Exome sequencing identifies the cause of a mendelian disorder

Abstract

We demonstrate the first successful application of exome sequencing to discover the gene for a rare mendelian disorder of unknown cause, Miller syndrome (MIM%263750). For four affected individuals in three independent kindreds, we captured and sequenced coding regions to a mean coverage of 40x and sufficient depth to call variants at approximately 97% of each targeted exome. Filtering against public SNP databases and eight HapMap exomes for genes with two previously unknown variants in each of the four individuals identified a single candidate gene, DHODH, which encodes a key enzyme in the pyrimidine de novo biosynthesis pathway. Sanger sequencing confirmed the presence of DHODH mutations in three additional families with Miller syndrome. Exome sequencing of a small number of unrelated affected individuals is a powerful, efficient strategy for identifying the genes underlying rare mendelian disorders and will likely transform the genetic analysis of monogenic traits.

Figures

Figure 1. Clinical characteristics of an individual with Miller syndrome (A,B) and an individual with methotrexate embryopathy (C,D)

A 9 year-old boy with Miller syndrome (A and B) caused by mutations in DHODH. Facial anomalies (A) include cupped ears, coloboma of the lower eyelids, prominent nose, micrognathia and absence of the 5th digits of the feet (B). A 26 year-old man with methotrexate embryopathy (C and D). Note the cupped ears, hypertelorism, sparse eyebrows, and prominent nose (C) accompanied by absence of the 4th and 5th digits of the feet (D). C and D are reprinted with permission from Bawle et al. Teratology 57:51-55 (1978).

Figure 2. Genomic structure of the exons encoding the open reading frame of DHODH

DHODH is composed of 9 exons that encode untranslated regions (orange) and protein coding sequence (blue). Arrows indicate the locations of 11 different mutations found in 6 families with Miller syndrome.