Clinical whole-exome sequencing for the diagnosis of mendelian disorders

Abstract

Background: Whole-exome sequencing is a diagnostic approach for the identification of molecular defects in patients with suspected genetic disorders.

Methods: We developed technical, bioinformatic, interpretive, and validation pipelines for whole-exome sequencing in a certified clinical laboratory to identify sequence variants underlying disease phenotypes in patients.

Results: We present data on the first 250 probands for whom referring physicians ordered whole-exome sequencing. Patients presented with a range of phenotypes suggesting potential genetic causes. Approximately 80% were children with neurologic phenotypes. Insurance coverage was similar to that for established genetic tests. We identified 86 mutated alleles that were highly likely to be causative in 62 of the 250 patients, achieving a 25% molecular diagnostic rate (95% confidence interval, 20 to 31). Among the 62 patients, 33 had autosomal dominant disease, 16 had autosomal recessive disease, and 9 had X-linked disease. A total of 4 probands received two nonoverlapping molecular diagnoses, which potentially challenged the clinical diagnosis that had been made on the basis of history and physical examination. A total of 83% of the autosomal dominant mutant alleles and 40% of the X-linked mutant alleles occurred de novo. Recurrent clinical phenotypes occurred in patients with mutations that were highly likely to be causative in the same genes and in different genes responsible for genetically heterogeneous disorders.

Conclusions: Whole-exome sequencing identified the underlying genetic defect in 25% of consecutive patients referred for evaluation of a possible genetic condition. (Funded by the National Human Genome Research Institute.).

Figure 1

Variants were identified with the use of Atlas-SNP and Atlas-Indel. ESP denotes ESP5400 data from the National Heart, Lung, and Blood Institute GO Exome Sequencing Project, HGMD Human Gene Mutation Database, MAF minor allele frequency, TG the 1000 Genomes Project, and VUS variants of unknown clinical significance.