Abstract
For human/SARS-CoV-2 interactome genes ACE2, TMPRSS2 and BSG, there is a convincing evidence of association in Asians with influenza-induced SARS for TMPRSS2-rs2070788, tag-SNP of the eQTL rs383510. This case illustrates the importance of population genetics and of sequencing data in the design of genetic association studies in different human populations: the high linkage disequilibrium (LD) between rs2070788 and rs383510 is Asian-specific. Leveraging on a combination of genotyping and sequencing data for Native Americans (neglected in genetic studies), we show that while their frequencies of the Asian tag-SNP rs2070788 is, surprisingly, the highest worldwide, it is not in LD with the eQTL rs383510, that therefore, should be directly genotyped in genetic association studies of SARS in populations with Native American ancestry.
Highlights
We performed a systematic review under the terms “[gene name] genetics infection]”, covering articles published until June 4th, 2020 in PubMed and in bioRxiv during 2020 (Figure 1A)
ACE2 and BSG allele frequencies and their regression analyses between population genomic ancestry (Native American, African, European and East Asian) and frequencies of functionally relevant SNPs are presented in Table S2 (A and B) and Table S3 (A and B), respectively
We examined our unpublished dataset of Native American and of admixed Latin Americans for the putative tag-SNP rs2070788 but not for rs383510 because there is no large dataset available for it
Summary
(ii) we annotated SNVs in ACE2, TMPRSS2, and BSG mining and integrating information from 24 biological and biomedical databases, using our bioinformatics tool (MASSA) [Multi-Agent System for SNP Annotation (Soares-Souza, 2014)], to identify functionally relevant variants (Table S1A). (iii) we performed a population genetics analysis of the 48 functionally relevant variants in the ACE2, TMPRSS2 and BSG genes in human populations to detect particular patterns of between-population genetic differentiation and independently of evidence of genetic association between ACE2, TMPRSS2 and BSG variants and infectious diseases, using published and unpublished data from different worldwide populations (Table S1-B), enriched for Latin Americans, who are mainly the product of admixture of Native Americans, Europeans and Africans.
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