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Editorial Board Members’ Collection Series: Human Traits and Genomics
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Editorial Board Members’ Collection Series: Human Traits and Genomics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 October 2025 | Viewed by 6151

Special Issue Editors

Dr. Giovanni Malerba

E-Mail Website
Guest Editor
GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
Interests: genomics and transcriptomics of Mendelian and complex traits; association and Linkage analyses; statistical genetics and bioinformatics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lidia Larizza

E-Mail Website
Guest Editor
Experimental Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Via Ariosto 13, 20145 Milan, Italy
Interests: rare disorders of chromatin regulators; Rubinstein-Taybi and related syndromes of the epigenetic machinery; chromosomal/genomic instability syndromes with cancer predisposition; imprinting disorders affecting growth; neurodevelopmental imprinting disorders; genomic disorders; MARK4 gene; c-kit gene
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Salvatore Saccone

E-Mail Website
Guest Editor
Department Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
Interests: genetics; genomics; molecular cytogenetics; chromosomes; nuclear chromatin organization; evolutionary genetics; developmental genetics; forensic genetics; environmental mutagenesis; epigenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Studies of the genetic component that is associated with human traits rely on a variety of strategies encompassing case–control and linkage (family-based) designs, along with the integration of evolutionary models to assess the likelihood of different classes of mutations. Despite the advances in genomic sequencing technology, a significant portion of the genetic causes of rare and common traits remain elusive, as functional variants often extend beyond coding regions; this poses challenges to identification. The availability of new data and tools, such as the telomere-to-telomere reference sequence of the human genome, the introduction of a human pangenome reflecting the haplotypic diversity of a population, and the utilization of cutting-edge technologies for genome analysis, such as long-read sequencing technology, single-cell sequencing, and the introduction of deep learning methods to extract knowledge from genomic data, offer new dimensions with which to unravel the molecular basis associated with trait inheritance and development in humans. This collection series aims to gather papers illustrating the latest and most innovative approaches in genetic data analysis for human traits. These approaches aim to uncover the patterns that associate genomic profiles with Mendelian or complex traits, thus contributing to a deeper understanding of the intricate mechanisms that govern trait inheritance in the human population.

Dr. Giovanni Malerba
Prof. Dr. Lidia Larizza
Prof. Dr. Salvatore Saccone
Guest Editors

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • genetic data analysis
  • genomic profiling
  • trait inheritance
  • DNA and RNA sequencing approaches
  • deep learning methods

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Published Papers (5 papers)

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Research

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19 pages, 7223 KiB  
Article
Identification of Novel Mutations in Patients Affected by Gaucher Disease
by Monia Anania, Miriam Giacomarra, Annalisa D’Errico, Massimo Marano, Immacolata Tartaglione, Marco Spada, Veronica Pagliardini, Maria Rosaria De Paolis, Gaetano Giuffrida, Giulia Duro, Tiziana Di Chiara, Daniele Francofonte, Emanuela Maria Marsana, Paolo Colomba, Giovanni Duro and Carmela Zizzo
Int. J. Mol. Sci. 2025, 26(8), 3918; https://doi.org/10.3390/ijms26083918 - 21 Apr 2025
Abstract
Gaucher disease is an autosomal recessive disorder caused by dysfunction of the enzyme glucocerebrosidase. The enzyme deficiency is mainly due to mutations in the GBA1 gene, and it is responsible for the accumulation of glucosylceramide within the lysosomes of monocyte macrophage-derived cells; causing [...] Read more.
Gaucher disease is an autosomal recessive disorder caused by dysfunction of the enzyme glucocerebrosidase. The enzyme deficiency is mainly due to mutations in the GBA1 gene, and it is responsible for the accumulation of glucosylceramide within the lysosomes of monocyte macrophage-derived cells; causing the associated symptomatology. In this paper, we describe six new mutations identified in the GBA1 gene, which, in combination with other mutations already documented, lead to absent or reduced glucocerebrosidase activity, resulting in pathological accumulation of the specific substrate and the clinical manifestations associated with Gaucher disease. We have identified three mutations (c.1578_1581dup, c.1308dup, and Y492X) that determine the formation of a premature stop codon in the translation process and three missense mutations (C342F, M280L, and Q247R) that lead to amino acid changes in proteins, resulting in decreased glucocerebrosidase activity. These mutations were never observed in our group of healthy control subjects > 1500 individuals. The patients examined had several clinical manifestations, which included hepatosplenomegaly and bone and hematologic involvement; considering the absence of enzyme activity, this suggests that the new mutations described here are associated with type I Gaucher disease. The identification of new mutations in patients with symptoms referable to Gaucher disease increases the molecular knowledge related to the GBA1 gene and offers to clinicians significant support for the accurate diagnosis of the pathology. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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19 pages, 1243 KiB  
Article
Medically Actionable Secondary Findings from Whole-Exome Sequencing (WES) Data in a Sample of 3972 Individuals
by Mafalda Melo, Mariana Ribeiro, Paulo Filipe Silva, Susana Valente, Filipe Alves, Margarida Venâncio, Jorge Sequeiros, João Parente Freixo, Diana Antunes and Jorge Oliveira
Int. J. Mol. Sci. 2025, 26(8), 3509; https://doi.org/10.3390/ijms26083509 - 9 Apr 2025
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Abstract
The application of whole-exome sequencing (WES) for diagnostic purposes has the potential to unravel secondary findings unrelated with the primary reason of testing. Some of those might be of high clinical utility and comprise disease-causing variants in genes, related to life-threatening and clinically [...] Read more.
The application of whole-exome sequencing (WES) for diagnostic purposes has the potential to unravel secondary findings unrelated with the primary reason of testing. Some of those might be of high clinical utility and comprise disease-causing variants in genes, related to life-threatening and clinically actionable diseases. Clarifying the allelic frequencies of such variants in specific populations is a crucial step for the large-scale deployment of genomic medicine. We analysed medically relevant variants in the 81 genes from the American College of Medical Genetics and Genomics (ACMG) v3.2 list of actionable loci, using WES data from a diagnostic laboratory cohort of 3972 persons, tentatively resampled to represent the Portuguese population geographic distribution. We identified medically actionable variants in 6.2% of our cohort, distributed across several disease domains: cardiovascular disorders (3.0%), cancer predisposition (2.0%), miscellaneous disorders (1.1%), and metabolic disorders (0.1%). Additionally, we estimated a frequency of heterozygotes for recessive disease alleles of 11.1%. Overall, our results suggest that medically actionable findings can be identified in approximately 6.2% of persons from our population. This is the first study estimating medically actionable findings in Portugal. These results provide valuable insight for patients, healthcare providers, and policymakers involved in advancing genomic medicine at the national and international level. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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14 pages, 648 KiB  
Article
Epigenome-Wide Association Study of Depressive Symptoms in Black Women in the InterGEN Study
by Brittany Taylor, Yihong Zhao, Nicole B. Perez, Stephanie Potts-Thompson, Cindy Crusto, Ruth Masterson Creber and Jacquelyn Y. Taylor
Int. J. Mol. Sci. 2024, 25(14), 7681; https://doi.org/10.3390/ijms25147681 - 12 Jul 2024
Cited by 2 | Viewed by 1407
Abstract
(1) The prevalence of depression is two times higher in women than men. Black women have an increased risk of depression due to stressors such as low socioeconomic status and perceived discrimination. Depression is likely influenced by both genetic and environmental factors. Psychosocial [...] Read more.
(1) The prevalence of depression is two times higher in women than men. Black women have an increased risk of depression due to stressors such as low socioeconomic status and perceived discrimination. Depression is likely influenced by both genetic and environmental factors. Psychosocial stressors can influence DNA methylation (DNAm), leading to changes in gene expression and ultimately, depression. The objective of this study was to examine associations between DNAm and depressive symptoms in Black women. (2) This study was a secondary analysis of data from the Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) Study. Perceived discrimination was assessed using Krieger’s Experiences of Discrimination and Waelde’s Race-Related Events Scale, and participants were screened for depressive symptoms with the Beck Depression Inventory. Raw data from saliva samples were analyzed using the Illumina Infinium Epic (850 K) BeadChip and then preprocessed in RStudio. (3) Differential methylation analysis identified DNAm sites and regions associated with depressive symptoms. Six DNAm sites had a q-value less than 0.05. Additionally, of the 25 regions identified, 12 were associated with neurological diseases or disorders. (4) These findings suggest that there is a neurological component to depression, which should be considered during treatment. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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15 pages, 3730 KiB  
Article
The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates
by Desiree Brancato, Francesca Bruno, Elvira Coniglio, Valentina Sturiale, Salvatore Saccone and Concetta Federico
Int. J. Mol. Sci. 2024, 25(12), 6602; https://doi.org/10.3390/ijms25126602 - 15 Jun 2024
Viewed by 2076
Abstract
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional [...] Read more.
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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12 pages, 2280 KiB  
Review
Placental–Heart Axis: An Evolutionary Perspective
by Jadyn Matthews, Brammy Rajakumar, Chrystalle Katte Carreon and Sarah U. Morton
Int. J. Mol. Sci. 2024, 25(20), 11212; https://doi.org/10.3390/ijms252011212 - 18 Oct 2024
Viewed by 1715
Abstract
To maintain its development, the growing fetus is directly dependent on the placenta, an organ that acts as both a modulator and mediator. As an essential component of pregnancy that is derived from both maternal and fetal tissues, the placenta facilitates the passage [...] Read more.
To maintain its development, the growing fetus is directly dependent on the placenta, an organ that acts as both a modulator and mediator. As an essential component of pregnancy that is derived from both maternal and fetal tissues, the placenta facilitates the passage of all oxygen and nutrients from the expecting parent to their fetuses. Further, the placenta conveys multiple impacts of the maternal environment to the growing fetus. The timing of placental development parallels that of the fetal cardiovascular system, and placental anomalies are implicated as a potential cause of congenital heart disease. For example, congenital heart disease is more common in pregnancies complicated by maternal preeclampsia, a condition characterized by placental dysfunction. Given the placenta’s intermediary links to the maternal environment and fetal health outcomes, it is an emerging focus of evolutionary medicine, which seeks to understand how interactions between humans and the environment affect our biology and give rise to disease. The present review provides an overview of the evolutionary and developmental courses of the placenta as well as their implications on infant health. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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