Poking COVID-19: Insights on Genomic Constraints among Immune-Related Genes between Qatari and Italian Populations

Host genomic information, specifically genomic variations, may characterize susceptibility to disease and identify people with a higher risk of harm, leading to better targeting of care and vaccination. Italy was the epicentre for the spread of COVID-19 in Europe, the first country to go into a national lockdown and has one of the highest COVID-19 associated mortality rates. Qatar, on the other hand has a very low mortality rate. In this study, we compared whole-genome sequencing data of 14398 adults and Qatari-national to 925 Italian individuals. We also included in the comparison whole-exome sequence data from 189 Italian laboratory-confirmed COVID-19 cases. We focused our study on a curated list of 3619 candidate genes involved in innate immunity and host-pathogen interaction. Two population-gene metric scores, the Delta Singleton-Cohort variant score (DSC) and Sum Singleton-Cohort variant score (SSC), were applied to estimate the presence of selective constraints in the Qatari population and in the Italian cohorts. Results based on DSC and SSC metrics demonstrated a different selective pressure on three genes (MUC5AC, ABCA7, FLNA) between Qatari and Italian populations. This study highlighted the genetic differences between Qatari and Italian populations and identified a subset of genes involved in innate immunity and host-pathogen interaction.

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Poking COVID-19: insights on genomic constraints among immune-related genes between Qatari and Italian populations

10.1101/2021.10.04.21264507 ◽

2021 ◽

Author(s):

Hamdi Mbarek ◽

Massimiliano Cocca ◽

Yasser Al Sarraj ◽

Chadi Saad ◽

Massimo Mezzavilla ◽

...

Keyword(s):

Innate Immunity ◽

Sequence Data ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Host Pathogen Interaction ◽

Whole Exome ◽

Exome Sequence Data ◽

Host Pathogen ◽

Immune Related Genes ◽

Exome Sequence

AbstractHost genomic information, specifically genomic variations, may characterize susceptibility to disease and identify people with a higher risk of harm, leading to better targeting of care and vaccination. Italy was the epicentre for the spread of COVID-19 in Europe, the first country to go into a national lockdown and has one of the highest COVID-19 associated mortality rates. Qatar, on the other hand has a very low mortality rate. In this study, we compared whole-genome sequencing data of 14398 adults and Qatari-national to 925 Italian individuals. We also included in the comparison whole-exome sequence data from 189 Italian laboratory confirmed COVID-19 cases. We focused our study on a curated list of 3619 candidate genes involved in innate immunity and host-pathogen interaction. Two population-gene metric scores, the Delta Singleton-Cohort variant score (DSC) and Sum Singleton-Cohort variant score (SSC), were applied to estimate the presence of selective constraints in the Qatari population and in the Italian cohorts. Results based on DSC SSC metrics demonstrated a different selective pressure on three genes (MUC5AC, ABCA7, FLNA) between Qatari and Italian populations. This study highlighted the genetic differences between Qatari and Italian populations and identified a subset of genes involved in innate immunity and host-pathogen interaction.

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ALSgeneScanner: a pipeline for the analysis and interpretation of DNA NGS data of ALS patients

10.1101/378158 ◽

2018 ◽

Author(s):

Alfredo Iacoangeli ◽

Ahmad Al Khleifat ◽

William Sproviero ◽

Aleksey Shatunov ◽

Ashley R Jones ◽

...

Keyword(s):

Motor Neurons ◽

Health Care Professionals ◽

Sequence Data ◽

Whole Genome Sequence ◽

Next Generation Sequencing Data ◽

Sequencing Data ◽

Whole Exome ◽

Exome Sequence Data ◽

Als Patients ◽

Ngs Data

AbstractAmyotrophic lateral sclerosis (ALS, MND) is a neurodegenerative disease of upper and lower motor neurons resulting in death from neuromuscular respiratory failure, typically within two years of first symptoms. Genetic factors are an important cause of ALS, with variants in more than 25 genes having strong evidence, and weaker evidence available for variants in more than 120 genes. With the increasing availability of Next-Generation sequencing data, non-specialists, including health care professionals and patients, are obtaining their genomic information without a corresponding ability to analyse and interpret it. Furthermore, the relevance of novel or existing variants in ALS genes is not always apparent. Here we present ALSgeneScanner, a tool that is easy to install and use, able to provide an automatic, detailed, annotated report, on a list of ALS genes from whole genome sequence data in a few hours and whole exome sequence data in about one hour on a readily available mid-range computer. This will be of value to non-specialists and aid in the interpretation of the relevance of novel and existing variants identified in DNA sequencing data.

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Comprehensive blood group antigen profile predictions for Western Desert Indigenous Australians from whole exome sequence data

Transfusion ◽

10.1111/trf.15047 ◽

2018 ◽

Vol 59 (2) ◽

pp. 768-778 ◽

Cited By ~ 3

Author(s):

Elizna M. Schoeman ◽

Eileen V. Roulis ◽

Maree A. Perry ◽

Robert L. Flower ◽

Catherine A. Hyland

Keyword(s):

Blood Group ◽

Sequence Data ◽

Blood Group Antigen ◽

Western Desert ◽

Indigenous Australians ◽

Whole Exome ◽

Exome Sequence Data ◽

Antigen Profile ◽

Exome Sequence

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Practical Experience of the Application of a Weighted Burden Test to Whole Exome Sequence Data for Obesity and Schizophrenia

Annals of Human Genetics ◽

10.1111/ahg.12135 ◽

2015 ◽

Vol 80 (1) ◽

pp. 38-49 ◽

Cited By ~ 13

Author(s):

David Curtis ◽

Keyword(s):

Sequence Data ◽

Practical Experience ◽

Whole Exome ◽

Exome Sequence Data ◽

Burden Test ◽

Exome Sequence

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Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort

Molecular Neuropsychiatry ◽

10.1159/000454773 ◽

2017 ◽

Vol 3 (1) ◽

pp. 1-11 ◽

Cited By ~ 4

Author(s):

Eric T. Monson ◽

Mehdi Pirooznia ◽

Jennifer Parla ◽

Melissa Kramer ◽

Fernando S. Goes ◽

...

Keyword(s):

Bipolar Disorder ◽

Attempted Suicide ◽

Sequence Data ◽

Whole Exome ◽

Exome Sequence Data ◽

Exome Sequence

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Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder

The American Journal of Human Genetics ◽

10.1016/j.ajhg.2013.09.001 ◽

2013 ◽

Vol 93 (4) ◽

pp. 607-619 ◽

Cited By ~ 105

Author(s):

Christopher S. Poultney ◽

Arthur P. Goldberg ◽

Elodie Drapeau ◽

Yan Kou ◽

Hala Harony-Nicolas ◽

...

Keyword(s):

Autism Spectrum Disorder ◽

Sequence Data ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Whole Exome ◽

Exome Sequence Data ◽

Exome Sequence

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Whole exome sequencing analysis reveals TRPV3 as a risk factor for cardioembolic stroke/subtitle

Thrombosis and Haemostasis ◽

10.1160/th16-02-0113 ◽

2016 ◽

Vol 116 (12) ◽

pp. 1165-1771 ◽

Cited By ~ 4

Author(s):

Caty Carrera ◽

Jordi Jiménez-Conde ◽

Sophia Derdak ◽

Kelly Rabionet ◽

Cristofol Vives-Bauzá ◽

...

Keyword(s):

Exome Sequencing ◽

Sequence Data ◽

Cardioembolic Stroke ◽

P Value ◽

Sequencing Analysis ◽

New Genes ◽

Whole Exome ◽

Exome Sequence Data ◽

Exome Sequence ◽

New Strategies

SummaryGenetic studies suggest that hundreds of genes associated with stroke remain unidentified. Exome sequencing proves useful for finding new genes associated with stroke. We aimed to find new genetic risk factors for cardioembolic stroke by analysing exome sequence data using new strategies. For discovery, we analysed 42 cardioembolic stroke cases and controls with extreme phenotypes (cohort 1), and for replication, 32 cardioembolic stroke cases and controls (cohort 2) using the SeqCapExome capture kit. We then analysed the replicated genes in two new cohorts that comprised 834 cardioembolic strokes and controls (cohort 3) and 64,373 cardioembolic strokes and controls (cohort 4). Transcriptomic in-silico functional analyses were also performed. We found 26 coding regions with a higher frequency of mutations in cardioembolic strokes after correcting for the number of mutations found in the whole exome of every patient. The TRPV3 gene was associated with cardioembolic stroke after replication of exome sequencing analysis (p-value-discovery: 0.018, p-value-replication: 0.014). The analysis of the TRPV3 gene using polymorphisms in cohort 3 and 4 revealed two polymorphisms associated with cardioembolic stroke in both cohorts, the most significant polymorphism being rs151091899 (p-value: 3.1 × 10−05; odds ratio: 5.4) in cohort 3. The genotype of one polymorphism of TRPV3 was associated with a differential expression of genes linked to cardiac malformations. In conclusion, new strategies using exome sequence data have revealed TRPV3 as a new gene associated with cardioembolic stroke. This strategy among others might be useful in finding new genes associated with complex genetic diseases.

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