Precision medicine and COVID-19: importance of host genome profiling and bioinformatics
Апстракт
Clinical picture and course of the disease in patients with COVID-19 vary from asymptomatic to lethal.
Precision medicine could discover the cause of this phenomenon by analyzing the individual genomic
profiles of the patients.
We aimed to understand a host genetic component of COVID-19 focusing on variants in genes encoding
proteases and genes involved in innate immunity, important for susceptibility and resistance to SARS-CoV-2
infection. Also, we wanted to identify phamracogenes and pharmacogenomics markers associated with
drugs used for COVID-19 treatment in different clinical protocols in Serbia, and to compare the results
with various world populations.
Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained
using TruSight One Gene Panel (Illumina). Variants in genes encoding proteases and genes involved in innate
immunity were identified and analysed in silico (PolyPhen-2, SIFT, MutPred2, Swiss-Pdb Viewer) to predict
t...he impact of the variants to the structure and/or function of proteins. Genotype data from Serbian population
was compared with European and 4 super-populations (total 2504 subjects). Data were extracted from
VCF files of Phase 3 variant calls of the 1000 Genomes Project (1kGP) sample collection via Ensembl Data
Slicer Tool. The level of population genetic variability at each selected loci was examined using the maximal
global differences in minor allele frequencies (delta MAF) calculated by subtracting the maximum and the
minimum MAF across analyzed population groups, and Fst statistics. Fisher exact test was used to measure
differences in genotypes distributions between Serbian and 1kGP populations, applying Bonferoni correction.
R software was utilized for genotype data manipulation and statistical calculations.
Based on high alternative allele frequencies in population and the functional effect of the variants, we identified
variants in genes encoding proteases and involved in the innate immunity that might be relevant for the
host response to SARS-CoV-2 infection. The potential pharmacogenomics markers in pharmacogenes relevant
for COVID-19 treatment were also identified. Bioinformatics tools integrated into precision medicine
could contribute to better understanding of inter-individual and population-specific genetic susceptibility and
resistance to the SARS-CoV-2 infection, therapy response inconsistencies, and could be applied to improve
the outcome of the COVID-19 patients.
Кључне речи:
COVID-19 / precision medicine / bioinformatics / host genomics / population pharmacogenomicsИзвор:
Biologia Serbica, 2021, 43, 1 (Special Edition), 31-Издавач:
- Novi Sad : Faculty of Sciences, Department of Biology and Ecology
Напомена:
- Book of Abstracts: Belgrade BioInformatics Conference 2021
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Zukić, Branka AU - Kotur, Nikola AU - Stanković, Biljana PY - 2021 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1878 AB - Clinical picture and course of the disease in patients with COVID-19 vary from asymptomatic to lethal. Precision medicine could discover the cause of this phenomenon by analyzing the individual genomic profiles of the patients. We aimed to understand a host genetic component of COVID-19 focusing on variants in genes encoding proteases and genes involved in innate immunity, important for susceptibility and resistance to SARS-CoV-2 infection. Also, we wanted to identify phamracogenes and pharmacogenomics markers associated with drugs used for COVID-19 treatment in different clinical protocols in Serbia, and to compare the results with various world populations. Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Variants in genes encoding proteases and genes involved in innate immunity were identified and analysed in silico (PolyPhen-2, SIFT, MutPred2, Swiss-Pdb Viewer) to predict the impact of the variants to the structure and/or function of proteins. Genotype data from Serbian population was compared with European and 4 super-populations (total 2504 subjects). Data were extracted from VCF files of Phase 3 variant calls of the 1000 Genomes Project (1kGP) sample collection via Ensembl Data Slicer Tool. The level of population genetic variability at each selected loci was examined using the maximal global differences in minor allele frequencies (delta MAF) calculated by subtracting the maximum and the minimum MAF across analyzed population groups, and Fst statistics. Fisher exact test was used to measure differences in genotypes distributions between Serbian and 1kGP populations, applying Bonferoni correction. R software was utilized for genotype data manipulation and statistical calculations. Based on high alternative allele frequencies in population and the functional effect of the variants, we identified variants in genes encoding proteases and involved in the innate immunity that might be relevant for the host response to SARS-CoV-2 infection. The potential pharmacogenomics markers in pharmacogenes relevant for COVID-19 treatment were also identified. Bioinformatics tools integrated into precision medicine could contribute to better understanding of inter-individual and population-specific genetic susceptibility and resistance to the SARS-CoV-2 infection, therapy response inconsistencies, and could be applied to improve the outcome of the COVID-19 patients. PB - Novi Sad : Faculty of Sciences, Department of Biology and Ecology C3 - Biologia Serbica T1 - Precision medicine and COVID-19: importance of host genome profiling and bioinformatics IS - 1 (Special Edition) SP - 31 VL - 43 UR - https://hdl.handle.net/21.15107/rcub_imagine_1878 ER -
@conference{ author = "Zukić, Branka and Kotur, Nikola and Stanković, Biljana", year = "2021", abstract = "Clinical picture and course of the disease in patients with COVID-19 vary from asymptomatic to lethal. Precision medicine could discover the cause of this phenomenon by analyzing the individual genomic profiles of the patients. We aimed to understand a host genetic component of COVID-19 focusing on variants in genes encoding proteases and genes involved in innate immunity, important for susceptibility and resistance to SARS-CoV-2 infection. Also, we wanted to identify phamracogenes and pharmacogenomics markers associated with drugs used for COVID-19 treatment in different clinical protocols in Serbia, and to compare the results with various world populations. Genotype information of 143 individuals of Serbian origin was extracted from database previously obtained using TruSight One Gene Panel (Illumina). Variants in genes encoding proteases and genes involved in innate immunity were identified and analysed in silico (PolyPhen-2, SIFT, MutPred2, Swiss-Pdb Viewer) to predict the impact of the variants to the structure and/or function of proteins. Genotype data from Serbian population was compared with European and 4 super-populations (total 2504 subjects). Data were extracted from VCF files of Phase 3 variant calls of the 1000 Genomes Project (1kGP) sample collection via Ensembl Data Slicer Tool. The level of population genetic variability at each selected loci was examined using the maximal global differences in minor allele frequencies (delta MAF) calculated by subtracting the maximum and the minimum MAF across analyzed population groups, and Fst statistics. Fisher exact test was used to measure differences in genotypes distributions between Serbian and 1kGP populations, applying Bonferoni correction. R software was utilized for genotype data manipulation and statistical calculations. Based on high alternative allele frequencies in population and the functional effect of the variants, we identified variants in genes encoding proteases and involved in the innate immunity that might be relevant for the host response to SARS-CoV-2 infection. The potential pharmacogenomics markers in pharmacogenes relevant for COVID-19 treatment were also identified. Bioinformatics tools integrated into precision medicine could contribute to better understanding of inter-individual and population-specific genetic susceptibility and resistance to the SARS-CoV-2 infection, therapy response inconsistencies, and could be applied to improve the outcome of the COVID-19 patients.", publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology", journal = "Biologia Serbica", title = "Precision medicine and COVID-19: importance of host genome profiling and bioinformatics", number = "1 (Special Edition)", pages = "31", volume = "43", url = "https://hdl.handle.net/21.15107/rcub_imagine_1878" }
Zukić, B., Kotur, N.,& Stanković, B.. (2021). Precision medicine and COVID-19: importance of host genome profiling and bioinformatics. in Biologia Serbica Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 31. https://hdl.handle.net/21.15107/rcub_imagine_1878
Zukić B, Kotur N, Stanković B. Precision medicine and COVID-19: importance of host genome profiling and bioinformatics. in Biologia Serbica. 2021;43(1 (Special Edition)):31. https://hdl.handle.net/21.15107/rcub_imagine_1878 .
Zukić, Branka, Kotur, Nikola, Stanković, Biljana, "Precision medicine and COVID-19: importance of host genome profiling and bioinformatics" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):31, https://hdl.handle.net/21.15107/rcub_imagine_1878 .