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Genomic Analysis of Common Disease

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Medicine".

Deadline for manuscript submissions: 31 July 2024 | Viewed by 5275

Special Issue Editor


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Guest Editor
Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, and KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
Interests: genomics; syndromology; connective tissue dysplasias; Ehlers–Danlos syndrome

Special Issue Information

Dear Colleagues,

The ability of NextGen or massive parallel sequencing technology to screen all genes in the human genome for mutations is changing the reductive one disease–one responsible gene paradigm to one of multifactorial (polygenic–environmental) causation. The multiple DNA changes defined by all-gene screening are particularly applicable to common diseases like intellectual disability (autism), diabetes, cardiomyopathy/arrhythmias, connective tissue dysplasias, and many cancers where changes in gene networks lead to spectra of disease. A combined genomic analysis of microarray and whole exome sequencing can define the respective duplication/deficiency of chromosome regions (copy number variants) and of gene sequence alterations (DNA sequence variants), the former being common in patients with intellectual disability (autism), and the latter being common in diseases affecting older children and adults. This Special Issue will begin with a brief introduction of genomics and an article contrasting its results when applied to patients with increased joint laxity (hypermobility). Patients with developmental disability and joint laxity from hypotonia of surrounding muscles will have a mixture of copy number and sequence variants, and those with laxity from dysplastic connective tissue in Ehlers–Danlos syndrome will have sequence variants in a different but overlapping network of genes. Accompanying articles that describe DNA results from genomic analysis of other common conditions ranging from cardiovascular diseases to cancer will be explored as well.

Dr. Golder N. Wilson
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Current Issues in Molecular Biology is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genomic analysis
  • microarray analysis
  • whole exome sequencing
  • pathogenic mutations
  • copy number variants
  • DNA sequence variation
  • intellectual disability
  • autism
  • connective tissue dysplasia

Published Papers (3 papers)

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Research

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24 pages, 3305 KiB  
Article
Clinical-Genomic Analysis of 1261 Patients with Ehlers–Danlos Syndrome Outlines an Articulo-Autonomic Gene Network (Entome)
by Golder N. Wilson and Vijay S. Tonk
Curr. Issues Mol. Biol. 2024, 46(3), 2620-2643; https://doi.org/10.3390/cimb46030166 - 19 Mar 2024
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Abstract
Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers–Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients [...] Read more.
Systematic evaluation of 80 history and 40 history findings diagnosed 1261 patients with Ehlers–Danlos syndrome (EDS) by direct or online interaction, and 60 key findings were selected for their relation to clinical mechanisms and/or management. Genomic testing results in 566 of these patients supported EDS relevance by their differences from those in 82 developmental disability patients and by their association with general rather than type-specific EDS findings. The 437 nuclear and 79 mitochondrial DNA changes included 71 impacting joint matrix (49 COL5), 39 bone (30 COL1/2/9/11), 22 vessel (12 COL3/8VWF), 43 vessel–heart (17FBN1/11TGFB/BR), 59 muscle (28 COL6/12), 56 neural (16 SCN9A/10A/11A), and 74 autonomic (13 POLG/25porphyria related). These genes were distributed over all chromosomes but the Y, a network analogized to an ‘entome’ where DNA change disrupts truncal mechanisms (skin constraint, neuromuscular support, joint vessel flexibility) and produces a mirroring cascade of articular and autonomic symptoms. The implied sequences of genes from nodal proteins to hypermobility to branching tissue laxity or dysautonomia symptoms would be ideal for large language/artificial intelligence analyses. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease)
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16 pages, 2657 KiB  
Article
Exploring the Functional Basis of Epigenetic Aging in Relation to Body Fat Phenotypes in the Norfolk Island Cohort
by Thao Van Cao, Heidi G. Sutherland, Miles C. Benton, Larisa M. Haupt, Rodney A. Lea and Lyn R. Griffiths
Curr. Issues Mol. Biol. 2023, 45(10), 7862-7877; https://doi.org/10.3390/cimb45100497 - 27 Sep 2023
Viewed by 795
Abstract
DNA methylation is an epigenetic factor that is modifiable and can change over a lifespan. While many studies have identified methylation sites (CpGs) related to aging, the relationship of these to gene function and age-related disease phenotypes remains unclear. This research explores this [...] Read more.
DNA methylation is an epigenetic factor that is modifiable and can change over a lifespan. While many studies have identified methylation sites (CpGs) related to aging, the relationship of these to gene function and age-related disease phenotypes remains unclear. This research explores this question by testing for the conjoint association of age-related CpGs with gene expression and the relation of these to body fat phenotypes. The study included blood-based gene transcripts and intragenic CpG methylation data from Illumina 450 K arrays in 74 healthy adults from the Norfolk Island population. First, a series of regression analyses were performed to detect associations between gene transcript level and intragenic CpGs and their conjoint relationship with age. Second, we explored how these age-related expression CpGs (eCpGs) correlated with obesity-related phenotypes, including body fat percentage, body mass index, and waist-to-hip ratio. We identified 35 age-related eCpGs associated with age. Of these, ten eCpGs were associated with at least one body fat phenotype. Collagen Type XI Alpha 2 Chain (COL11A2), Complement C1s (C1s), and four and a half LIM domains 2 (FHL2) genes were among the most significant genes with multiple eCpGs associated with both age and multiple body fat phenotypes. The COL11A2 gene contributes to the correct assembly of the extracellular matrix in maintaining the healthy structural arrangement of various components, with the C1s gene part of complement systems functioning in inflammation. Moreover, FHL2 expression was upregulated under hypermethylation in both blood and adipose tissue with aging. These results suggest new targets for future studies and require further validation to confirm the specific function of these genes on body fat regulation. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease)
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Review

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11 pages, 1782 KiB  
Review
Effect of Carcinomas on Autosomal Trait Screening: A Review Article
by Husein Alhatim, Muhammad Nazrul Hakim Abdullah, Suhaili Abu Bakar and Sayed Amin Amer
Curr. Issues Mol. Biol. 2023, 45(9), 7275-7285; https://doi.org/10.3390/cimb45090460 - 04 Sep 2023
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Abstract
This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements [...] Read more.
This review highlights the effect of carcinomas on the results of the examination of autosomal genetic traits for identification and paternity tests when carcinoid tissue is the only source and no other samples are available. In DNA typing or genetic fingerprinting, variable elements are isolated and identified within the base pair sequences that form the DNA. The person’s probable identity can be determined by analysing nucleotide sequences in particular regions of DNA unique to everyone. Genetics plays an increasingly important role in the risk stratification and management of carcinoma patients. The available information from previous studies has indicated that in some incidents, including mass disasters and crimes such as terrorist incidents, biological evidence may not be available at the scene of the accident, except for some unknown human remains found in the form of undefined human tissues. If these tissues have cancerous tumours, it may affect the examination of the genetic traits derived from these samples, thereby resulting in a failure to identify the person. Pathology units, more often, verify the identity of the patients who were diagnosed with cancer in reference to their deceased tumorous relatives. Genetic fingerprinting (GF) is also used in paternity testing when the alleged parent disappeared or died and earlier was diagnosed and treated for cancer. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease)
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