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Genomics of Disease Risk in Diverse Populations
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Genomics of Disease Risk in Diverse Populations

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

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 10594

Special Issue Editors

Prof. Dr. Nora Franceschini

E-Mail Website
Guest Editor
Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
Interests: diverse population; genetics; omics; trans-ethnic analyses; admixture bioinformatics; complex traits
Prof. Dr. Elizabeth Blue

E-Mail Website
Guest Editor
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
Interests: statistical genetics; genetic epidemiology; complex traits; rare disease genetics; variant annotation and interpretation; population genetics

Special Issue Information

There has been an increased interest in studying the genetic determinants of complex traits in diverse populations to uncover mechanisms explaining the uneven distribution in disease risk across populations. Recent studies suggest that the landscape of genetic regulation of gene expression varies across populations. Populations also vary in their DNA make-up. The Special Issue on Genomics of Disease Risk in Diverse Populations will accept manuscript submissions of human studies that highlight populations of diverse (non-European) ancestry. Topics of interest include but are not limited to: genome-wide studies of complex traits using association and admixture approaches, gene expression variation across populations, studies that integrate high-dimensional multi-omics with genotypes and traits, bioinformatics studies using gene expression or epigenetic data that are specific to a diverse population, and statistical methods that account for genetic differences across populations. Trans-ethnic studies should demonstrate the contribution of a diverse population to main findings. Studies of selected populations for which the genetic architecture is less known are encouraged to apply.

Prof. Dr. Nora Franceschini
Prof. Dr. Elizabeth Blue
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. 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

  • Admixture mapping
  • Trans-ethnic analyses
  • Diverse Populations
  • Genetic architecture
  • Disease Risk
  • Personalized Medicine
  • Human diversity

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Published Papers (2 papers)

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Research

21 pages, 3624 KiB  
Article
Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations
by Jia Wen, Munan Xie, Bryce Rowland, Jonathan D. Rosen, Quan Sun, Jiawen Chen, Amanda L. Tapia, Huijun Qian, Madeline H. Kowalski, Yue Shan, Kristin L. Young, Marielisa Graff, Maria Argos, Christy L. Avery, Stephanie A. Bien, Steve Buyske, Jie Yin, Hélène Choquet, Myriam Fornage, Chani J. Hodonsky, Eric Jorgenson, Charles Kooperberg, Ruth J. F. Loos, Yongmei Liu, Jee-Young Moon, Kari E. North, Stephen S. Rich, Jerome I. Rotter, Jennifer A. Smith, Wei Zhao, Lulu Shang, Tao Wang, Xiang Zhou, Alexander P. Reiner, Laura M. Raffield and Yun Liadd Show full author list remove Hide full author list
Genes 2021, 12(7), 1049; https://doi.org/10.3390/genes12071049 - 8 Jul 2021
Cited by 9 | Viewed by 4583
Abstract
Background: Thousands of genetic variants have been associated with hematological traits, though target genes remain unknown at most loci. Moreover, limited analyses have been conducted in African ancestry and Hispanic/Latino populations; hematological trait associated variants more common in these populations have likely been [...] Read more.
Background: Thousands of genetic variants have been associated with hematological traits, though target genes remain unknown at most loci. Moreover, limited analyses have been conducted in African ancestry and Hispanic/Latino populations; hematological trait associated variants more common in these populations have likely been missed. Methods: To derive gene expression prediction models, we used ancestry-stratified datasets from the Multi-Ethnic Study of Atherosclerosis (MESA, including n = 229 African American and n = 381 Hispanic/Latino participants, monocytes) and the Depression Genes and Networks study (DGN, n = 922 European ancestry participants, whole blood). We then performed a transcriptome-wide association study (TWAS) for platelet count, hemoglobin, hematocrit, and white blood cell count in African (n = 27,955) and Hispanic/Latino (n = 28,324) ancestry participants. Results: Our results revealed 24 suggestive signals (p < 1 × 10−4) that were conditionally distinct from known GWAS identified variants and successfully replicated these signals in European ancestry subjects from UK Biobank. We found modestly improved correlation of predicted and measured gene expression in an independent African American cohort (the Genetic Epidemiology Network of Arteriopathy (GENOA) study (n = 802), lymphoblastoid cell lines) using the larger DGN reference panel; however, some genes were well predicted using MESA but not DGN. Conclusions: These analyses demonstrate the importance of performing TWAS and other genetic analyses across diverse populations and of balancing sample size and ancestry background matching when selecting a TWAS reference panel. Full article
(This article belongs to the Special Issue Genomics of Disease Risk in Diverse Populations)
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12 pages, 1287 KiB  
Article
Genetic Variant c.245A>G (p.Asn82Ser) in GIPC3 Gene Is a Frequent Cause of Hereditary Nonsyndromic Sensorineural Hearing Loss in Chuvash Population
by Nika V. Petrova, Andrey V. Marakhonov, Natalia V. Balinova, Anna V. Abrukova, Fedor A. Konovalov, Sergey I. Kutsev and Rena A. Zinchenko
Genes 2021, 12(6), 820; https://doi.org/10.3390/genes12060820 - 27 May 2021
Cited by 5 | Viewed by 3232
Abstract
Hereditary nonsyndromic sensorineural hearing loss is a disease in which hearing loss occurs due to damage to the organ of the inner ear, the auditory nerve, or the center in the brain that is responsible for the perception of sound, characterized by wide [...] Read more.
Hereditary nonsyndromic sensorineural hearing loss is a disease in which hearing loss occurs due to damage to the organ of the inner ear, the auditory nerve, or the center in the brain that is responsible for the perception of sound, characterized by wide locus and allelic heterogeneity and different types of inheritance. Given the diversity of population of the Russian Federation, it seems necessary to study the ethnic characteristics of the molecular causes of the disease. The aim is to study the molecular and genetic causes of hereditary sensorineural hearing loss in Chuvash, the fifth largest ethnic group in Russia. DNA samples of 26 patients from 21 unrelated Chuvash families from the Republic of Chuvashia, in whom the diagnosis of hereditary sensorineural hearing loss had been established, were analyzed using a combination of targeted Sanger sequencing, multiplex ligase-dependent probe amplification, and whole exome sequencing. The homozygous variant NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) is the major molecular cause of hereditary sensorineural hearing loss in 23% of Chuvash patients (OMIM #601869). Its frequency was 25% in patients and 1.1% in healthy Chuvash population. Genotyping of the NM_133261.3(GIPC3):c.245A>G (p.Asn82Ser) variant in five neighboring populations from the Volga-Ural region (Russian, Udmurt, Mary, Tatar, Bushkir) found no evidence that this variant is common in those populations. Full article
(This article belongs to the Special Issue Genomics of Disease Risk in Diverse Populations)
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