Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data

Abstract

Background: The -α3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study, we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.

Non-glycemic genetic effects on HbA1c and clinical glycemic status in African ancestry: VA Million Veteran Program

“…6,8,24 Fifth, -α3.7 is difficult to impute and its R 2 from MVP imputation was only 0.773, but that should result in false negatives rather than false positives. 11,25,26 Finally, due to the paucity in capturing pre-diabetes by ICD codes in the CDW, we could not determine whether G202A carriers had been clinically designated as having pre-diabetes. Consequently, we may have over-estimated the proportion of patients in pre-diabetes who are misguided by HbA1c as having normoglycemia due to G202A.…”

The impact of malaria-protective red blood cell polymorphisms on parasite biomass in children with severe Plasmodium falciparum malaria

“…Severe malaria cases were genotyped for the rs334 SNP and for the common African form of α-thalassaemia (a 3.7kb deletion in HBA1 and HBA2 ; -α 3.7 -thalassaemia 17 ) by PCR at the KEMRI-Wellcome Trust Laboratories, Kenya, as described in detail previously 7,18,19 . Genotyping for a further 119 candidate SNPs was conducted at the Wellcome Centre for Human Genetics in Oxford, UK, by use of the Sequenom iPLEX MassARRAY platform, using DNA extracted from frozen samples of whole blood as previously described 7 .…”

Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha globin region at Chr16p13.3

“…These methods have been highly successful at calling variants throughout the genome, but because they are trained on genome-wide data and rely on accurately-aligned reads to make their predictions, they may not perform as well in repetitive regions. In addition, alignment-free methods for genotyping medically relevant variants have been developed (13)(14)(15), but so far these have been more applicable to calling smaller variants.…”