The development and application of methods to prevent the transmission of damaging mutations through the human germ line would have considerable health benefits. In an attempt to correct a paternal pathogenic mutation using CRISPR–Cas9 technology in human embryos, Ma et al. 1 assert that the maternal allele is an efficient repair template for gene correction, including when Cas9 is applied in metaphase II (MII) oocytes. As the maternal and paternal genomes undergo distinct developmental programs and are in separate nuclei before the first mitotic division, which would seem to preclude inter-homologue interactions, we believe that it is crucial to provide a comprehensive analysis of the molecular outcomes of double-strand break (DSB) repair in human embryos. In the absence of direct molecular evidence for the inferred events, the consideration of using such methods for correction of the human germ line should proceed with extreme caution. There is a Reply to this Comment by Ma, H. et al. Nature 560, https://doi. org/10.1038/s41586-018-0381-y (2018). Ma et al. 1 use two approaches to attempt gene correction in human embryos. In one approach, which is deemed to be more promising because it is thought to give rise to non-mosaic embryos, MII oocytes were injected with donor sperm from a heterozygous mutation carrier together with Cas9 complexes to direct the cleavage of the mutant paternal allele. About 72% of embryos arising from Cas9 injection were thought to be wild type compared with 50% of control embryos. The authors argue that this excess of apparently wild-type embryos (22%) arose by correction of the paternal allele, by using the maternal allele as a repair template, a process termed inter-homologue homologous recombination (abbreviated here as IH-HR). In the other approach, Ma et al. 1 again used sperm from the mutation carrier to fertilize wild-type oocytes; when the pronuclear-stage zygotes were completing S phase, they were injected with Cas9 complexes, again directed to the mutant paternal allele. In contrast to the previous approach, embryos derived from fertilization with mutant sperm could be conclusively identified because mosaic embryos were obtained. Some cells of these mosaic embryos contained a mutant paternal locus, either unmodified or with small indels, together with the wild-type maternal allele. Other cells in these mosaic embryos contained only a detectable wild-type allele. The authors inferred that these cells arose by IH-HR of the mutant paternal allele using the wild-type maternal allele as a template, leading to gene correction. Considering the data presented in Ma et al. 1, alternatives to IH-HR are possible. Genotyping involved the amplification of an approximately 534-base-pair (bp) fragment in which the MYBPC3ΔGAGT mutation is approximately 200 bp from one of the primer-binding sites. Deletions larger than 200 bp would be sufficient to remove this primer-binding site and lead to amplification of only the maternal allele (Fig. 1a, b), giving the misleading appearance of gene correction of the paternal allele. Although typically not as common as small indels, long deletions and other events have been detected in cultured cells and in both mouse and pig zygotes 2–4. To detect longer deletions, a matrix of primer pairs needs to be tiled at increasing distances from both sides of the mutation; linkage analysis performed on the long-range PCR products would confirm whether amplification is from both the maternal and the paternal chromosomes. In a study designed to score these events systematically, Cas9-induced double-strand breaks in mouse embryonic stem cells were found to resolve …