Resolving genotype-phenotype mismatches in whole-exome based genetic testing.

Abstract

Purpose: In recent years, clinical genetic testing for inherited eye diseases has moved to genome-wide approaches like whole exome sequencing (WES) that have the power to detect unexpected phenotype-genotype correlations. We have discovered many cases of non-syndromic disease caused by genes usually associated with syndromic disease.

Methods: To date, WES has been obtained for 652 probands with inherited eye diseases. All putative disease-causing mutations in genes relevant to a patient’s disease are confirmed with bidirectional sequencing and phase is established using samples from family when available.

Results: 4/502 photoreceptor-disease exome patients were homozygous for BBS1 M390R, yet escaped the clinical diagnosis of Bardet-Biedl syndrome (BBS), including a case of a patient with apparent Usher Syndrome caused by homozygous BBS1 M390R and compound heterozygous variants in SLC26A4. On re-examination, several of these patients had BBS stigmata that were subtle enough to escape previous detection, and other patients had no detectable signs of BBS aside from RP. An additional screen of 219 patients revealed three non-syndromic RP patients with homozygous M390R. Similarly, in FLVCR1, a gene reported to cause PCARP, a syndrome consisting of posterior column ataxia and RP, we discovered plausible disease-causing genotypes in 5/502 patients that escaped clinical PCARP diagnosis. These patients again had a mix of subtle syndromic features and non-syndromic disease. Interestingly, four of these patients have c.1092+5G>A on one allele with a more severe mutation in repulsion, suggesting the former variant could be hypomorphic.

Conclusions: Genome-scale experiments like WES in patients with non-syndromic photoreceptor diseases can lead to discoveries of genotypes in genes previously suspected to cause only syndromic disease. These genotype/phenotype mismatches need to be resolved either by a careful clinical reevaluation that discovers subtle syndromic stigmata that escaped previous detection (thus increasing confidence in the accuracy of the genetic test result), or by gathering enough non-syndromic patients to expand the phenotypic scope of the disease. Deciphering these cases requires a close coupling between clinicians and the diagnostic laboratory.