Molecular findings among patients referred for clinical whole-exome sequencing: Editorial comment

Whole-exome sequencing can identify variations in an individual’s DNA sequence and compare them with a normal reference sequence, a process that can help to determine the cause of a patient’s medical disorder. Although results of prior studies on clinical applications of these techniques have been promising, many questions remain unanswered. This study was undertaken to determine clinical findings of whole-exome sequencing in 2000 consecutive patients. The unrelated patients were referred from physicians for clinical whole-exome sequencing. Peripheral blood, tissue, or extracted DNA samples were collected from patients or their parents. The phenotypes were categorized into 4 groups: (1) neurologic, findings only in neurologic or developmental systems; (2) neurologic plus other organ systems, findings for the neurologic group plus at least 1 finding from another organ system; (3) specific neurologic, more defined neurologic signs and symptoms than the neurologic category; and (4) nonneurologic, findings from organ systems other than neurologic. Interpretations considered the specific variant, gene involved, and clinical case history. The format for reporting sequencing data used a 2-tier strategy. The focused tier 1 report included deleterious mutations related to the disease phenotype, variants of unknown clinical significance related to the disease phenotype, medically actionable mutations in genes with potential therapies or established surveillance protocols, autosomal recessive carrier status for genes, pharmacogenetic variants, and clinically relevant pathogenic mutations in the mitochondrial genome. Tier 2 included deleterious mutations or variants of unknown clinical significance unrelated to the disease phenotype and predicted deleterious mutations such as nonsense or splice site mutations in nondisease genes. The cohort included 900 children younger than 5 years (45.0%), 845 children and adolescents aged 5 to 18 years (42.2%), 244 adults older than 18 years (12.2%), and 11 fetal samples from terminated pregnancies (0.6%). Most patients (87.8%) had neurologic disorders or developmental delay (groups 1, 2, and 3); 12.2% of patients had nonneurologic disorders. Overall, 1808 families (90.4%) requested all aspects of the tier 1 report. The tier 2 report was ordered by physicians for 524 patients (26.2%). About ~1,750,800 variants were analyzed for the 2000 samples (average of ~875 variants/sample), including ~52,000 deleterious mutations (3.0%), 153,230 variants of unknown clinical significance (8.8%), and 1,545,000 benign variants (88.3%). Molecular diagnoses were reported for 504 patients (25.2%; 95% confidence interval, 23.3%–27.2%). The rates for molecular diagnosis varied with clinical presentation, with the lowest yield in patients in the nonneurologic group (20.1%) and the highest in the specific neurologic group (36.1%). Modes of inheritance of the molecular diagnoses included 280 autosomal dominant (53.1%), 181 autosomal recessive (34.3%), 65 X-linked (12.3%), and 1 mitochondrial (0.2%). Of the 280 autosomal dominant conditions, 208 (74.3%) resulted from de novomutations, 32 (11.4%) were inherited, and 40 (14.3%) were undetermined. Of the 65 X-linked disorders, 34 (52.3%) occurred in males, and 31 (47.7%) in females; 40 X-linked alleles (61.5%) resulted from de novo mutations, including 17 (42.5%) in males and 23 in females (57.5%). Among the 181 autosomal recessive disorders, 108 (59.7%) demonstrated compound heterozygosity of 2 distinct mutations, and 73 (40.3%) had apparently homozygous mutations, including 5 patients with uniparental disomy. From the 504 positive cases, 708 presumptive causative variant alleles were identified, with 409 (57.8%) of these defined as novel. Mutant alleles included 346 missense, 149 frameshift, 134 nonsense, 57 splice, 8 in-frame deletions or duplications, 6 large deletions, 5 start codon defects, 1 stop loss (loss of stop codon), 1 promoter region, and 1 mitochondrial DNAmutation. Twenty-three patients had mutations at 2 distinct disease loci related to the phenotype. Whole-exome sequencing provided a potential molecular diagnosis for 25% of patients and detected rare genetic events and new mutations contributing to disease. The technique may offer advantages over traditional molecular diagnostic approaches in certain patients. Debate continues regarding the definition of medically actionable findings and the threshold for reporting.