Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders

Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1 retrotransposition; 80% of the larger inversions are balanced and affect twice as many nucleotides as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or retrotransposons. Since flanking repeats promote non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7 3 10-4 per locus per generation. Recurrent inversions exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes specific haplotypes to disease-causing CNVs.

Automated summary

Unlike copy number variants, inversions are a less studied form of genetic variation. Through the integration of multiple genomic technologies, researchers have discovered 729 inversions in 41 human genomes. The majority of these inversions are formed through twin-priming during L1 retrotransposition. It is found that inversions have an excess of common variants and a high percentage of them are flanked by segmental duplications or retrotransposons. Additionally, researchers have identified 40 recurrent inversions, accounting for 0.6% of the genome, which exhibit a sex-chromosomal bias and co-localize with genomic disorder critical regions. Recurrent inversions lead to an increase in mutability in the population and predispose specific haplotypes to disease-causing copy number variants.