Sperm sequencing reveals extensive positive selection in the human germline

Abstract

Over the course of life, cells of the human body accumulate DNA mutations due to damage from intrinsic causes or exposure to mutagens. Mutations that occur in reproductive cell lineages are known as germline mutations and have the potential to be transmitted to offspring. Germline mutations serve as the origin of all heritable genetic variation, making them crucial in the study of evolution and disease. The majority (~80%) of germline mutations in humans are paternal in origin. However, direct observation of mutations in sperm, the gametes of the paternal germline, has been limited by the need for a low error rate sequencing technology. Using the duplex sequencing method known as NanoSeq, which achieves a sufficiently low error rate, we sequenced bulk sperm and whole blood from the same individuals. We show that mutation rates and mutation signatures in sperm are consistent with results from trio studies and we contrast mutation rates in the germline to that in blood. Applying a targeted version of NanoSeq, we then generated a large dataset of coding mutations from sperm. Our findings reveal extensive positive selection in the male germline, implicating new genes, pathways, and mutational mechanisms in this process. Annotation of positively selected genes identified in our study found that most are known to cause pathogenic disorders when transmitted as a germline mutation to an offspring. Furthermore, we quantified the fraction of sperm carrying pathogenic variants per individual, highlighting an increased disease risk for children born to fathers of advanced age. These findings shed light on the dynamics of germline mutations and have important implications for our understanding of human disease.