Copy number variation is highly correlated with differential gene expression: a pan-cancer study

Shao, Xin; Lv, Ning; Liao, Jie; Long, Jinbo; Xue, Rui; Ni, Ai; Xu, Donghang; Fan, Xiaohui

doi:10.1186/s12881-019-0909-5

Cited by 220 publications

(191 citation statements)

References 58 publications

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“…CNAs change the dosage of affected genes and can lead to transcriptome changes 58 . We sought to determine whether ancestry-associated CNAs have such downstream mRNA associations.…”

Section: Changesmentioning

confidence: 99%

Ancestry Influences on the Molecular Presentation of Tumours

Haider

Boutros

2020

Preprint

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Epidemiological studies have identified innumerable ways in which cancer presentation and behaviour is associated with patient ancestry. The molecular bases for these relationships remain largely unknown. We analyzed ancestry associations in the somatic mutational landscape of 12,774 tumours across 33 tumour-types, including 2,562 with whole-genome sequencing. Ancestry influences both the number of mutations in a tumour and the evolutionary timing of when they occur. Specific mutational signatures are associated with ancestry, reflecting potential differences in exogenous and endogenous oncogenic processes. A subset of known cancer driver genes was mutated in ancestry-associated patterns, with transcriptomic consequences. Cancer genome sequencing data is not well-balanced in epidemiologic factors; these data suggest ancestry strongly shapes the somatic mutational landscape of cancer, with potential functional implications.

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“…CNAs change the dosage of affected genes and can lead to transcriptome changes 58 . We sought to determine whether ancestry-associated CNAs have such downstream mRNA associations.…”

Section: Changesmentioning

confidence: 99%

Ancestry Influences on the Molecular Presentation of Tumours

Haider

Boutros

2020

Preprint

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“…It has been demonstrated that modulating gene expression is one of the most important ways for CNV to play diversi ed roles in diseases [11][12][13][14]. In this study, the results showed that 5022 gene expressions in TCGA were signi cantly modulated by CNV (p <0.05, adjusted p <0.2) and 577 genes in TARGET were signi cantly associated with CNV (p <0.05, adjusted p <0.2).…”

Section: Integrative Analysis Of Gene Expressions In Concordance Withmentioning

confidence: 58%

Identification of Prognostic Signature Based on the Copy Number Variation (CNV) and Expression in Acute Myeloid Leukemia

Niu¹,

Wu²,

Li³

et al. 2020

Preprint

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Purpose Acute myeloid leukemia (AML) is caused by multiple genetic alterations in the hematopoietic progenitors, and molecular genetic analysis has provided useful information for AML diagnosis and prognosis. However, an integrative understanding about the prognosis value of specific copy number variation (CNV) and CNV-modulated gene expression has been limited. Methods We conducted an integrative analysis of CNV profiling and gene expression using data from the TARGET and TCGA AML cohorts. The CNV data from TCGA were analyzed using the GISTIC. CNV survival analysis and mRNA survival analysis were conducted with the Multivariate Cox proportional hazards regression model using R software with “survminer” and “survival” packages. KEGG cancer panel genes were extracted from the cancer related pathways from Kyoto Encyclopedia of Genes and Genomes (KEGG). The R package “circlize” was used for mapping the CNV genes to chromosomes. Results From this investigation, we observed distinct CNV patterns in the AML risk groups as well as the expression of 251 genes significantly modulated by CNV in both cohorts. There were 102 CNV genes (located at 7q31-34, 16q24) associated with clinical outcomes in AML, which were identified in the TARGET cohort and validated in the TCGA cohort, three of which being miRNA genes (MIR29A, MIR183, MIR335) that overlapped with a KEGG cancer panel. Five genes were identified whose expressions were modulated by CNV and significantly associated with clinical outcomes, and among them, the deletion of SEMA4D and CBFB were found to potentially have protective effects against AML. Moreover, the distribution of CNV in these five CNV-modulated genes was independent of the risk groups, which suggests that they are independent prognosis factors. Conclusion Overall, this study identified 102 CNV genes and five CNV-modulated gene expressions that are crucial for developing new modes of prognosis evaluation and target therapy for AML.

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“…However, the evolutionary advantage of CNAs is based on the expression of particular genes located within the CNA genomic region. Therefore, analysis of gene expression data provides additional valuable information [20][21][22][23][24] . Some among the list of the consistently co-expressed genes, including the first and the last when sorted in terms of their genomic location, play some role in tumorigenesis and it is possible that this role is due to their synergistic functions.…”

Section: Analysis Of Large Gene Expression Datasets From Biopsies Of mentioning

confidence: 99%

Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis

Wang

Anastassiou

2020

Sci Rep

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Analysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.

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Copy number variation is highly correlated with differential gene expression: a pan-cancer study

Cited by 220 publications

References 58 publications

Ancestry Influences on the Molecular Presentation of Tumours

Ancestry Influences on the Molecular Presentation of Tumours

Identification of Prognostic Signature Based on the Copy Number Variation (CNV) and Expression in Acute Myeloid Leukemia

Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis

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