worldwide. The study of GC-alterations is crucial to understand tumor biology, to establish important aspects of cancer prognosis and treatment response. Here, we purified DNA and performed whole-genome analysis with high-density arrays in samples from Mexican patients diagnosed with GC: diffuse (DGC) or intestinal (IGC), or non-atrophic gastritis (NAG) samples that served as controls. We identified shared and unique copy number alterations (CNA) between these altered tissues involving key genes and signaling pathways associated with cancer, allowing their molecular distinction and identification of the most relevant molecular functions impacted. When focused on epithelial-mesenchymal transition (EMT) genes, our bioinformatic analysis revealed that the altered network associated with chromosomal alterations included 11 genes shared between DGC, IGC, and NAG, as well as 19 DGC- and 7 IGC-exclusive genes, whose main molecular functions included adhesion, angiogenesis, migration, metastasis, morphogenesis, proliferation, and survival. This study presents the first whole-genome high-density array study in GC from Mexican patients and reveals shared and exclusive CNA-genes in DGC and IGC. In addition, we provide a bioinformatically predicted network focused on CNA-altered genes involved in the EMT, associated with the hallmarks of cancer, as well as precancerous alterations that could lead to gastric cancer. Implications: Molecular signatures of diffuse and intestinal GC, predicted bioinformatically, involve common and distinct CNA-EMT genes related to the hallmarks of cancer that are potential candidates for screening GC biomarkers, including early stages.

15. Interpreting TP53 variants identified by NGS in the setting of complex karyotypes: examples of potential cryptic copy number alterations and copy-neutral loss of heterozygosity

2021 ◽  
Vol 252-253 ◽  
pp. S5-S6
Author(s):  
Celeste C. Eno ◽  
P. Nagesh Rao ◽  
Fabiola Quintero-Rivera ◽  
Sung Hae L. Kang ◽  
Sophie X. Song ◽  
...  
Keyword(s):  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Neutral Loss ◽  
Copy Number Alterations

Whole genome SNP arrays for best practice for detection of diagnostic, prognostic and therapy related copy number changes and copy neutral-loss of heterozygosity across solid tumors and hematologic malignancies.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e15575-e15575
Author(s):  
Patrick Alan Lennon ◽  
Gordana Raca ◽  
Min Fang ◽  
Daynna Wolff ◽  
Marilyn M. Li ◽  
...  
Keyword(s):  
Solid Tumors ◽  
Loss Of Heterozygosity ◽  
Copy Number ◽  
Neutral Loss ◽  
Chromosome Analysis ◽  
Hematologic Malignancies ◽  
Whole Genome ◽  
Clinical Tool ◽  
Entire Genome ◽  
Copy Number Changes

e15575 Background: High resolution single nucleotide polymorphism (SNP) chromosomal microarrays (CMA) detect copy number changes and copy neutral-loss of heterozygosity (CN-LOH) across the entire genome, currently providing the best assessment for these types of genomic variants. Chromosomal microarrays are first tier tests utilized in the postnatal detection of microdeletions, microduplications and uniparental disomy/regions of homozygosity in constitutional disorders involving congenital abnormalities, developmental delay and intellectual disability. Methods: In the oncology setting, aberrations detected may be diagnostic, prognostic, and therapeutic. Because CMA assesses the entire genome and can readily detect aberrations as small as a single exon to as large as a whole chromosome, this is an important clinical tool to bridge the gap between low resolution of metaphase chromosome analysis and PCR-based short read sequencing-based assays. Results: No single genomic technique (metaphase chromosome analysis, FISH, CMA or Next Generation Sequencing, including large targeted gene panels) has the ability to detect all relevant information. Therefore, CMA should be considered an important clinical tool for solid and liquid tumors. Across a wide variety of solid tumors, whole genome assessment (including oncogene amplification, tumor suppressor loss, and copy number burden) leads not only to possible therapy targets but also to opportunities for participation in active clinical trials. Recently, the Cancer Genomics Consortium has published evidenced-based reviews on the clinical utility of CMA for copy number and CN-LOH assessment in a variety of hematologic malignancies, and similar papers in solid tumors are in review. Recognizing the growing evidence for CMA, the American Medical Association (AMA) CPT editorial board recently created a new Tier 1 test for cytogenomic arrays in neoplasia, and Centers for Medicare and Medicaid Services (CMS) approved crosswalking the price of the new code to the well-established constitutional cytogenomic array CPT code. Conclusions: For this presentation, examples of diagnostic, prognostic, and therapeutic utility and inclusion in clinical trials across many hematologic and solid tumor neoplasms will be presented to demonstrate the efficacy, cost effectiveness and sensitivity of whole genome assessment of copy number and copy neutral loss of heterozygosity

scholarly journals Whole genome microarray analysis ofC. elegans rrf-3anderi-1mutants

FEBS Letters ◽  
2007 ◽  
Vol 581 (26) ◽  
pp. 5050-5054 ◽  
Author(s):  
Suvi Asikainen ◽  
Markus Storvik ◽  
Merja Lakso ◽  
Garry Wong
Keyword(s):  
Microarray Analysis ◽  
Whole Genome ◽  
Whole Genome Microarray
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