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Genomic Research of Rare Diseases

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: 30 December 2024 | Viewed by 1324

Special Issue Editors


E-Mail Website
Guest Editor
Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
Interests: genomics; rare disease; bioinformatics; epigenomics

E-Mail Website
Guest Editor
Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
Interests: genomics; rare disease; mechanistic and structural biology; bioinformatics

Special Issue Information

Dear Colleagues,

There are over 7000 rare diseases impacting over 300 million people worldwide. The ubiquity of whole exome and genome sequencing has transformed rare disease research and shortened lengthy diagnostic odysseys and are leading to changes in disease management, yet 60–70% of rare disease patients remain undiagnosed after genomic testing. Furthermore, the validation of variants of uncertain significance in candidate genes remains a tedious and lengthy process. Increasingly, the integration of multi-omics data, the reanalysis of prior genomic testing, emerging technologies, and computational approaches are contributing to rare disease diagnostics and enabling precision medicine.

This Special Issue aims to highlight the latest research and innovation in rare diseases, in particular, in the areas of genomic and multi-omics approaches as well as mechanistic research that aims to validate genomic findings. We invite original research, innovative methodologies, case studies, up-to-date reviews, meta-analyses, and discussions about therapeutic implications of genomic findings.

Dr. Shira Rockowitz
Dr. Piotr Sliz
Guest Editors

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Keywords

  • rare disease ontology
  • variants of uncertain significance
  • candidate genes
  • whole genome sequencing
  • long read whole genome sequencing
  • machine learning
  • multi-omics

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Published Papers (2 papers)

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Research

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11 pages, 2266 KiB  
Article
Erythropoiesis and Gene Expression Analysis in Erythroid Progenitor Cells Derived from Patients with Hemoglobin H/Constant Spring Disease
by Narawich Wongkhammul, Pinyaphat Khamphikham, Siripong Tongjai, Adisak Tantiworawit, Kanda Fanhchaksai, Somsakul Pop Wongpalee, Alisa Tubsuwan, Supawadee Maneekesorn and Pimlak Charoenkwan
Int. J. Mol. Sci. 2024, 25(20), 11246; https://doi.org/10.3390/ijms252011246 - 19 Oct 2024
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Abstract
Hemoglobin H/Constant Spring (Hb H/CS) disease represents a form of non-deletional Hb H disease characterized by chronic hemolytic anemia that ranges from moderate to severe and may lead to transfusion-dependent thalassemia. To study the underlying mechanisms of this disease, we conducted an analysis [...] Read more.
Hemoglobin H/Constant Spring (Hb H/CS) disease represents a form of non-deletional Hb H disease characterized by chronic hemolytic anemia that ranges from moderate to severe and may lead to transfusion-dependent thalassemia. To study the underlying mechanisms of this disease, we conducted an analysis of erythropoiesis and gene expression in erythroid progenitor cells derived from CD34+ hematopoietic stem/progenitor cells from patients with Hb H/CS disease and normal controls. Twelve patients with Hb H/CS disease and five normal controls were enrolled. Peripheral blood samples were collected to isolate CD34+ hematopoietic stem/progenitor cells for the analysis of cell proliferation and differentiation. Six samples from patients with Hb H/CS disease and three controls were subsequently studied for gene expression by next generation sequencing analysis. Erythroid progenitor cells derived from patients with Hb H/CS disease exhibited a trend towards increased rates of erythroid proliferation and decreased cell viability compared to those from controls. Moreover, erythroid progenitor cells derived from patients with Hb H/CS disease demonstrated delayed terminal differentiation. Gene expression profiling revealed elevated levels of genes encoding molecular chaperones, including the heat shock protein genes (HSPs) and the chaperonin containing TCP-1 subunit genes (CCTs) in the Hb H/CS disease group. In summary, erythroid progenitor cells derived from patients with Hb H/CS disease exhibit a trend towards heightened erythroid proliferation, diminished cell viability, and delayed terminal differentiation. Additionally, the increased expression of genes encoding molecular chaperones was observed, providing information on potential underlying pathophysiological mechanisms. Full article
(This article belongs to the Special Issue Genomic Research of Rare Diseases)
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23 pages, 1191 KiB  
Perspective
Estimating the Number of Polygenic Diseases Among Six Mutually Exclusive Entities of Non-Tumors and Cancer
by C. I. Edvard Smith, Jan A. Burger and Rula Zain
Int. J. Mol. Sci. 2024, 25(22), 11968; https://doi.org/10.3390/ijms252211968 - 7 Nov 2024
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Abstract
In the era of precision medicine with increasing amounts of sequenced cancer and non-cancer genomes of different ancestries, we here enumerate the resulting polygenic disease entities. Based on the cell number status, we first identified six fundamental types of polygenic illnesses, five of [...] Read more.
In the era of precision medicine with increasing amounts of sequenced cancer and non-cancer genomes of different ancestries, we here enumerate the resulting polygenic disease entities. Based on the cell number status, we first identified six fundamental types of polygenic illnesses, five of which are non-cancerous. Like complex, non-tumor disorders, neoplasms normally carry alterations in multiple genes, including in ‘Drivers’ and ‘Passengers’. However, tumors also lack certain genetic alterations/epigenetic changes, recently named ‘Goners’, which are toxic for the neoplasm and potentially constitute therapeutic targets. Drivers are considered essential for malignant transformation, whereas environmental influences vary considerably among both types of polygenic diseases. For each form, hyper-rare disorders, defined as affecting <1/108 individuals, likely represent the largest number of disease entities. Loss of redundant tumor-suppressor genes exemplifies such a profoundly rare mutational event. For non-tumor, polygenic diseases, pathway-centered taxonomies seem preferable. This classification is not readily feasible in cancer, but the inclusion of Drivers and possibly also of epigenetic changes to the existing nomenclature might serve as initial steps in this direction. Based on the detailed genetic alterations, the number of polygenic diseases is essentially countless, but different forms of nosologies may be used to restrict the number. Full article
(This article belongs to the Special Issue Genomic Research of Rare Diseases)
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