Whole Exome Sequencing Identifies New Host Genomic Susceptibility Factors in Empyema Caused by Streptococcus pneumoniae in Children: A Pilot Study

Genes
Antonio SalasGENDRES network

Abstract

Pneumonia is the leading cause of death amongst infectious diseases. Streptococcus pneumoniae is responsible for about 25% of pneumonia cases worldwide, and it is a major cause of childhood mortality. We carried out a whole exome sequencing (WES) study in eight patients with complicated cases of pneumococcal pneumonia (empyema). An initial assessment of statistical association of WES variation with pneumonia was carried out using data from the 1000 Genomes Project (1000G) for the Iberian Peninsula (IBS) as reference controls. Pseudo-replication statistical analyses were carried out using different European control groups. Association tests pointed to single nucleotide polymorphism (SNP) rs201967957 (gene MEIS1; chromosome 2; p-valueIBS = 3.71 × 10-13) and rs576099063 (gene TSPAN15; chromosome 10; p-valueIBS = 2.36 × 10-8) as the best candidate variants associated to pneumococcal pneumonia. A burden gene test of pathogenicity signaled four genes, namely, OR9G9, MUC6, MUC3A and APOB, which carry significantly increased pathogenic variation when compared to controls. By analyzing various transcriptomic data repositories, we found strong supportive evidence for the role of MEIS1, TSPAN15 and APOBR (encoding the receptor of the APOB...Continue Reading

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Citations

Jun 4, 2019·Human Vaccines & Immunotherapeutics·Federico Martinón-TorresRobb Butler
Feb 9, 2020·Intensive Care Medicine·Elie AzoulayUNKNOWN Nine-i Investigators
Apr 25, 2020·International Journal of Molecular Sciences·Ruth Barral-ArcaAntonio Salas

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Datasets Mentioned

BETA
GSE45644

Methods Mentioned

BETA
exome sequencing
X ray
genotyping
Exon Sequencing
PCR
MDS

Software Mentioned

PolyPhen
HaplotypeCaller
Wheeler Aligner ( BWA )
stats
GATK
house R
oligo
Burrows
R
Ensembl

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