What to do with a negative exome?.

Background: Individuals with suspected monogenic disease remain unsolved after exome sequencing (ES) for reasons including technical challenges and difficulty in variant interpretation. Aim(s): To evaluate systematic reanalysis of singleton ES data for unsolved cases. Method(s): Data from unsolved cases referred for clinical ES at Victorian Clinical Genetics Services between 01/2016 and 03/2017 was systematically reanalyzed. First reanalysis at 4-13 months after the initial report looked at genes newly associated with disease since the original analysis; second reanalysis at 9-18 months looked at all disease-associated genes. At 25-34 months we reviewed the status of all cases and collated the strategies which solved cases through means other than reanalysis of singleton ES data. Result(s): Fifty-six unsolved cases were referred for syndromic (45%) and non-syndromic (3.5%) neurodevelopmental conditions, multiple congenital anomalies (12.5%), and single system disorders (39%). Reanalysis of existing ES data alone did not yield new diagnoses. Over the same timeframe, nine new diagnoses were obtained (16%): two intragenic deletions not tractable by ES but detected on array (ATAD3A/3B, NIPBL); two missense variants with low coverage in the original singleton ES, detected on trio ES/GS (CHD7; SCN8A); one in-frame deletion detected with a low variant fraction on singleton ES, highlighted as a de novo variant of interest on trio ES (WDR45); and four novel gene discoveries (unpublished). Conclusion(s): All additional diagnoses in this study were derived from strategies other than reanalysis of singleton ES data, illustrating the need to implement a multifaceted strategy for cases remaining unsolved after singleton ES.