scholarly journals Systematic Prioritization and Integrative Analysis of Copy Number Variations in Schizophrenia Reveal Key Schizophrenia Susceptibility Genes

2014 ◽  
Vol 40 (6) ◽  
pp. 1285-1299 ◽  
Author(s):  
Xiongjian Luo ◽  
Liang Huang ◽  
Leng Han ◽  
Zhenwu Luo ◽  
Fang Hu ◽  
...  
Keyword(s):  
Copy Number ◽  
Susceptibility Genes ◽  
Copy Number Variations ◽  
Integrative Analysis ◽  
Schizophrenia Susceptibility

22q11-q13 as a hot spot for prediction of disease-free survival in bile duct cancer: integrative analysis of copy number variations

2014 ◽  
Vol 207 (3) ◽  
pp. 57-69 ◽  
Author(s):  
Mee Joo Kang ◽  
Jayoun Kim ◽  
Jin-Young Jang ◽  
Taesung Park ◽  
Kyoung Bun Lee ◽  
...  
Keyword(s):  
Bile Duct ◽  
Bile Duct Cancer ◽  
Copy Number ◽  
Hot Spot ◽  
Disease Free Survival ◽  
Copy Number Variations ◽  
Integrative Analysis ◽  
Free Survival ◽  
Duct Cancer ◽  
Disease Free

scholarly journals Integrative Analysis and Identification of an Excellent lncRNA Signature to Predict Prognosis in Patients with COAD

2021 ◽  
Author(s):  
ZhiHua Chen ◽  
YiLin Lin ◽  
SuYong Lin ◽  
Ji Gao ◽  
Shao-Qin Chen
Keyword(s):  
Copy Number ◽  
Cox Regression ◽  
Gene Expression Omnibus ◽  
Copy Number Variations ◽  
Integrative Analysis ◽  
Transcriptome Data ◽  
Cox Regression Analysis ◽  
Number Variation ◽  
Cancer Genome Atlas ◽  
Internal Mechanism

Abstract Backgroud: Tumour recurrence and metastasis lead to poor prognosis incolon cancer(COAD). Therefore We aimed to identify a lncRNA signature through an integrative analysis of copy number variation, mutation and transcriptome data to predict prognosis and explore its internal mechanism.Methods: The lncRNA expression profile were collected fromThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). TCGA data was randomly divided 3:1 intotraining andtesting cohort. In the training, weperformed integrated analyses of three candidate lncRNA sets that correlated with prognosis, copy number variations and mutations to establish a signature through Cox regression analysis. The robustness was determined in the testing and GEO.Results: An 11-lncRNA signature that was significantly associated with prognosiswas constructed in the training (P<0.0001, HR=2.014) , And this signature was validated in the testing(P=0.0019, HR=3.374) and GSE17536(P=0.0076, HR=1.864). The signature is significantly related to MSI status and clinical prognostic factors. The prognostic-relatedrisk scores were significantly excellent than the other five models have been reported. Furthermore, GSEA suggested that the signature was involved in COAD development and metastasis-related pathways.Conclusions: We identifiedansignature has strong robustness and can stably predict the prognosis of COAD in different platformsand may be implicated in COAD pathogenesis and metastasis and applied clinically as a prognostic marker.

scholarly journals Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas

Cancers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 269
Author(s):  
Mouna Tabebi ◽  
Małgorzata Łysiak ◽  
Ravi Kumar Dutta ◽  
Sandra Lomazzi ◽  
Maria V. Turkina ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Copy Number ◽  
Nuclear Dna ◽  
Genome Instability ◽  
Genetic Alterations ◽  
Susceptibility Genes ◽  
Copy Number Variations ◽  
Mitochondrial Mutations ◽  
Mtdna Sequence ◽  
Gene And Protein Expression

Background: Somatic mutations, copy-number variations, and genome instability of mitochondrial DNA (mtDNA) have been reported in different types of cancers and are suggested to play important roles in cancer development and metastasis. However, there is scarce information about pheochromocytomas and paragangliomas (PCCs/PGLs) formation. Material: To determine the potential roles of mtDNA alterations in sporadic PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of seventy-seven human tumors, using next-generation sequencing, and compared the results with normal adrenal medulla tissues. We also performed an analysis of copy-number alterations, large mtDNA deletion, and gene and protein expression. Results: Our results revealed that 53.2% of the tumors harbor a mutation in at least one of the targeted susceptibility genes, and 16.9% harbor complementary mitochondrial mutations. More than 50% of the mitochondrial mutations were novel and predicted pathogenic, affecting mitochondrial oxidative phosphorylation. Large deletions were found in 26% of tumors, and depletion of mtDNA occurred in more than 87% of PCCs/PGLs. The reduction of the mitochondrial number was accompanied by a reduced expression of the regulators that promote mitochondrial biogenesis (PCG1α, NRF1, and TFAM). Further, P62 and LC3a gene expression suggested increased mitophagy, which is linked to mitochondrial dysfunction. Conclusion: The pathogenic role of these finding remains to be shown, but we suggest a complementarity and a potential contributing role in PCCs/PGLs tumorigenesis.

scholarly journals Integrative Analysis and Identification of an Excellent lncRNA Signature to Predict Prognosis in Patients With Colon Cancer

2021 ◽  
Author(s):  
ZhiHua Chen ◽  
YiLin Lin ◽  
SuYong Lin ◽  
YiSu Liu ◽  
Yan Zheng ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Copy Number ◽  
Cox Regression ◽  
Gene Expression Omnibus ◽  
Copy Number Variations ◽  
Integrative Analysis ◽  
The Cancer Genome Atlas ◽  
Risk Scores ◽  
Cox Regression Analysis ◽  
Number Variation

Abstract Backgroud: Tumour recurrence and metastasis lead to poor prognosis in colon cancer (COAD). Therefore We aimed to identify a lncRNA signature through an integrative analysis of copy number variation, mutation and transcriptome data to predict prognosis and explore its internal mechanism.Methods: The lncRNA expression profile were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). TCGA data was randomly divided 3:1 into training and testing cohort. In the training, we performed integrated analyses of three candidate lncRNA sets that correlated with prognosis, copy number variations and mutations to establish a signature through Cox regression analysis. The robustness was determined in the testing and GEO. Results: An 11-lncRNA signature that was significantly associated with prognosis was constructed in the training (P<0.0001, HR=2.014) , And this signature was validated in the testing (P=0.0019, HR=3.374) and GSE17536 (P=0.0076, HR=1.864). The signature is significantly related to MSI status and clinical prognostic factors. The prognostic-related risk scores were significantly excellent than the other five models have been reported. Furthermore, GSEA suggested that the signature was involved in COAD development and metastasis-related pathways.Conclusions: We identified an signature has strong robustness and can stably predict the prognosis of COAD in different platforms and may be implicated in COAD pathogenesis and metastasis and applied clinically as a prognostic marker.

scholarly journals Horizontal and vertical integrative analysis methods for mental disorders omics data

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shuaichao Wang ◽  
Xingjie Shi ◽  
Mengyun Wu ◽  
Shuangge Ma
Keyword(s):  
Mental Disorders ◽  
Mental Disorder ◽  
Copy Number ◽  
Principal Component ◽  
Copy Number Variations ◽  
Integrative Analysis ◽  
Single Type ◽  
Horizontal Integration ◽  
Gene Expressions ◽  
Disease Etiology

Abstract In recent biomedical studies, omics profiling has been extensively conducted on various types of mental disorders. In most of the existing analyses, a single type of mental disorder and a single type of omics measurement are analyzed. In the study of other complex diseases, integrative analysis, both vertical and horizontal integration, has been conducted and shown to bring significantly new insights into disease etiology, progression, biomarkers, and treatment. In this article, we showcase the applicability of integrative analysis to mental disorders. In particular, the horizontal integration of bipolar disorder and schizophrenia and the vertical integration of gene expression and copy number variation data are conducted. The analysis is based on the sparse principal component analysis, penalization, and other advanced statistical techniques. In data analysis, integration leads to biologically sensible findings, including the disease-related gene expressions, copy number variations, and their associations, which differ from the “benchmark” analysis. Overall, this study suggests the potential of integrative analysis in mental disorder research.

X-linked CNV and skewed X-chromosome inactivation

2020 ◽  
pp. 19-21
Author(s):  
Е.А. Фонова ◽  
Е.Н. Толмачева ◽  
А.А. Кашеварова ◽  
М.Е. Лопаткина ◽  
К.А. Павлова ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Intellectual Disability ◽  
X Chromosome ◽  
Copy Number ◽  
Copy Number Variations ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Chromosome X ◽  
Skewed X Chromosome Inactivation

Смещение инактивации Х-хромосомы может быть следствием и маркером нарушения клеточной пролиферации при вариациях числа копий ДНК на Х-хромосоме. Х-сцепленные CNV выявляются как у женщин с невынашиванием беременности и смещением инактивации Х-хромосомы (с частотой 33,3%), так и у пациентов с умственной отсталостью и смещением инактивацией у их матерей (с частотой 40%). A skewed X-chromosome inactivation can be a consequence and a marker of impaired cell proliferation in the presence of copy number variations (CNV) on the X chromosome. X-linked CNVs are detected in women with miscarriages and a skewed X-chromosome inactivation (with a frequency of 33.3%), as well as in patients with intellectual disability and skewed X-chromosome inactivation in their mothers (with a frequency of 40%).

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