Copy number variation in the human genome is dynamic across generations and tissues
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Peer-reviewed literature and reference texts establish that DNA copy number variations in the human genome are dynamic, occurring both between individuals across generations and within the somatic cells and tissues of the same individual.
Abstract
Purpose
This study analyzes the rise of genome instability in the life sciences and traces the problematic of instability as it relates to the sociology of health. Genome instability is the study of how genomes change and become variable between generations and within organisms over the life span. Genome instability reflects a significant departure from the Platonic genome imagined during the Human Genome Project. The aim of this chapter is to explain and analyze research on copy number variation and somatic mosaicism to consider the implications of these sciences for sociologists interested in genomics.
Methodology/approach
This chapter draws on two multi-sited ethnographies of contemporary biomedical science and literature in the sociology of health, science, and biomedicine to document a shift in thinking about the genome from fixed and universal to highly variable and influenced by time and context.
Findings
Genomic instability has become a framework for addressing how genomes change and become variable between generations and within organisms over the life span. Instability is a useful framework for analyzing changes in the life sciences in the post-genomic era.
Research implications
Genome instability requires life scientists to address how differences both within and between individuals articulate with shifting disease categories and classifications. For sociologists, these findings have implications for studies of identity, sociality, and clinical experience.
Originality/value
This is the first sociological analysis of genomic instability. It identifies practical and conceptual implications of genomic instability for life scientists and helps sociologists delineate new approaches to the study of genomics in the post-genomic era.
Understanding genomic function has historically relied on sequence conservation across evolutionary time. However, advances in genomics have revealed that functional innovations often arise from rapidly evolving, nonconserved elements that are frequently overlooked by conservation-based approaches. Among these, variable number tandem repeats (VNTRs) act as engines of both functional innovation and phenotypic consequence. VNTRs are repetitive genomic sequences whose copy numbers can vary significantly between individuals and species, influencing gene regulation, protein structure, and eventually, phenotypic diversity. Recent long-read assemblies and pangenomes now resolve VNTR loci accurately, enabling robust evolutionary reconstruction and functional associations. Here, we synthesize emerging insights into the functional and evolutionary impact of VNTRs in mammals. Specifically, we outline pressing questions on the mutational mechanisms driving VNTR evolution in humans, the selective forces maintaining their structural heterogeneity, and propose a theoretical framework for their persistence through evolutionary tradeoffs.
Abstract Mitotic catastrophe (MC) is a novel form of cell death that plays an important role in the treatment and drug resistance of colon adenocarcinoma (COAD). However, MC related genes in COAD treatment and prognosis evaluation are rarely studied. In this study, the transcriptome data, somatic mutation and copy number variation data were obtained from The Cancer Genome Atlas (TCGA) database. The mitotic catastrophe related genes (MCRGs) were obtained from GENCARDS website. Differential gene analysis was conducted with LIMMA package. Univariate Cox regression analysis was used to identify prognostic related genes. Mutation analysis was performed and displayed by maftools package. RCircos package was used for localizing the position of genes on chromosomes. “Glmnet” R package was applied for constructing a risk model via the LASSO regression method. Consensus clustering analyses was implemented for clustering different subtypes. Functional enrichment analysis through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) methods, immune infiltration analysis via single sample gene set enrichment analysis (ssGSEA), tumor mutation burden and drug sensitivity analysis by pRRophetic R package were also carried out for risk model or molecular subtype’s assessment. Additionally, the connections between the expression of hub genes and overall survival (OS) were obtained from online Human Protein Atlas (HPA) website. Real-Time Quantitative Polymerase Chain Reaction (R
Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.
The human genome is a dynamic structure, recently recognized to present with significant large-scale structural variation. DNA-copy number changes represent one common type of such variation and is found both between individuals and within the somatic cells of the same individual, especially in disease states like cancer. Apart from DNA-rearrangements, epigenomic changes are increasingly acknowledged as important events in the maintenance of genomic integrity. In this thesis, different array-based methods have been applied for global genomic and epigenomic profiling of both normal and cancer c
Whole genome sequencing enables a high resolution view of the human genome and enables unique insights into copy number variations on an unprecedented scale. Numerous tools and studies have already been introduced that provide confirmatory evidence and new genomic structure variation data in individuals as well as across populations. We utilize two such tools, CNV-seq and FREEC to compare their outputs when applied to five whole genome sequences representing four populations. We focus on the ability of these tools to detect segments from two sets of segments known to vary across populations, and discuss the direction and the challenges in developing tools that detect copy number variation in collections of human genomes.
Background: Fc gamma receptors (FcγRs) play a crucial role in immunity by linking IgG antibody-mediated responses with cellular effector and regulatory functions. Genetic variants in these receptors have been previously identified as risk factors for several chronic inflammatory conditions. The present study aimed to investigate the presence of copy number variations (CNVs) in the FCGR3B gene and its potential association with the autoimmune disease rheumatoid arthritis (RA). Methodology/Principal Findings: CNV of the FCGR3B gene was studied using Multiplex Ligation Dependent Probe Amplificati
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