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Precision Medicine and Genetics
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Precision Medicine and Genetics

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

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 8316

Special Issue Editor

Dr. Honey Reddi

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
Interests: tools for genetic diagnostics, variant interpretation, clinical assay validation precision medicine; genetic association studies; genetic predisposition to disease; genetic testing for somatic cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Precision Medicine is an emerging science for the treatment and prevention of disease considering the variability in an individual’s genetic makeup in the context of their environment and lifestyle. Precision medicine allows for the identification of genetic causation in case of inherited disorders, the determination of variants for cancer diagnosis and treatment of disease, as well as risk assessment for disease, enabling individualized or tailored applications for disease management.

This Special Issue entitled “Precision Medicine and Genetics” is intended to provide a platform for a wide range of reviews, research articles, communications, case reports and technical notes related to genetics and genomic studies in clinical diagnostics. We encourage submissions that focus on a strong precision medicine component and are devoted to assay validation, novel variants in disease, functional studies that impact variant evaluation for clinical pathogenicity, and machine learning of the genetic markers associated with inherited diseases and cancer. Please contact the Guest Editors should you have any questions related to the scope of this Special Issue.

Dr. Honey Reddi
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

  • genetics
  • clinical assay validation
  • precision medicine
  • genomics

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Published Papers (4 papers)

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Research

18 pages, 2036 KiB  
Article
The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population
by Iskra A. Signore, Gerardo Donoso, Pamela Bocchieri, Eduardo A. Tobar-Calfucoy, Cristian E. Yáñez, Laura Carvajal-Silva, Andrea X. Silva, Carola Otth, Claudio Cappelli, Héctor Valenzuela Jorquera, Daniela Zapata-Contreras, Yolanda Espinosa-Parrilla, Paula Zúñiga-Pacheco, Macarena Fuentes-Guajardo, Virginia A. Monardes-Ramírez, Pia Kochifas Velasquez, Christian A. Muñoz, Cristina Dorador, Jonathan García-Araya, Claudia P. Campillay-Véliz, Cesar Echeverria, Rodolfo Alejandro Santander, Leslie C. Cerpa, Matías F. Martínez, Luis Abel Quiñones, Eduardo Roberto Lamoza Galleguillos, Juan Saez Hidalgo, Estefanía Nova-Lamperti, Sergio Sanhueza, Annesi Giacaman, Gerardo Acosta-Jamett, Cristóbal Verdugo, Anita Plaza, Claudio Verdugo, Carolina Selman, Ricardo Alejandro Verdugo and Alicia Colomboadd Show full author list remove Hide full author list
Genes 2024, 15(11), 1352; https://doi.org/10.3390/genes15111352 - 22 Oct 2024
Viewed by 2086
Abstract
Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical [...] Read more.
Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America’s largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online. Full article
(This article belongs to the Special Issue Precision Medicine and Genetics)
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13 pages, 20689 KiB  
Article
Diagnosis of Two Unrelated Syndromes of Prader-Willi and Calpainopathy: Insight from Trio Whole Genome Analysis and Isodisomy Mapping
by Mario Cuk, Busra Unal, Andjela Bevanda, Connor P. Hayes, McKenzie Walker, Feruza Abraamyan, Robert Beluzic, Kristina Crkvenac Gornik, David Ozretic, Maja Prutki, Qian Nie, Honey V. Reddi and Arezou A. Ghazani
Genes 2024, 15(7), 946; https://doi.org/10.3390/genes15070946 - 19 Jul 2024
Cited by 1 | Viewed by 1580
Abstract
Purpose: An investigation for the co-occurrence of two unrelated genetic disorders of muscular dystrophy and Prader-Willi syndrome (PWS) (OMIM#176270) using joint whole genome sequencing (WGS). Methods: Trio WGS joint analysis was performed to investigate the genetic etiology in a proband with PWS, prolonged [...] Read more.
Purpose: An investigation for the co-occurrence of two unrelated genetic disorders of muscular dystrophy and Prader-Willi syndrome (PWS) (OMIM#176270) using joint whole genome sequencing (WGS). Methods: Trio WGS joint analysis was performed to investigate the genetic etiology in a proband with PWS, prolonged muscular hypotonia associated hyperCKemia, and early-onset obesity. The parents were unaffected. Results: Results showed maternal isodisomy uniparental disomy (UPD) in chromosome 15, expanding from 15q11.2 to 15q22.2, including PWS regions at 15q11.2–15q13. Maternal heterodisomy was detected from 15q22.2 to 15q26.3. A pathogenic variant, NM_000070.3(CAPN3):c.550del (p.Thr184fs), was identified at 15q15.1 in a heterozygous state in the mother that was homozygous in the proband due to maternal isodisomy. Conclusion: This is the first study of the concurrent molecular etiology of PWS and calpainopathy (OMIM#253600) in the same patient. This report highlights the utility of joint analysis and the need for the assessment of autosomal recessive disease in regions of isodisomy in patients with complex and unexplained phenotypes. Full article
(This article belongs to the Special Issue Precision Medicine and Genetics)
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12 pages, 1106 KiB  
Article
Resolving Discrepancies in Idylla BRAF Mutational Assay Results Using Targeted Next-Generation Sequencing
by Giby V. George, Huijie Liu, Audrey N. Jajosky and Zoltán N. Oltvai
Genes 2024, 15(5), 527; https://doi.org/10.3390/genes15050527 - 23 Apr 2024
Cited by 1 | Viewed by 1510
Abstract
BRAF mutation identification is important for the diagnosis and treatment of several tumor types, both solid and hematologic. Rapid identification of BRAF mutations is required to determine eligibility for targeted BRAF inhibitor therapy. The Idylla BRAF mutation assay is a rapid, multiplex allele-specific [...] Read more.
BRAF mutation identification is important for the diagnosis and treatment of several tumor types, both solid and hematologic. Rapid identification of BRAF mutations is required to determine eligibility for targeted BRAF inhibitor therapy. The Idylla BRAF mutation assay is a rapid, multiplex allele-specific PCR test designed to detect the most common oncogenic BRAF V600 mutations in formalin-fixed paraffin-embedded (FFPE) tissue samples. Here, we describe the validation of the Idylla BRAF mutation assay in our laboratory. During routine clinical practice, we noticed cases in which BRAF V600 mutations were identified with unusual amplification curves, with three cases displaying a delayed amplification within a double amplification pattern and two false-positive calls. We therefore initiated a quality improvement effort to systematically and retrospectively evaluate next-generation sequencing (NGS)-tested cases with BRAF mutations identified within five amino acids of BRAF codon V600 and did not identify additional false-positive cases. We hypothesize that late amplification in a double amplification pattern may represent non-specific amplification, whereas cases displaying single delayed amplification curves may stem from the presence of either non-V600 variants, very low-level V600 variants, cytosine deamination artifacts, and/or non-specific amplification by an allele-specific PCR primer. Regardless, we recommend that Idylla BRAF cases with non-classical amplification curves undergo reflex NGS testing. These findings are likely relevant for other Idylla assays interrogating hotspot mutations in genes such as EGFR, IDH1/2, KRAS, and NRAS. Full article
(This article belongs to the Special Issue Precision Medicine and Genetics)
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10 pages, 1279 KiB  
Communication
Paternally Inherited Noonan Syndrome Caused by a PTPN11 Variant May Exhibit Mild Symptoms: A Case Report and Literature Review
by Ji Yoon Han and Joonhong Park
Genes 2024, 15(4), 445; https://doi.org/10.3390/genes15040445 - 31 Mar 2024
Cited by 2 | Viewed by 2377
Abstract
Background: Noonan syndrome (NS)/Noonan syndrome with multiple lentigines (NSML) is commonly characterized by distinct facial features, a short stature, cardiac problems, and a developmental delay of variable degrees. However, as many as 50% of individuals diagnosed with NS/NSML have a mildly affected parent [...] Read more.
Background: Noonan syndrome (NS)/Noonan syndrome with multiple lentigines (NSML) is commonly characterized by distinct facial features, a short stature, cardiac problems, and a developmental delay of variable degrees. However, as many as 50% of individuals diagnosed with NS/NSML have a mildly affected parent or relative due to variable expressivity and possibly incomplete penetrance of the disorder, and those who are recognized to have NS only after a diagnosis are established in a more obviously affected index case. Methods: In order to collect intergenerational data reported from previous studies, electronic journal databases containing information on the molecular genetics of PTPN11 were searched from 2000 to 2022. Results: We present a case of a proband with a PTPN11 variant (c.1492C > T/p.Arg498Trp) inherited from an asymptomatic father, displaying only mild intellectual disability without classical symptoms of NS. Among our cases and the reported NS cases caused by the PTPN11 p.Arg498Trp variant, cardiac abnormalities (6/11), facial dysmorphism (7/11), skin pigmentation (4/11), growth problems (4/11), and sensorineural hearing loss (2/11) have been observed. NS/NSML patients with the PTPN11 p.Arg498Trp variant tend to exhibit relatively lower frequencies of skin pigmentation, facial dysmorphism and cardiac abnormalities and mild symptoms compared to those carrying any other mutated PTPN11. Conclusions: Paternally inherited NS/NSML caused by a PTPN11 p.Arg498Trp variant, including our cases, may exhibit relatively lower frequencies of abnormal features and mild symptoms. This could be ascribed to potential gene–gene interactions, gene–environment interactions, the gender and phenotype of the transmitting parent, or ethnic differences that influence the clinical phenotype. Full article
(This article belongs to the Special Issue Precision Medicine and Genetics)
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