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From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of...
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From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of Genomics Research

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Genetic Diagnosis".

Deadline for manuscript submissions: closed (25 November 2025) | Viewed by 6630

Special Issue Editors

Dr. Kathleen D. Valverde

E-Mail Website
Guest Editor
Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Interests: continuing education; professional development; coping and resiliency; standardized patient education; financing genetic counseling education
Prof. Deb A. Duquette

E-Mail Website
Guest Editor
Feinberg School of Medicine, Northwestern University, Chicago, IL 60208, USA
Interests: public health genomics; precision public health; access to genetic counseling services; genetic counseling education; population genetic screening; health disparities related to genetic services

Special Issue Information

Dear Colleagues,

Genomic medicine is rapidly advancing, driven by breakthroughs in understanding genetic mechanisms, technological innovations, and the growing clinical applicability of genomic research. As our knowledge of disease-associated variants, functional genomics, and molecular pathways expands, these discoveries are increasingly translated into patient-centered care, enabling precise diagnostics, targeted therapies, and personalized risk assessment.

This progress relies on interdisciplinary collaboration, integrating foundational genetic research with clinical implementation. From elucidating pathogenic variants to developing therapeutic interventions, genomics research now spans diverse medical specialties, reshaping how we diagnose, treat, and prevent genetic conditions. At the same time, advances in genomic technologies—such as multi-omics integration, CRISPR-based editing, and AI-driven variant interpretation—are accelerating the translation of mechanistic discoveries into real-world applications.

However, challenges remain in ensuring equitable access, optimizing clinical utility, and bridging gaps between research and practice. Efforts to diversify genomic datasets, refine functional assays, and improve variant classification are critical to delivering inclusive, evidence-based care.

This Special Issue invites original research, reviews, and perspectives that explore the full spectrum of genomics research, from fundamental genetic discoveries to their clinical and therapeutic implementation. We welcome submissions on novel disease mechanisms, genotype–phenotype analysis, functional genomics, translational bioinformatics, implementation science, and strategies for advancing precision medicine. By highlighting these themes, we aim to foster discussions on how genomic research can evolve to better serve patient needs worldwide.

Dr. Kathleen D. Valverde
Prof. Deb A. Duquette
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 250 words) can be sent to the Editorial Office for assessment.

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

  • Genomic Medicine
  • Precision Medicine
  • Functional Genomics
  • Variant Interpretation
  • Genetic Mechanisms

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Published Papers (4 papers)

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Research

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12 pages, 1357 KB  
Article
22q11.2 Deletion Syndrome in Offspring Conceived via Assisted Reproductive Technology Versus Spontaneously
by Jennifer Borowka, Terrence Blaine Crowley, Ashika Mani, Victoria Guinta, Daniel E. McGinn, Bekah Wang, Audrey Green, Lydia Rockart, Oanh Tran, Beverly S. Emanuel, Elaine H. Zackai, Lorraine Dugoff, Kathleen Valverde and Donna M. McDonald-McGinn
Genes 2026, 17(1), 68; https://doi.org/10.3390/genes17010068 - 6 Jan 2026
Viewed by 848
Abstract
Background/Objectives: The majority of chromosome 22q11.2 deletions are de novo, resulting from meiotic non-allelic homologous recombination (NAHR). While 22q11.2 deletion syndrome (22q11.2DS)-associated phenotypes are well characterized, risk factors leading to NAHR are poorly understood, including the possible relationship with assisted reproductive technology [...] Read more.
Background/Objectives: The majority of chromosome 22q11.2 deletions are de novo, resulting from meiotic non-allelic homologous recombination (NAHR). While 22q11.2 deletion syndrome (22q11.2DS)-associated phenotypes are well characterized, risk factors leading to NAHR are poorly understood, including the possible relationship with assisted reproductive technology (ART). Here we examined the prevalence of ART conceptions and medical comorbidities in patients with 22q11.2DS vs. spontaneously conceived (SC) patients with 22q11.2DS. Methods: Retrospective analysis, under IRB approval, of medical records on 1184 patients with laboratory-confirmed de novo chromosome 22q11.2 deletions was performed. ART conceptions included IVF with and without ICSI. Deletion size and obstetric, family, and medical histories were examined. Results: We identified 30 pregnancies conceived using ART (2.57%) compared with the U.S. general population rate of 2.3% (p-value = 0.6603). ART and SC sub-cohorts demonstrated no significant differences in deletion size or perinatal outcomes, including preterm birth, multiples, polyhydramnios, or congenital heart disease. Controlling for these factors, neonates conceived via ART were more likely to be admitted to the ICU (aOR = 6.3). Conclusions: Pregnancies conceived via ART, and later found to have 22q11.2DS, demonstrated no significant differences in prevalence or perinatal outcomes compared with the U.S. general population. Moreover, NAHR is unrelated to ART in this population. Likewise, associated phenotypic features are unrelated. These data will be reassuring to those families where ART was employed to conceive children who were later found to have 22q11.2DS. Full article
(This article belongs to the Special Issue From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of Genomics Research)
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16 pages, 1499 KB  
Article
A Plot Twist: When RNA Yields Unexpected Findings in Paired DNA-RNA Germline Genetic Testing
by Heather Zimmermann, Terra Brannan, Colin Young, Jesus Ramirez Castano, Carolyn Horton, Alexandra Richardson, Bhuvan Molparia and Marcy E. Richardson
Genes 2025, 16(11), 1382; https://doi.org/10.3390/genes16111382 - 13 Nov 2025
Cited by 1 | Viewed by 1218
Abstract
Background: Germline genetic variants impacting splicing are a frequent cause of disease. The clinical interpretation of such variants is challenging for many reasons including the immense complexity of splicing mechanisms. While recent advances in splicing algorithms have improved the accuracy of splice prediction, [...] Read more.
Background: Germline genetic variants impacting splicing are a frequent cause of disease. The clinical interpretation of such variants is challenging for many reasons including the immense complexity of splicing mechanisms. While recent advances in splicing algorithms have improved the accuracy of splice prediction, predicting the nature and abundance of aberrant splicing remains challenging. As RNA testing becomes more mainstream in the clinical diagnostic setting, the complexities of interpretation are coming to light. Methods: Data from patients undergoing concurrent DNA and RNA testing were retrospectively reviewed for unusual splicing impacts to underscore some of these complexities and serve as exemplars in how to avoid pitfalls in the interpretation of sequence variants. Results: Seven rare variants with unusual splicing impacts are presented: a variant at a consensus donor nucleotide position lacking a splice impact (NF1 c.888+2T>C); a mid-exonic missense variant creating a novel donor site and a cryptic acceptor site resulting in pseudo-intronization (BRIP1 c.727A<G p.Ile243Val); one variant creating a spliceosome switch from U12 to U2 (LZTR1 c.2232G>A p.Ala744Ala); two variants that would be expected to result in nonsense-mediated-mRNA-decay triggering splicing impacts that obviated nonsense-mediated-decay (APC c.1042C>T p.Arg348Ter and BRCA2 c.6762del; c.6816_6841+1534del); and two variants causing splicing impacts through pyrimidine tract optimization (NF1 c.5750-184_5750-178dup and ATM c.3480G>T p.Val1160Val). Conclusions: Paired DNA and RNA testing revealed unexpected splice events altering variant interpretation, expanding our knowledge of clinically important splicing mechanisms and highlighting the benefit of RNA testing. Full article
(This article belongs to the Special Issue From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of Genomics Research)
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Review

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20 pages, 1389 KB  
Review
Psychosocial Factors Involved in Genetic Testing for Rare Diseases: A Scoping Review
by Samantha Strasser, Isabella R. McDonald, Melissa K. Uveges, Sharlene Hesse-Biber, Jordan Keels, Neil Smith and Andrew A. Dwyer
Genes 2025, 16(6), 614; https://doi.org/10.3390/genes16060614 - 22 May 2025
Cited by 1 | Viewed by 2912
Abstract
Background/Objectives: Rare diseases are predominantly genetic in etiology and characterized by a prolonged ‘diagnostic odyssey’. Advances in genetic testing (GT) have helped shorten the time to diagnosis for rare/undiagnosed conditions. We aimed to synthesize the evidence on psychosocial factors related to GT [...] Read more.
Background/Objectives: Rare diseases are predominantly genetic in etiology and characterized by a prolonged ‘diagnostic odyssey’. Advances in genetic testing (GT) have helped shorten the time to diagnosis for rare/undiagnosed conditions. We aimed to synthesize the evidence on psychosocial factors related to GT for rare diseases to inform more person-centered approaches to care. Methods: We conducted a systematic literature search in six databases using structured terms (September 2024). Retrieved articles underwent independent dual review. Data were extracted and collated in tables for analysis. Thematic analysis was used to identify promoters/barriers to GT for patients and families. Findings were validated by a patient advocate and were reported using PRISMA-ScR guidelines. Synthesized findings were mapped to the Theory of Planned Behavior to inform intervention development. Results: Of 1730 retrieved articles, 32 were included for data extraction/synthesis. Studies employed qualitative (n = 19), quantitative (n = 10), and mixed-methods (n = 3) approaches. Nearly all (29/32, 91%) were non-interventional, reporting on decision-making cognitions/processes (19/32, 59%), attitudes/preferences (15/32, 47%), psychosocial impact (6/32, 19%), and knowledge/awareness (4/32, 8%) of pre-conception/prenatal/diagnostic GT and carrier screening. Promoters included understanding GT, ending the diagnostic odyssey, actionable outcomes, personal/family history, altruism, and reproductive decision-making. Barriers included logistical (e.g., distance, cost), psychological burden, perceived lack of benefit, and discrimination/social stigma concerns. Conclusions: Some psychosocial factors related to GT for rare diseases overlap with those in literature on GT for common conditions. Identified factors represent targets for theory-informed, person-centered interventions to support high-quality GT decisions that are informed and aligned with patient/family values and preferences. Full article
(This article belongs to the Special Issue From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of Genomics Research)
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Other

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12 pages, 1239 KB  
Case Report
A Complex Case of Langer–Giedion Syndrome, Cornelia de Lange Syndrome Type 4, and Hereditary Multiple Osteochondromas with Mosaic 8q23.1–q24.12 Deletion
by Samuel David Amio Valientes and Hua Wang
Genes 2026, 17(2), 175; https://doi.org/10.3390/genes17020175 - 31 Jan 2026
Viewed by 788
Abstract
Langer–Giedion syndrome (LGS), also known as trichorhinophalangeal syndrome type II (TRPS II; OMIM #150230), is a contiguous-gene deletion disorder caused by haploinsufficiency of TRPS1 and EXT1. Cornelia de Lange syndrome (CdLS) is genetically heterogeneous; heterozygous variants in RAD21 cause the milder CdLS [...] Read more.
Langer–Giedion syndrome (LGS), also known as trichorhinophalangeal syndrome type II (TRPS II; OMIM #150230), is a contiguous-gene deletion disorder caused by haploinsufficiency of TRPS1 and EXT1. Cornelia de Lange syndrome (CdLS) is genetically heterogeneous; heterozygous variants in RAD21 cause the milder CdLS type 4 phenotype (OMIM #614701). Because RAD21 lies between TRPS1 and EXT1, overlapping phenotypes may arise when all three genes are deleted. We report a unique case of a 4-year-old female presenting with a blended phenotype of Langer–Giedion Syndrome (LGS) and Cornelia de Lange Syndrome (CdLS) type 4. This case is distinct from previously reported 8q deletions in three key aspects: (1) Complex Genomic Architecture: Chromosomal microarray revealed a novel complex rearrangement consisting of a 13.01 Mb mosaic interstitial deletion at 8q23.1–q24.12, flanked by two large duplications (21.5 Mb at 8q11.23–q23.1 and 25.78 Mb at 8q24.12–q24.3). (2) Rare Mosaicism: This represents only the second reported case of mosaicism affecting this contiguous gene region. Notably, the patient demonstrates a “mosaic rescue” effect, where the mosaicism appears to have mitigated the neurodevelopmental phenotype (the patient is bilingual and ambulatory) while failing to protect the skeleton. (3) First Bone-Specific Therapy: The patient suffered from severe, recurrent fractures due to a synergistic “double hit” of TRPS1-related osteopenia and EXT1-related exostoses. We report the first successful use of bisphosphonate therapy (pamidronate) in this specific mosaic profile, which resulted in a complete cessation of fractures during a 12-month follow-up. This case underscores the utility of detailed microarray analysis in complex phenotypes and suggests bisphosphonates as a viable rescue therapy for refractory syndromic osteoporosis. Full article
(This article belongs to the Special Issue From Genetic Mechanisms Discovery to Patient-Centered Care: The Expanse of Genomics Research)
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