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Significance Despite a growing number of reports of rare disorders not fully explained by monogenic lesions, digenic inheritance has been reported for only 54 diseases to date. The very few existing methods for detecting gene × gene interactions from next-generation sequencing data were generally examined in rare-variant association studies with limited simulation analyses for short genomic regions, under a case-control design. We describe a case-only approach designed specifically to search for digenic inheritance, which avoids recruitment of controls. We show, through both extensive simulation studies on real whole-exome sequencing datasets and application to a real example of craniosynostosis, that our method is robust and powerful for the genome-wide identification of digenic lesions.

A genome-wide case-only test for the detection of digenic inheritance in human exomes