scholarly journals Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

2012 ◽  
Vol 44 (6) ◽  
pp. 694-698 ◽  
Author(s):  
Cécile Guichard ◽  
Giuliana Amaddeo ◽  
Sandrine Imbeaud ◽  
Yannick Ladeiro ◽  
Laura Pelletier ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Somatic Mutations ◽  
Integrated Analysis ◽  
Key Genes ◽  
Copy Number Changes

scholarly journals Simultaneous FLT3, NPM1 and DNMT3A mutations in adult patients with acute myeloid leukemia – case study

2019 ◽  
Vol 27 (3) ◽  
pp. 245-254 ◽  
Author(s):  
Florin Tripon ◽  
George Andrei Crauciuc ◽  
Valeriu George Moldovan ◽  
Alina Bogliș ◽  
István Benedek ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Cytogenetic Analysis ◽  
Copy Number ◽  
Myeloid Leukemia ◽  
Somatic Mutations ◽  
Molecular Technique ◽  
Chromosomal Anomalies ◽  
Copy Number Changes ◽  
Next Generation Sequencing Ngs ◽  
Acute Myeloid

Abstract Background: Nowadays, cytogenetics and molecular genetics, but not only, are mandatory in acute myeloid leukemia (AML) management, as a consequence of their impact on AML pathogenesis, classification, risk-stratification, prognosis and treatment. Objective: The aim of our study was to present our algorithm for the analysis of copy number changes, aneuploidies and somatic mutations focusing on a rare AML case positive for four somatic mutations. Methods: Cytogenetic analysis, Multiplex Ligationdependent Probe Amplification (MLPA) analysis, somatic mutation analysis (for FLT3 ITD, FLT3 D835, DNMT3A R882 and NPM1 c.863_864ins) by using several PCR techniques and also next-generation sequencing (NGS) analysis were performed. Results: Cytogenetic analysis did not reveal structural or numerical chromosomal anomalies. The patient’s DNA showed no copy number changes or aberrations (CNAs) following the MLPA analysis. By using several molecular technologies we found four mutations: FLT3-ITD, FLT3 D835 (c.2504A>T, D835V), DNMT3A R882C, and NPM1 c.863_864insTCTG. Challenges, benefits, applications and the limitations of each molecular technique used for the investigation of the mentioned mutation, and not only, are also described. Conclusion: All these techniques can be useful in the diagnosis of AML patients, each of them covering the limits of the other technique. New strategies for a positive, fast, accurate and reliable diagnosis are mandatory in cases with AML.

scholarly journals A comprehensive genome-wide profiling comparison between HBV and HCV infected hepatocellular carcinoma

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Suofeng Sun ◽  
Yuan Li ◽  
Shuangyin Han ◽  
Hongtao Jia ◽  
Xiuling Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Survival Rates ◽  
Gene Expression Pattern ◽  
Asian Population ◽  
Copy Number Variations ◽  
The Cancer Genome Atlas ◽  
Integrated Analysis ◽  
Immune Related Genes

Abstract Background Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, especially in East Asia. Even with the progress in therapy, 5-year survival rates remain unsatisfied. Chronic infection with the hepatitis B virus (HBV) or hepatitis C virus (HCV) has been epidemiologically associated with HCC and is the major etiology in the East Asian population. The detailed mechanism, especially the changes of DNA methylation and gene expression between the two types of virus-related HCC, and their contributions to the HCC development, metastasis, and recurrence remain largely unknown. Methods In this integrated analysis, we characterized genome-scale profiles of HBV and HCV infected HCC by comparing their gene expression pattern, methylation profiles, and copy number variations from the publicly accessible data of The Cancer Genome Atlas Program (TCGA). Results The HLA-A, STAT1, and OAS2 genes were highly enriched and up-regulated discovered in the HCV-infected HCC. Hypomethylation but not copy number variations might be the major factor for the up-regulation of these immune-related genes in HCV-infected HCC. Conclusions The results indicated the different epigenetic changes of HBV/HCV related hepatocarcinogenesis. The top up-regulated genes in HCV group were significantly clustered in the immune-related and defense response pathways. These findings will help us to understand the pathogenesis of HBV/HCV associated hepatocellular carcinoma.

Clonal Heterogeneity and Genetic Instability of Multiple Myeloma and Impact on Treatment

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. SCI-53-SCI-53
Author(s):  
Jonathan J Keats
Keyword(s):  
Multiple Myeloma ◽  
Copy Number ◽  
Somatic Mutations ◽  
Conflicts Of Interest ◽  
Tumor Evolution ◽  
Clonal Heterogeneity ◽  
Genetic Complexity ◽  
Impact On Treatment ◽  
Copy Number Changes ◽  
Individual Disease

Multiple myeloma is a pathological definition for a series of distinct genetic entities with similar phenotypic and clinical characteristics. Multiple studies have now identified distinct subtypes of the disease, which are associated with different clinical outcomes. The genetic complexity underlying these different subtypes is very diverse. Some subtypes like those characterized by immunoglobulin translocations targeting cyclin D1 are associated with very minimal changes or no copy number changes. Conversely, subtypes defined by translocations targeting WHSC1/MMSET or the MAF and MAFB transcription factors often have highly complex and diverse copy number changes. With the substantial advances in DNA sequencing technology we now know there is a diverse array of somatic mutations in multiple myeloma tumors. Through the integration of copy number changes and somatic mutations multiple groups have now shown the existence of multiple co-existing subclones within individual tumors. Additional studies following patients through their individual disease courses have shown these subclones can ebb and flow with time through multiple rounds of therapeutic selection. This session will highlight our current understanding of how the interplay between tumor evolution and clonal heterogeneity should influence our treatment decisions, particularly when applying a personalized medicine approach. Disclosures No relevant conflicts of interest to declare.

scholarly journals Integrated Analysis of Mutation Data from Various Sources Identifies Key Genes and Signaling Pathways in Hepatocellular Carcinoma

PLoS ONE ◽  
2014 ◽  
Vol 9 (7) ◽  
pp. e100854 ◽  
Author(s):  
Yuannv Zhang ◽  
Zhaoping Qiu ◽  
Lin Wei ◽  
Ruqi Tang ◽  
Baofeng Lian ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Signaling Pathways ◽  
Integrated Analysis ◽  
Key Genes ◽  
Mutation Data

Transcriptional profiling of iPSC-derived neurons with reciprocal monogenic CNV in 3p26.3 region

2020 ◽  
pp. 10-11
Author(s):  
М.Е. Лопаткина ◽  
В.С. Фишман ◽  
М.М. Гридина ◽  
Н.А. Скрябин ◽  
Т.В. Никитина ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
System Development ◽  
Transcriptional Profiling ◽  
Global Gene Expression ◽  
Nervous System Development ◽  
Number Variation ◽  
The Central Nervous System ◽  
Cntn6 Gene ◽  
Copy Number Changes

Проведен анализ генной экспрессии в нейронах, дифференцированных из индуцированных плюрипотентных стволовых клеток пациентов с идиопатическими интеллектуальными нарушениями и реципрокными хромосомными мутациями в регионе 3p26.3, затрагивающими единственный ген CNTN6. Для нейронов с различным типом хромосомных аберраций была показана глобальная дисрегуляция генной экспрессии. В нейронах с вариациями числа копий гена CNTN6 была снижена экспрессия генов, продукты которых вовлечены в процессы развития центральной нервной системы. The gene expression analysis of iPSC-derived neurons, obtained from patients with idiopathic intellectual disability and reciprocal microdeletion and microduplication in 3p26.3 region affecting the single CNTN6 gene was performed. The global gene expression dysregulation was demonstrated for cells with CNTN6 copy number variation. Gene expression in neurons with CNTN6 copy number changes was downregulated for genes, whose products are involved in the central nervous system development.

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