Autozygome Sequencing Expands the Horizon of Human Knockout Research and Provides Novel Insights into Human Phenotypic Variation

摘要

The use of autozygosity as a mapping tool in the search for autosomal recessive disease genes is well established. We hypothesized that autozygosity not only unmasks the recessiveness of disease causing variants, but can also reveal natural knockouts of genes with less obvious phenotypic consequences. To test this hypothesis, we exome sequenced 77 well phenotyped individuals born to first cousin parents in search of genes that are biallelically inactivated. Using a very conservative estimate, we show that each of these individuals carries biallelic inactivation of 22.8 genes on average. For many of the 169 genes that appear to be biallelically inactivated, available data support involvement in modulating metabolism, immunity, perception, external appearance and other phenotypic aspects, and appear therefore to contribute to human phenotypic variation. Other genes with biallelic inactivation may contribute in yet unknown mechanisms or may be on their way to conversion into pseudogenes due to true recent dispensability. We conclude that sequencing the autozygome is an efficient way to map the contribution of genes to human phenotypic variation that goes beyond the classical definition of disease. Author Summary Identification of disease-causing gene variants by taking advantage of autozygosity mapping in consanguineous pedigrees is well established. However, autozygous intervals can also result in making homozygous those loss of function variants in genes that may not result in a discernible phenotype even under a complete knockout. The advent of next-generation sequencing makes it possible to systematically sequence all autozygous intervals per individual (the autozygome) and uncover all apparent homozygous loss of function variants therein. By applying this approach on well phenotyped offspring of first cousin marriages, we were able to uncover >160 genes that appear to be completely inactivated, and we show that the apparent lack of phenotype may be context-dependent. This work expands the spectrum of phenotypic consequence of human knockout to include apparent lack of discernible phenotypes.