Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

TLDR

Protein‑coding genes comprise only ~1 % of the human genome yet harbor ~85 % of disease‑causing mutations, so efficient whole‑exome sequencing can advance understanding of rare and common diseases and has not yet been applied for clinical diagnosis. The authors developed a whole‑exome sequencing method that couples Roche/NimbleGen capture arrays with Illumina sequencing. They used Roche/NimbleGen exome capture arrays to enrich coding regions and sequenced the enriched DNA on an Illumina platform. The approach captured ~95 % of targeted coding sequences with high sensitivity and specificity, enabling the discovery of a homozygous D652N mutation in SLC26A3 that caused congenital chloride diarrhea in a patient and identifying deleterious SLC26A3 mutations in five additional patients, thereby demonstrating clinical utility for disease gene discovery and diagnosis.

Abstract

Protein coding genes constitute only approximately 1% of the human genome but harbor 85% of the mutations with large effects on disease-related traits. Therefore, efficient strategies for selectively sequencing complete coding regions (i.e., “whole exome”) have the potential to contribute to the understanding of rare and common human diseases. Here we report a method for whole-exome sequencing coupling Roche/NimbleGen whole exome arrays to the Illumina DNA sequencing platform. We demonstrate the ability to capture approximately 95% of the targeted coding sequences with high sensitivity and specificity for detection of homozygous and heterozygous variants. We illustrate the utility of this approach by making an unanticipated genetic diagnosis of congenital chloride diarrhea in a patient referred with a suspected diagnosis of Bartter syndrome, a renal salt-wasting disease. The molecular diagnosis was based on the finding of a homozygous missense D652N mutation at a position in SLC26A3 (the known congenital chloride diarrhea locus) that is virtually completely conserved in orthologues and paralogues from invertebrates to humans, and clinical follow-up confirmed the diagnosis. To our knowledge, whole-exome (or genome) sequencing has not previously been used to make a genetic diagnosis. Five additional patients suspected to have Bartter syndrome but who did not have mutations in known genes for this disease had homozygous deleterious mutations in SLC26A3 . These results demonstrate the clinical utility of whole-exome sequencing and have implications for disease gene discovery and clinical diagnosis.