PMC:6218809 / 25661-29110 JSONTXT

{"project":"2_test","denotations":[{"id":"30388403-28450586-2049251","span":{"begin":372,"end":373},"obj":"28450586"},{"id":"30388403-30033078-2049252","span":{"begin":1845,"end":1847},"obj":"30033078"},{"id":"30388403-26432246-2049253","span":{"begin":2528,"end":2530},"obj":"26432246"},{"id":"30388403-22974163-2049254","span":{"begin":2532,"end":2534},"obj":"22974163"},{"id":"30388403-22374857-2049255","span":{"begin":2652,"end":2654},"obj":"22374857"},{"id":"30388403-25087610-2049256","span":{"begin":3059,"end":3061},"obj":"25087610"},{"id":"30388403-26481646-2049257","span":{"begin":3063,"end":3065},"obj":"26481646"}],"text":"Discussion\nIn summary, we directly demonstrate that the DUP4 variant has a complex structure involving a duplication of GYPE, deletion of GYPB, and generation of two GYPB/GYPA fusion genes. The evolution of this particular rearrangement remains unclear. A model involving three intermediates has been suggested but none of these putative intermediates have yet been found.5 Given the relatively limited numbers of individuals analyzed for glycophorin structural variation so far, it is possible that these intermediate variants are rare or have been lost from the population. Indeed, given the extensive structural variation seen already at this locus, it seems likely that a high rate of genomic rearrangement generates complex variants that are mostly lost by genetic drift, with a few, such as DUP4, increasing in frequency due to positive selection. Further studies on the extensive variation in Africa are needed to fully characterize the variation at this locus.\nWe show that the DUP4 variant is associated with hemoglobin levels in a community setting indicating protection from malaria. Low levels of hemoglobin indicate anemia, which can reflect sub-clinical levels of malaria infection, and the village studied has a very high prevalence of P. falciparum infection, so our study supports the importance of the DUP4 variant in malaria protection. However, the absence of an association with either the number of clinical episodes of malaria or the parasite load is perhaps more puzzling. This may reflect the lower heritability of these traits compared to hemoglobin levels, and therefore the increased effect of non-genetic variation (Table 1). A recent case-control study of severe malaria in Kenyan children found an association of DUP4 with higher hemoglobin levels but not with parasite load, repeating the results we present here.39 How DUP4 protects against malaria is unknown and alternatively these results may point to a role in directly affecting erythrocyte invasion by the parasite, which is detectable in our cohort, rather than the more general phenotypes such as number of clinical malaria episodes or parasite load.\nWe also show that a novel somatic variant exists (DUP4b) with an extra GYPB/GYPA fusion gene, suggesting that this region may be prone to somatic rearrangements. We cannot rule out a somatic rearrangement in the transformation and culturing of the lymphoblastoid cell line, although it has been shown previously that such genetic changes introduced by EBV transformation are either rare15, 42 or overlap with regions known to undergo extensive programmed somatic rearrangement, such as the immunoglobulin loci.43 It is possible, therefore, that the somatic variant originated in the donor patient given that the HG02554 B-lymphoblastoid cells from Oxford and the Wellcome Sanger Institute were both from the same batch of cells (passage #4, according to Coriell Cell Repositories); recent evidence suggests that such structural variant mosaics are likely to occur at a significant frequency, at least at certain loci.44, 45 We demonstrate that this somatic variant is able to be detected from high coverage short read sequence data, which will allow further analysis of somatic variation at this locus without cell material. Our data raise the intriguing possibility of heightened somatic instability and somatic mosaicism at this locus in DUP4 carriers, which might confer added protection against malaria."}