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No statistical evidence for an effect of CCR5-∆32 on lifespan in the UK Biobank cohort

By Robert Maier, Ali Akbari, Xinzhu Wei, Nick Patterson, Rasmus Nielsen, David Reich

Posted 02 Oct 2019
bioRxiv DOI: 10.1101/787986 (published DOI: 10.1038/s41591-019-0710-1)

A recent study reported that a 32-base-pair deletion in the CCR5 gene (CCR5-∆32) is deleterious in the homozygous state in humans. Evidence for this came from a survival analysis in the UK Biobank cohort, and from deviations from Hardy-Weinberg equilibrium at a polymorphism tagging the deletion (rs62625034). Here, we carry out a joint analysis of whole-genome genotyping data and whole-exome sequencing data from the UK Biobank, which reveals that technical artifacts are a more plausible cause for deviations from Hardy-Weinberg equilibrium at this polymorphism. Specifically, we find that individuals homozygous for the deletion in the sequencing data are underrepresented in the genotyping data due to an elevated rate of missing data at rs62625034, possibly because the probe for this SNP overlaps with the ∆32 deletion. Another variant which has a higher concordance with the deletion in the sequencing data shows no associations with mortality. A phenome-wide scan for effects of variants tagging this deletion shows an overall inflation of association p-values, but identifies only one trait at p < 5×10−8, and no mediators for an effect on mortality. These analyses show that the original reports of a recessive deleterious effect of CCR5-∆32 are affected by a technical artifact, and that a closer investigation of the same data provides no positive evidence for an effect on lifespan.

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