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Genomic Analysis of Common Disease, 2nd Edition
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Genomic Analysis of Common Disease, 2nd Edition

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 August 2025 | Viewed by 2563

Special Issue Editor

Dr. Golder N. Wilson

E-Mail Website
Guest Editor
1. Department of Pediatrics, Texas Tech University Health Sciences Center, Lubbock, TX, USA
2. KinderGenome Genetics Private Practice, 5347 W Mockingbird, Dallas, TX 75209, USA
Interests: genomics; syndromology; connective tissue dysplasias; Ehlers–Danlos syndrome
Special Issues, Collections and Topics in MDPI journals

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 transforming 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.

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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

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Published Papers (4 papers)

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Editorial

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3 pages, 168 KiB  
Editorial
Introduction to Special Issue: Genomic Analysis of Common Disease
by Golder N. Wilson
Curr. Issues Mol. Biol. 2025, 47(2), 112; https://doi.org/10.3390/cimb47020112 - 10 Feb 2025
Viewed by 644
Abstract
The development of NextGen or massive parallel sequencing [...] Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)

Research

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12 pages, 1531 KiB  
Article
Association of DROSHA Variants with Susceptibility and Outcomes in Childhood Acute Lymphoblastic Leukemia
by Ioannis Kyriakidis, Iordanis Pelagiadis, Charalampos Pontikoglou, Helen A. Papadaki and Eftichia Stiakaki
Curr. Issues Mol. Biol. 2025, 47(6), 473; https://doi.org/10.3390/cimb47060473 - 19 Jun 2025
Abstract
MicroRNAs are key regulators of lymphoid differentiation, exhibiting a pivotal role in acute lymphoblastic leukemia (ALL) biology and prognosis. The initial steps of canonical miRNA biogenesis involve the microprocessor complex processing the primary miRNA transcripts into precursor miRNAs via Drosha. DROSHA polymorphisms have [...] Read more.
MicroRNAs are key regulators of lymphoid differentiation, exhibiting a pivotal role in acute lymphoblastic leukemia (ALL) biology and prognosis. The initial steps of canonical miRNA biogenesis involve the microprocessor complex processing the primary miRNA transcripts into precursor miRNAs via Drosha. DROSHA polymorphisms have been implicated in pediatric ALL and linked with cancer risk. This study investigated the role of rs642321, rs3805500, and rs10035440 DROSHA polymorphisms in ALL susceptibility, relapse, and outcomes in children and adolescents of Greek descent. The study included 252 children and adolescents (115 ALL cases and 137 controls). Genotyping was performed using RT-qPCR and the TaqMan Genotyping Assay. Homozygotes for the minor allele in DROSHA rs642321 were nominally associated with ALL susceptibility (TT vs. CC+CT; OR 4.5; 95% CI: 1.2–21.2; padj = 0.034). Likewise, homozygotes for the minor allele in rs3805500 were linked with ALL risk (GG vs. AA+AG; OR 2.7; 95% CI: 1.3–6.1; padj = 0.012). A suggestive association was observed between the rs3805500 AG genotype and both relapsed (OR 5.8; 95% CI: 1.6–24.3; padj = 0.011) and deceased cases (OR 5; 95% CI: 1.1–26.3; padj = 0.038). Patients with the rs3805500 AG and GG genotypes showed a trend toward poorer overall survival rates. In summary, certain haplotypes of DROSHA polymorphisms may be modestly associated with the occurrence of childhood ALL and its outcomes, although these findings require validation in larger, independent cohorts. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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20 pages, 1887 KiB  
Article
Microarray Analysis Reveals Sepsis Is a Syndrome with Hyperactivity of TH17 Immunity, with Over-Presentation of the Treg Cell Cytokine TGF-β
by Yu-Ju Chen, Jang-Jih Lu, Chih-Pei Lin and Wan-Chung Hu
Curr. Issues Mol. Biol. 2025, 47(6), 435; https://doi.org/10.3390/cimb47060435 - 9 Jun 2025
Viewed by 235
Abstract
Currently, there are two major theories regarding the pathogenesis of sepsis: hyperimmune and hypoimmune. The hyperimmune theory suggests that a cytokine storm causes the symptoms of sepsis. On the contrary, the hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By conducting [...] Read more.
Currently, there are two major theories regarding the pathogenesis of sepsis: hyperimmune and hypoimmune. The hyperimmune theory suggests that a cytokine storm causes the symptoms of sepsis. On the contrary, the hypoimmune theory suggests that immunosuppression causes the manifestations of sepsis. By conducting a microarray analysis on peripheral leukocytes from patients with sepsis, this study found that hyperactivity of TH17 immunity was noted in sepsis patients. Innate immunity-related genes are significantly upregulated, including CD14, TLR1,2,4,5,8, HSP70, CEBP proteins, AP1 (JUNB and FOSL2), TGFB1, IL6, TGFA, CSF2 receptor, TNFRSF1A, S100A binding proteins, CCR2, FPR2, amyloid proteins, pentraxin, defensins, CLEC5A, whole complement machinery, CPD, NCF, MMP, neutrophil elastase, caspases, IgG and IgA Fc receptors (CD64, CD32), ALOX5, PTGS, LTB4R, LTA4H, and ICAM1. The majority of adaptive immunity genes were downregulated, including MHC-related genes, TCR genes, granzymes/perforin, CD40, CD8, CD3, TCR signaling, BCR signaling, T and B cell-specific transcription factors, NK killer receptors, and TH17 helper-specific transcription factors (STAT3, RORA, and REL), as well as Treg-related genes, including TGFB1, IL15, STAT5B, SMAD2/4, CD36, and thrombospondin. The findings of this study show that Th17 with Treg over-presentation play an important role in the pathophysiology of sepsis. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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Other

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11 pages, 1472 KiB  
Case Report
The Novel Association of a Single Nucleotide Variant in the COL3A1 Gene with Diffuse Coronary Aneurysms
by Charlene Norgan Radler, Kevin Ku, Alison Hodge, Tianci Wang, Peyton Moore and Mohanakrishnan Sathyamoorthy
Curr. Issues Mol. Biol. 2025, 47(2), 82; https://doi.org/10.3390/cimb47020082 - 27 Jan 2025
Viewed by 1305
Abstract
The COL3A1 gene, encoding the pro-alpha chain of type III collagen, has been implicated in a range of collagen-mediated diseases such as Ehlers–Danlos syndrome and aortic aneurysms. In this report, we present evidence for the first time associating a single nucleotide variant p.P517R [...] Read more.
The COL3A1 gene, encoding the pro-alpha chain of type III collagen, has been implicated in a range of collagen-mediated diseases such as Ehlers–Danlos syndrome and aortic aneurysms. In this report, we present evidence for the first time associating a single nucleotide variant p.P517R in exon 22 of COL3A1 with the development of diffuse coronary aneurysms in a human subject without prior atherosclerotic cardiovascular disease, connective tissue disorder, or phenotypic characteristics diagnostic for vascular Ehlers–Danlos syndrome. Computational modeling of this specific variant in AlphaFold and in silico analyses predict deleterious alterations in the structure and function of the COL3A1 gene product, alpha 1 chain of type III collagen. This novel phenotype-to-genotype correlation should prompt further investigation into the mechanistic basis of this association. Full article
(This article belongs to the Special Issue Genomic Analysis of Common Disease, 2nd Edition)
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