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Genetic Architecture in Complex Traits
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Genetic Architecture in Complex Traits

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

Deadline for manuscript submissions: closed (25 August 2023) | Viewed by 6491

Special Issue Editor

Dr. Oleg S. Glotov

E-Mail
Guest Editor
Children’s Scientific and Clinical Center for Infectious Diseases of the Federal Medical and Biological Agency, 197022 St. Petersburg, Russia
Interests: searching new genes for disorders; molecular medicine; genetic tests; monogenic diseases; multifactorial diseases; SNV/SNP; COVID-19; host genome; biobanks

Special Issue Information

Dear Colleagues,

We would like to invite you to participate in this Special Issue, “Genetic Architecture in Complex Traits”.

The emergence of new genetic technologies is a key aspect of progress in the development of molecular medicine. Thanks to these technologies, it is possible to identify the causes of rare monogenic diseases, improve prevention, and improve the effectiveness of the treatment of common complex and infectious diseases.

Today, with an idea of inheritance type, the pathogenetic mechanism of disease development, and the population frequency of SNVs/SNPs, it is possible to annotate and clinically interpret pathogenic variants. However, the natures of these diseases remain unclear: polygenic, oligogenic or multifactorial? It is assumed that this is determined by the contribution of different gene variants, as well as their expressiveness and penetrance. An important feature of the results of modern NGS research methods is that we can detect several hereditary diseases in one person at once. Such findings create difficulties for clinical interpretation, but are extremely important when consulting patients.

Unfortunately, neither new antibiotics nor new vaccines can fundamentally become a solution to the problem of fighting infectious diseases. Therefore, it is necessary to study not only the virus itself and its genome, but also the genome of the host (humans). The COVID-19 pandemic has stimulated large-scale genome-wide research of this kind.

The aim of this Special Issue is to provide an updated view of the current research on the underlying genetic mechanisms of monogenic and common complex and infectious diseases.

Dr. Oleg S. Glotov
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. Genes 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 2600 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

  • searching new genes for disorders
  • NGS
  • molecular medicine
  • monogenic diseases
  • common complex diseases
  • SNV/SNP
  • COVID-19
  • large-scale genome-wide research
  • genetic susceptibility
  • host genome

Published Papers (5 papers)

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11 pages, 284 KiB  
Article
From Feeding Challenges to Oral-Motor Dyspraxia: A Comprehensive Description of 10 New Cases with CTNNB1 Syndrome
by Roberta Onesimo, Elisabetta Sforza, Valentina Trevisan, Chiara Leoni, Valentina Giorgio, Donato Rigante, Eliza Maria Kuczynska, Francesco Proli, Cristiana Agazzi, Domenico Limongelli, Maria Cistina Digilio, Maria Lisa Dentici, Maria Macchiaiolo, Antonio Novelli, Andrea Bartuli, Lorenzo Sinibaldi, Marco Tartaglia and Giuseppe Zampino
Genes 2023, 14(10), 1843; https://doi.org/10.3390/genes14101843 - 22 Sep 2023
Viewed by 986
Abstract
CTNNB1 syndrome is an autosomal-dominant neurodevelopmental disorder featuring developmental delay; intellectual disability; behavioral disturbances; movement disorders; visual defects; and subtle facial features caused by de novo loss-of-function variants in the CTNNB1 gene. Due to paucity of data, this study intends to describe feeding [...] Read more.
CTNNB1 syndrome is an autosomal-dominant neurodevelopmental disorder featuring developmental delay; intellectual disability; behavioral disturbances; movement disorders; visual defects; and subtle facial features caused by de novo loss-of-function variants in the CTNNB1 gene. Due to paucity of data, this study intends to describe feeding issues and oral-motor dyspraxia in an unselected cohort of 10 patients with a confirmed molecular diagnosis. Pathogenic variants along with key information regarding oral-motor features were collected. Sialorrhea was quantified using the Drooling Quotient 5. Feeding abilities were screened using the Italian version of the Montreal Children’s Hospital Feeding Scale (I-MCH-FS). Mild-to-severe coordination difficulties in single or in a sequence of movements involving the endo-oral and peri-oral muscles were noticed across the entire cohort. Mild-to-profuse drooling was a commonly complained-about issue by 30% of parents. The mean total I-MCH-FS t-score equivalent was 43.1 ± 7.5. These findings contribute to the understanding of the CTNNB1 syndrome highlighting the oral motor phenotype, and correlating specific gene variants with clinical characteristics. Full article
(This article belongs to the Special Issue Genetic Architecture in Complex Traits)
12 pages, 2847 KiB  
Article
Clinical and Genetic Characteristics of a Patient with Cystic Fibrosis with a Complex Allele [E217G;G509D] and Functional Evaluation of the CFTR Channel
by Elena Kondratyeva, Yuliya Melyanovskaya, Anna Efremova, Mariya Krasnova, Diana Mokrousova, Nataliya Bulatenko, Nika Petrova, Alexander Polyakov, Tagui Adyan, Valeriia Kovalskaia, Tatiana Bukharova, Andrey Marakhonov, Rena Zinchenko, Elena Zhekaite, Artem Buhonin and Dmitry Goldshtein
Genes 2023, 14(9), 1705; https://doi.org/10.3390/genes14091705 - 28 Aug 2023
Cited by 3 | Viewed by 1078
Abstract
The intricate nature of complex alleles presents challenges in the classification of CFTR gene mutations, encompassing potential disease-causing, neutral, or treatment-modulating effects. Notably, the complex allele [E217G;G509D] remains absent from international databases, with its pathogenicity yet to be established. Assessing the functionality of [...] Read more.
The intricate nature of complex alleles presents challenges in the classification of CFTR gene mutations, encompassing potential disease-causing, neutral, or treatment-modulating effects. Notably, the complex allele [E217G;G509D] remains absent from international databases, with its pathogenicity yet to be established. Assessing the functionality of apical membrane ion channels in intestinal epithelium employed the intestinal current measurements (ICM) method, using rectal biopsy material. The effectivity of CFTR-targeted therapy was evaluated using a model of intestinal organoids of a patient harboring the genotype F508del/[E217G;G509D]. ICM analysis revealed diminished chloride channel function. Remarkably, [E217G;G509D] presence within intestinal organoids correlated with heightened residual CFTR function. Employing CFTR modulators facilitated the restoration of the functional CFTR protein. This multifaceted study intertwines genetic investigations, functional analyses, and therapeutic interventions, shedding light on the intricate interplay of complex alleles within CFTR mutations. The results highlight the potential of targeted CFTR modulators to restore functional integrity, offering promise for advancing precision treatments in cystic fibrosis management. Full article
(This article belongs to the Special Issue Genetic Architecture in Complex Traits)
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10 pages, 336 KiB  
Article
The Telomeric Repeats of HHV-6A Do Not Determine the Chromosome into Which the Virus Is Integrated
by Aleksey V. Kusakin, Olga V. Goleva, Lavrentii G. Danilov, Andrey V. Krylov, Victoria V. Tsay, Roman S. Kalinin, Natalia S. Tian, Yuri A. Eismont, Anna L. Mukomolova, Alexei B. Chukhlovin, Aleksey S. Komissarov and Oleg S. Glotov
Genes 2023, 14(2), 521; https://doi.org/10.3390/genes14020521 - 18 Feb 2023
Viewed by 1409
Abstract
Human herpes virus 6A (HHV-6A) is able to integrate into the telomeric and subtelomeric regions of human chromosomes representing chromosomally integrated HHV-6A (ciHHV-6A). The integration starts from the right direct repeat (DRR) region. It has been shown experimentally that perfect telomeric [...] Read more.
Human herpes virus 6A (HHV-6A) is able to integrate into the telomeric and subtelomeric regions of human chromosomes representing chromosomally integrated HHV-6A (ciHHV-6A). The integration starts from the right direct repeat (DRR) region. It has been shown experimentally that perfect telomeric repeats (pTMR) in the DRR region are required for the integration, while the absence of the imperfect telomeric repeats (impTMR) only slightly reduces the frequency of HHV-6 integration cases. The aim of this study was to determine whether telomeric repeats within DRR may define the chromosome into which the HHV-6A integrates. We analysed 66 HHV-6A genomes obtained from public databases. Insertion and deletion patterns of DRR regions were examined. We also compared TMR within the herpes virus DRR and human chromosome sequences retrieved from the Telomere-to-Telomere consortium. Our results show that telomeric repeats in DRR in circulating and ciHHV-6A have an affinity for all human chromosomes studied and thus do not define a chromosome for integration. Full article
(This article belongs to the Special Issue Genetic Architecture in Complex Traits)
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12 pages, 301 KiB  
Article
Suicide-Related Single Nucleotide Polymorphisms, rs4918918 and rs10903034: Association with Dementia in Older Adults
by Olga Abramova, Kristina Soloveva, Yana Zorkina, Dmitry Gryadunov, Anna Ikonnikova, Elena Fedoseeva, Marina Emelyanova, Aleksandra Ochneva, Nika Andriushchenko, Konstantin Pavlov, Olga Pavlova, Valeriya Ushakova, Timur Syunyakov, Alisa Andryushchenko, Olga Karpenko, Victor Savilov, Marat Kurmishev, Denis Andreuyk, Olga Gurina, Vladimir Chekhonin, Georgy Kostyuk and Anna Morozovaadd Show full author list remove Hide full author list
Genes 2022, 13(11), 2174; https://doi.org/10.3390/genes13112174 - 21 Nov 2022
Cited by 2 | Viewed by 1576
Abstract
Dementia has enormous implications for patients and the health care system. Genetic markers are promising for detecting the risk of cognitive impairment. We hypothesized that genetic variants associated with suicide risk might significantly increase the risk of cognitive decline because suicide in older [...] Read more.
Dementia has enormous implications for patients and the health care system. Genetic markers are promising for detecting the risk of cognitive impairment. We hypothesized that genetic variants associated with suicide risk might significantly increase the risk of cognitive decline because suicide in older adults is often a consequence of cognitive impairment. We investigated several single-nucleotide polymorphisms that were initially associated with suicide risk in dementia older adults and identified the APOE gene alleles. The study was performed with subjects over the age of 65: 112 patients with dementia and 146 healthy volunteers. The MMSE score was used to assess cognitive functions. Study participants were genotyped using real-time PCR (APOE: rs429358, rs7412; genes associated with suicide: rs9475195, rs7982251, rs2834789, rs358592, rs4918918, rs3781878, rs10903034, rs165774, rs16841143, rs11833579 rs10898553, rs7296262, rs3806263, and rs2462021). Genotype analysis revealed the significance of APOEε4, APOEε2, and rs4918918 (SORBS1) when comparing dementia and healthy control groups. The association of APOEε4, APOEε2, and rs10903034 (IFNLR1) with the overall MMSE score was indicated. The study found an association with dementia of rs4918918 (SORBS1) and rs10903034 (IFNLR1) previously associated with suicide and confirmed the association of APOEε4 and APOEε2 with dementia. Full article
(This article belongs to the Special Issue Genetic Architecture in Complex Traits)

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9 pages, 1250 KiB  
Case Report
In Tandem Intragenic Duplication of Doublesex and Mab-3-Related Transcription Factor 1 (DMRT1) in an SRY-Negative Boy with a 46,XX Disorder of Sex Development
by Veronica Bertini, Fulvia Baldinotti, Pietro Parma, Nina Tyutyusheva, Margherita Sepich, Giulia Bertolucci, Camillo Rosano, Maria Adelaide Caligo, Diego Peroni, Angelo Valetto and Silvano Bertelloni
Genes 2023, 14(11), 2067; https://doi.org/10.3390/genes14112067 - 12 Nov 2023
Viewed by 872
Abstract
Disorders of sexual development (DSDs) encompass a group of congenital conditions associated with atypical development of internal and external genital structures. Among those with DSDs are 46,XX males, whose condition mainly arises due to the translocation of SRY onto an X chromosome or [...] Read more.
Disorders of sexual development (DSDs) encompass a group of congenital conditions associated with atypical development of internal and external genital structures. Among those with DSDs are 46,XX males, whose condition mainly arises due to the translocation of SRY onto an X chromosome or an autosome. In the few SRY-negative 46,XX males, overexpression of other pro-testis genes or failure of pro-ovarian/anti-testis genes may be involved, even if a non-negligible number of cases remain unexplained. A three-year-old boy with an SRY-negative 46,XX karyotype showed a normal male phenotype and normal prepubertal values for testicular hormones. A heterozygous de novo in tandem duplication of 50,221 bp, which encompassed exons 2 and 3 of the Doublesex and Mab-3-related transcription factor 1 (DMRT1) gene, was detected using MPLA, CGH-array analysis, and Sanger sequencing. Both breakpoints were in the intronic regions, and this duplication did not stop or shift the coding frame. Additional pathogenic or uncertain variants were not found in a known pro-testis/anti-ovary gene cascade using a custom NGS panel and whole genome sequencing. The duplication may have allowed DMRT1 to escape the transcriptional repression that normally occurs in 46,XX fetal gonads and thus permitted the testicular determination cascade to switch on. So far, no case of SRY-negative 46,XX DSD with alterations in DMRT1 has been described. Full article
(This article belongs to the Special Issue Genetic Architecture in Complex Traits)
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