Increased rate of de novo single nucleotide mutation in house mice born through assisted reproduction

Approximately 2.6% of live births in the United States are conceived using assisted reproductive technologies (ARTs). While some ART procedures, including in vitro fertilization (IVF) and intracytoplasmic sperm injection, are known to alter the epigenetic landscape of early embryonic development, their impact on DNA sequence stability is unclear. Here, we leverage the strengths of the laboratory mouse model system to investigate whether a standard ART regimen-ovarian hyperstimulation, gamete isolation, IVF, embryo culture, and embryo transfer-affects genome stability. Age-matched cohorts of ART-derived and naturally conceived C57BL/6J inbred mice were reared in a controlled setting and whole genome sequenced to ~50x coverage. Using a rigorous pipeline for de novo single nucleotide variant (dnSNV) discovery, we observe a ~30% increase in the dnSNV rate in ART-compared to naturally-conceived mice. Analysis of the dnSNV mutation spectrum identified signature contributions related to germline DNA repair activity, affirming expectations and evidencing the quality of our dnSNV calls. We observed no enrichment of dnSNVs in specific genomic contexts, suggesting that the observed rate increase in ART-derived mice is a general genome-wide phenomenon. Similarly, we show that the developmental timing of dnSNVs is similar in ART- and natural-born cohorts. Together, our findings show that ART is moderately mutagenic in house mice and motivate future work to define the precise procedure(s) associated with this increased mutational vulnerability. While we caution that our findings cannot be immediately translated to humans, they nonetheless emphasize a pressing need for investigations on the potential mutagenicity of ART in our species.