Health and population effects of rare gene knockouts in adult humans with related parents

Abstract

Examining complete gene knockouts within a viable organism can inform on gene function. We sequenced the exomes of 3222 British adults of Pakistani heritage with high parental relatedness, discovering 1111 rare-variant homozygous genotypes with predicted loss of function (knockouts) in 781 genes. We observed 13.7% fewer homozygous knockout genotypes than we expected, implying an average load of 1.6 recessive-lethal-equivalent loss-of-function (LOF) variants per adult. When genetic data were linked to the individuals' lifelong health records, we observed no significant relationship between gene knockouts and clinical consultation or prescription rate. In this data set, we identified a healthy PRDM9-knockout mother and performed phased genome sequencing on her, her child, and control individuals. Our results show that meiotic recombination sites are localized away from PRDM9-dependent hotspots. Thus, natural LOF variants inform on essential genetic loci and demonstrate PRDM9 redundancy in humans.

Fig. 1. Discovery and annotation of rhLOF variants

(A) Autozygous segment numbers and length for Pakistani heritage subjects in the UK, and 1000 Genomes project European (CEPH Utah residents with ancestry from northern and western Europe; CEU) individuals. (B) Autozygosity and rhLOF in 3,222 individuals. Count of number of individuals (left Y axis, blue columns) binned by fraction of autozygous genome (X axis, showing values from 0.00 to 0.12), with mean number of rhLOF genotypes per individual (right Y axis, orange circles). (C) Distribution of LOF variants by allele frequency, heterozygous or homozygous genotype, predicted protein consequence, and whether predicted for a full or partial set of GENCODE Basic transcripts for the gene.

Fig. 2. Population genetic analysis of rhLOF variants

(A) Comparison of number of LOF variants per unit length in autozygous regions (LOF A) with expected rate from non-autozygous sections (LOF NA) showing suppression of rhLOFs (t-test). A similar analysis of synonymous (Syn) variants shows no significant differences. (B) Observed number of variants with homozygote genotypes in 16,708 rare LOF variants (orange circle) versus a frequency matched subsampling of synonymous variants (blue violin plot). (C) Quantification of the recessive lethal load carried on average by a single individual. Direct subsampling estimate for rhLOF variants from current study (orange circle); epidemiological estimates from correlating infant mortality rates to estimated autozygosity in current and published data (blue circles); direct estimate from large Hutterite pedigree (green circle). 95% confidence intervals as black bars. (D) Relative number of derived LOF alleles that are frequent in one population and not another (under neutrality the expectation is 1.0), calculated for 1000 Genomes Project populations and the current Birmingham/Bradford Pakistani heritage population (BB), compared to the CEU population. Error bars represent ±1 (black) or 2 (grey) standard errors, and significant differences (R_A/B jackknife test) versus CEU population are highlighted in orange circles.