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Genetic Variants in Human Population and Diseases
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Genetic Variants in Human Population and Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (25 July 2023) | Viewed by 21725

Special Issue Editor

Prof. Dr. Marijana Peričić Salihović

E-Mail Website
Guest Editor
Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
Interests: isolated populations; genetic diversity; pharmacogenomics; ancestry; molecular anthropology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Contemporary populations’ genomic diversity reflects past demographic and evolutionary events such as migrations, admixtures, bottlenecks, geographic and sociocultural isolations, genetic drift and natural selection. Their different temporal and spatial occurrence defines the genetic profiles causing differences among human populations but at the same time they highlight the worldwide pattern consistent with the migration history that corresponds to the Out of Africa hypothesis. Studies of human genetic diversity have also enabled better understanding of the influence of genetic variation on disease risk and drug response, with both having public health repercussions. Accumulated knowledge in line with technological improvements have allowed the progress of personalized medicine as well. Since genetic distinctiveness is especially pronounced in isolated populations where the exchange of genes with other populations is minimal and where the increased frequency of otherwise rare or private alleles emerges, such populations should also be studied to enable their members to benefit from genomic diversity research as well. This Special Issue on “Genetic Variants in Human Population and Diseases” aims to present a collection of original articles or reviews on various aspect of human genetic variation at the gene and/or genome level.

Prof. Dr. Marijana Peričić Salihović
Guest Editor

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Keywords

  • population diversity
  • human genome
  • mutation
  • evolution
  • complex traits
  • ancestry
  • polygenic risk score
  • isolated populations

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Published Papers (7 papers)

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Research

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12 pages, 2881 KiB  
Article
Variants of IFNL4 Gene in Amazonian and Northern Brazilian Populations
by Carolina Cabral Angelim, Letícia Dias Martins, Álesson Adam Fonseca Andrade, Fabiano Cordeiro Moreira, João Farias Guerreiro, Paulo Pimentel de Assumpção, Sidney Emanuel Batista dos Santos and Greice de Lemos Cardoso Costa
Genes 2023, 14(11), 2075; https://doi.org/10.3390/genes14112075 - 14 Nov 2023
Cited by 1 | Viewed by 1559
Abstract
Since the discovery of the polymorphic nature of the IFNL4 gene, its variants have been investigated and associated with several viral diseases, with an emphasis on hepatitis C. However, the impacts of these variants on mixed-race and native populations in the northern region [...] Read more.
Since the discovery of the polymorphic nature of the IFNL4 gene, its variants have been investigated and associated with several viral diseases, with an emphasis on hepatitis C. However, the impacts of these variants on mixed-race and native populations in the northern region of Brazil are scarce. We investigated three variants of the IFNL4 gene in populations from this location, which were among the 14 most frequent variants in worldwide populations, and compared the frequencies obtained to populational data from the 1000 Genomes Project, gnomAD and ABraOM databases. Our results demonstrate that mixed-race and native populations from the northern region of Brazil present frequencies like those of European and Asian groups for the rs74597329 and rs11322783 variants, and like all populations presented for the rs4803221 variant. These data reinforce the role of world populations in shaping the genetic profile of Brazilian populations, indicate patterns of illness according to the expressed genotype, and infer an individual predisposition to certain diseases. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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16 pages, 334 KiB  
Article
Genes Involved in DNA Damage Cell Pathways and Health of the Oldest-Old (85+)
by Maja Šetinc, Matea Zajc Petranović, Goran Slivšek, Sandra Mijač, Željka Celinščak, Anita Stojanović Marković, Vesna Bišof, Marijana Peričić Salihović and Tatjana Škarić-Jurić
Genes 2023, 14(9), 1806; https://doi.org/10.3390/genes14091806 - 15 Sep 2023
Viewed by 1929
Abstract
Some sources report a connection of cellular senescence with chronic pathological conditions; however, the association between particular cellular processes and general health is rarely examined. This study aims to test the relationship of general health with DNA damage pathways that play a crucial [...] Read more.
Some sources report a connection of cellular senescence with chronic pathological conditions; however, the association between particular cellular processes and general health is rarely examined. This study aims to test the relationship of general health with DNA damage pathways that play a crucial role in senescence. The association of ten selected SNPs with subjective and objective general health and functional ability indicators has been tested in 314 oldest-old people from Croatia. Multivariate logistic regression was employed to simultaneously test the impact of variables potentially influencing targeted health and functional ability variables. The best model, explaining 37.1% of the variance, has six independent significant predictors of functional ability scores: rs16847897 in TERC, rs533984 in MRE11A, and rs4977756 in CDKN2B, chronic disease count, Mini-Mental State Examination scores, and age at surveying. In conclusion, the examined ten loci involved in DNA damage repair pathways showed a more significant association with self-rated health and functional ability than with the number of disease or prescribed medicaments. The more frequent, longevity-related homozygote (GG) in rs16847897 was associated with all three aspects of self-assessments—health, mobility, and independence—indicating that this TERC locus might have a true impact on the overall vitality of the oldest-old persons. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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11 pages, 573 KiB  
Article
Genetic Determinants of Atherogenic Indexes
by Tomas Texis, Susana Rivera-Mancía, Eloisa Colín-Ramírez, Raul Cartas-Rosado, David Koepsell, Kenneth Rubio-Carrasco, Mauricio Rodríguez-Dorantes and Vanessa Gonzalez-Covarrubias
Genes 2023, 14(6), 1214; https://doi.org/10.3390/genes14061214 - 1 Jun 2023
Cited by 4 | Viewed by 2275
Abstract
Atherogenesis and dyslipidemia increase the risk of cardiovascular disease, which is the leading cause of death in developed countries. While blood lipid levels have been studied as disease predictors, their accuracy in predicting cardiovascular risk is limited due to their high interindividual and [...] Read more.
Atherogenesis and dyslipidemia increase the risk of cardiovascular disease, which is the leading cause of death in developed countries. While blood lipid levels have been studied as disease predictors, their accuracy in predicting cardiovascular risk is limited due to their high interindividual and interpopulation variability. The lipid ratios, atherogenic index of plasma (AIP = log TG/HDL-C) and the Castelli risk index 2 (CI2 = LDL-C/HDL-C), have been proposed as better predictors of cardiovascular risk, but the genetic variability associated with these ratios has not been investigated. This study aimed to identify genetic associations with these indexes. The study population (n = 426) included males (40%) and females (60%) aged 18–52 years (mean 39 years); the Infinium GSA array was used for genotyping. Regression models were developed using R and PLINK. AIP was associated with variation on APOC3, KCND3, CYBA, CCDC141/TTN, and ARRB1 (p-value < 2.1 × 10−6). The three former were previously associated with blood lipids, while CI2 was associated with variants on DIPK2B, LIPC, and 10q21.3 rs11251177 (p-value 1.1 × 10−7). The latter was previously linked to coronary atherosclerosis and hypertension. KCND3 rs6703437 was associated with both indexes. This study is the first to characterize the potential link between genetic variation and atherogenic indexes, AIP, and CI2, highlighting the relationship between genetic variation and dyslipidemia predictors. These results also contribute to consolidating the genetics of blood lipid and lipid indexes. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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12 pages, 1060 KiB  
Article
Comprehensive Genetic Analysis of Druze Provides Insights into Carrier Screening
by Eden Avnat, Guy Shapira, Shelly Shoval, Ifat Israel-Elgali, Anna Alkelai, Alan R. Shuldiner, Claudia Gonzaga-Jauregui, Jamal Zidan, Taiseer Maray, Noam Shomron and Eitan Friedman
Genes 2023, 14(4), 937; https://doi.org/10.3390/genes14040937 - 18 Apr 2023
Cited by 1 | Viewed by 2092
Abstract
Background: Druze individuals, like many genetically homogeneous and isolated populations, harbor recurring pathogenic variants (PV) in autosomal recessive (AR) disorders. Methods: Variant calling of whole-genome sequencing (WGS) of 40 Druze from the Human Genome Diversity Project (HGDP) was performed (HGDP-cohort). Additionally, we performed [...] Read more.
Background: Druze individuals, like many genetically homogeneous and isolated populations, harbor recurring pathogenic variants (PV) in autosomal recessive (AR) disorders. Methods: Variant calling of whole-genome sequencing (WGS) of 40 Druze from the Human Genome Diversity Project (HGDP) was performed (HGDP-cohort). Additionally, we performed whole exome sequencing (WES) of 118 Druze individuals: 38 trios and 2 couples, representing geographically distinct clans (WES-cohort). Rates of validated PV were compared with rates in worldwide and Middle Eastern populations, from the gnomAD and dbSNP datasets. Results: Overall, 34 PVs were identified: 30 PVs in genes underlying AR disorders, 3 additional PVs were associated with autosomal dominant (AD) disorders, and 1 PV with X-linked-dominant inherited disorder in the WES cohort. Conclusions: The newly identified PVs associated with AR conditions should be considered for incorporation into prenatal-screening options offered to Druze individuals after an extension and validation of the results in a larger study. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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11 pages, 2716 KiB  
Article
A Biallelic Truncating Variant in the TPR Domain of GEMIN5 Associated with Intellectual Disability and Cerebral Atrophy
by Nazia Ibrahim, Shagufta Naz, Francesca Mattioli, Nicolas Guex, Saima Sharif, Afia Iqbal, Muhammad Ansar and Alexandre Reymond
Genes 2023, 14(3), 707; https://doi.org/10.3390/genes14030707 - 13 Mar 2023
Cited by 4 | Viewed by 2094
Abstract
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing [...] Read more.
GEMIN5 is a multifunctional RNA-binding protein required for the assembly of survival motor neurons. Several bi-allelic truncating and missense variants in this gene are reported to cause a neurodevelopmental disorder characterized by cerebellar atrophy, intellectual disability (ID), and motor dysfunction. Whole exome sequencing of a Pakistani consanguineous family with three brothers affected by ID, cerebral atrophy, mobility, and speech impairment revealed a novel homozygous 3bp-deletion NM_015465.5:c.3162_3164del that leads to the loss of NM_015465.5 (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) amino acid in one of the α-helixes of the tetratricopeptide repeats of GEMIN5. In silico 3D representations of the GEMIN5 dimerization domain show that this variant likely affects the orientation of the downstream sidechains out of the helix axis, which would affect the packing with neighboring helices. The phenotype of all affected siblings overlaps well with previously reported patients, suggesting that NM_015465.5: c.3162_3164del (NP_056280.2):p. (Asp1054_Ala1055delinsGlu) is a novel GEMIN5 pathogenic variant. Overall, our data expands the molecular and clinical phenotype of the recently described neurodevelopmental disorder with cerebellar atrophy and motor dysfunction (NEDCAM) syndrome. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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23 pages, 9342 KiB  
Article
High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania
by Noémi Borbély, Orsolya Székely, Bea Szeifert, Dániel Gerber, István Máthé, Elek Benkő, Balázs Gusztáv Mende, Balázs Egyed, Horolma Pamjav and Anna Szécsényi-Nagy
Genes 2023, 14(1), 133; https://doi.org/10.3390/genes14010133 - 3 Jan 2023
Cited by 4 | Viewed by 8990
Abstract
Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back [...] Read more.
Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th–9th centuries AD) and Hungarian Conquest Period (10th century AD) populations. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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Review

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16 pages, 610 KiB  
Review
Circadian Gene Variants in Diseases
by Paula Gršković and Petra Korać
Genes 2023, 14(9), 1703; https://doi.org/10.3390/genes14091703 - 27 Aug 2023
Cited by 4 | Viewed by 2013
Abstract
The circadian rhythm is a self-sustaining 24 h cycle that regulates physiological processes within the body, including cycles of alertness and sleepiness. Cells have their own intrinsic clock, which consists of several proteins that regulate the circadian rhythm of each individual cell. The [...] Read more.
The circadian rhythm is a self-sustaining 24 h cycle that regulates physiological processes within the body, including cycles of alertness and sleepiness. Cells have their own intrinsic clock, which consists of several proteins that regulate the circadian rhythm of each individual cell. The core of the molecular clock in human cells consists of four main circadian proteins that work in pairs. The CLOCK-BMAL1 heterodimer and the PER-CRY heterodimer each regulate the other pair’s expression, forming a negative feedback loop. Several other proteins are involved in regulating the expression of the main circadian genes, and can therefore also influence the circadian rhythm of cells. This review focuses on the existing knowledge regarding circadian gene variants in both the main and secondary circadian genes, and their association with various diseases, such as tumors, metabolic diseases, cardiovascular diseases, and sleep disorders. Full article
(This article belongs to the Special Issue Genetic Variants in Human Population and Diseases)
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