High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies
No Thumbnail Available
Date
2020
Journal Title
Journal ISSN
Volume Title
Publisher
Experimental Biology and Medicine
Abstract
Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as
receptors for pathogens of major public health interest, including Plasmodium sp., Babesia
sp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural
rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in
East African populations, has been linked with a 40% reduction in risk for severe malaria.
Apart from Dantu, other large structural variants exist, with the most common being deletion
of the whole GYPB gene and its surrounding region, resulting in multiple different deletion
forms. In West Africa particularly, these deletions are estimated to account for between 5
and 15% of the variation in different populations, mostly attributed to the forms known as
DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution
of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the
development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well
as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from
three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and
DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying
specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic
association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and
other diseases.
Description
Keywords
Glycophorins, WACCBIP_NCDS, University of Ghana, Felix Ansah, Nicholas Amoako, malaria, Plasmodium, red blood cell, invasion, GYPB deletion
Citation
Amuzu DS, Rockett KA, Leffler EM, et al. High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies. Experimental Biology and Medicine. 2021;246(8):916-928. doi:10.1177/1535370220968545