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Utilizing RNA-Seq and Genome Sequencing to Uncover Complexities of Genetic Disorders

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: closed (30 November 2020) | Viewed by 6674

Special Issue Editors

Ms. Divya Kalra

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Guest Editor
Baylor College of Medicine, Houston, TX, USA
Dr. Vipin Menon

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Guest Editor
Baylor College of Medicine, Houston, TX, USA

Special Issue Information

Dear Colleagues,

With lowering sequencing costs, next-generation sequencing (NGS) technologies have been extensively implemented, leading to the generation of a substantial amount of sequencing data. Mining this data by investigating mechanisms and variations in the genome can help us better understand how certain variants contribute to a phenotype and the genetic pathways involved to determine the underlying causes of a genetic disorder.

Various NGS applications, particularly whole-genome (WGS) and exome sequencing, are powerful tools for diagnosing the underlying causes of genetic disorders. However, despite the recent advances in NGS technologies, their diagnostic rate is limited. Augmenting it with RNA-Seq can facilitate in resolving the genetic basis of unsolved diseases, narrowing the diagnostic gap. Additionally, RNA-Seq can detect a wide variety of RNA species, including pre-mRNA, mRNA, and non-coding RNAs (ncRNAs), allowing for a deeper understanding of their role in the progression of a genetic disorder. 

This Special Issue invites original research and reviews on topics utilizing the power of RNA-Seq in addition to other sequencing methods to determine causative variants in different diseases, including cancer, in research as well as in clinical applications. This encompasses the use of short- and long-read sequencing technologies, implementation of innovative sequencing methodologies, robust quality control methods and bioinformatics tools, and approaches to analyze the data and develop pipelines.

Ms. Divya Kalra
Dr. Vipin Menon
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 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • RNA-Seq
  • genomics
  • transcriptomics
  • long-read sequencing
  • short-read sequencing
  • Mendelian disorders
  • cancer
  • genetic disorders
  • clinical
  • diagnosis
  • non-coding RNA

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Published Papers (2 papers)

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Research

17 pages, 1461 KiB  
Article
A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes
by Gennady Vasiliev, Irina Chadaeva, Dmitry Rasskazov, Petr Ponomarenko, Ekaterina Sharypova, Irina Drachkova, Anton Bogomolov, Ludmila Savinkova, Mikhail Ponomarenko, Nikolay Kolchanov, Alexander Osadchuk, Dmitry Oshchepkov and Ludmila Osadchuk
Int. J. Mol. Sci. 2021, 22(5), 2346; https://doi.org/10.3390/ijms22052346 - 26 Feb 2021
Cited by 7 | Viewed by 2457
Abstract
Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq [...] Read more.
Earlier, after our bioinformatic analysis of single-nucleotide polymorphisms of TATA-binding protein-binding sites within gene promoters on the human Y chromosome, we suggested that human reproductive potential diminishes during self-domestication. Here, we implemented bioinformatics models of human diseases using animal in vivo genome-wide RNA-Seq data to compare the effect of co-directed changes in the expression of orthologous genes on human reproductive potential and during the divergence of domestic and wild animals from their nearest common ancestor (NCA). For example, serotonin receptor 3A (HTR3A) deficiency contributes to sudden death in pregnancy, consistently with Htr3a underexpression in guinea pigs (Cavia porcellus) during their divergence from their NCA with cavy (C. aperea). Overall, 25 and three differentially expressed genes (hereinafter, DEGs) in domestic animals versus 11 and 17 DEGs in wild animals show the direction consistent with human orthologous gene-markers of reduced and increased reproductive potential. This indicates a reliable association between DEGs in domestic animals and human orthologous genes reducing reproductive potential (Pearson’s χ2 test p < 0.001, Fisher’s exact test p < 0.05, binomial distribution p < 0.0001), whereas DEGs in wild animals uniformly match human orthologous genes decreasing and increasing human reproductive potential (p > 0.1; binomial distribution), thus enforcing the norm (wild type). Full article
(This article belongs to the Special Issue Utilizing RNA-Seq and Genome Sequencing to Uncover Complexities of Genetic Disorders)
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24 pages, 1934 KiB  
Article
Transcriptomic Changes Related to Cellular Processes with Particular Emphasis on Cell Activation in Lysosomal Storage Diseases from the Group of Mucopolysaccharidoses
by Estera Rintz, Lidia Gaffke, Magdalena Podlacha, Joanna Brokowska, Zuzanna Cyske, Grzegorz Węgrzyn and Karolina Pierzynowska
Int. J. Mol. Sci. 2020, 21(9), 3194; https://doi.org/10.3390/ijms21093194 - 30 Apr 2020
Cited by 22 | Viewed by 3689
Abstract
Although mucopolysaccharidoses (MPS), inherited metabolic diseases from the group of lysosomal storage diseases (LSD), are monogenic disorders, recent studies indicated that their molecular mechanisms are complicated. Storage of glycosaminoglycans (GAGs), arising from a deficiency in one of the enzymes involved in the degradation [...] Read more.
Although mucopolysaccharidoses (MPS), inherited metabolic diseases from the group of lysosomal storage diseases (LSD), are monogenic disorders, recent studies indicated that their molecular mechanisms are complicated. Storage of glycosaminoglycans (GAGs), arising from a deficiency in one of the enzymes involved in the degradation of these compounds, is the primary cause of each MPS type. However, dysfunctions of various cellular organelles and disturbance of cellular processes have been reported which contribute considerably to pathomechanisms of the disease. Here, we present a complex transcriptomic analysis in which all types and subtypes of MPS were investigated, with special emphasis on genes related to cell activation processes. Complex changes in expression of these genes were found in fibroblasts of all MPS types, with number of transcripts revealing higher or lower levels (relative to control fibroblasts) between 19 and over 50, depending on MPS type. Genes in which expression was significantly affected in most MPS types code for proteins involved in following processes, classified according to Gene Ontology knowledge database: cell activation, cell growth, cell recognition, and cell division. Levels of some transcripts (including CD9, CLU, MME and others) were especially significantly changed (over five times relative to controls). Our results are discussed in the light of molecular pathomechanisms of MPS, indicating that secondary and/or tertiary changes, relative to GAG storage, might significantly modulate cellular dysfunctions and contribute to molecular mechanisms of the disease. This may influence the efficacy of various therapies and suggests why various treatments are not fully effective in improving the complex symptoms of MPS. Full article
(This article belongs to the Special Issue Utilizing RNA-Seq and Genome Sequencing to Uncover Complexities of Genetic Disorders)
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