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 40× and sufficient depth to call variants at ~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.
At a glance
- Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145 (2008). &
- Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009). et al.
- Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc. Natl. Acad. Sci. USA published online, doi:10.1073/pnas.0910672106 (27 October 2009). et al.
- Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 1522–1527 (2007). et al.
- The human gene mutation database: 2008 update. Genome Med 1, 13 (2009). et al.
- Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am. J. Hum. Genet. 80, 727–739 (2007). , &
- The strength of selection on ultraconserved elements in the human genome. Am. J. Hum. Genet. 80, 692–704 (2007). , &
- Deletion of ultraconserved elements yields viable mice. PLoS Biol. 5, e234 (2007). et al.
- The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 19, 1316–1323 (2009). et al.
- Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nat. Genet. 38, 561–565 (2006). et al.
- Postaxial acrofacial dysostosis syndrome. J. Pediatr. 95, 970–975 (1979). , &
- TCOF1 mutations excluded from a role in other first and second branchial arch-related disorders. Am. J. Med. Genet. 111, 324–327 (2002). , , , &
- Recurrence of the postaxial acrofacial dysostosis syndrome in a sibship: implications for genetic counseling. J. Pediatr. 98, 87–88 (1981).
- Miller syndrome (postaxial acrofacial dysostosis): further evidence for autosomal recessive inheritance and expansion of the phenotype. J. Med. Genet. 28, 695–700 (1991). &
- Postaxial acrofacial dysostosis (Miller) syndrome. J. Med. Genet. 24, 422–425 (1987). , &
- Une forme extensive de dysostose mandibulo-faciale. J. Genet. Hum. 17, 45–52 (1969).
- Postaxial acrofacial dysostosis: report on two patients. Am. J. Med. Genet. 44, 274–279 (1992). , , &
- Robin sequence and oligodactyly in mother and son. Am. J. Med. Genet. 25, 293–297 (1986). , &
- Dihydroorotate dehydrogenase polymorphism influences the toxicity of leflunomide treatment in patients with rheumatoid arthritis. Ann. Rheum. Dis. 68, 1367–1368 (2009). , , , &
- Orotic acid excretion and arginine metabolism. J. Nutr. 137, 1656S–1661S (2007). &
- Leflunomide: mode of action in the treatment of rheumatoid arthritis. Ann. Rheum. Dis. 59, 841–849 (2000). &
- Sex limited inheritance in Drosophila . Science 32, 120–122 (1910).
- Functional diversity within the rudimentary locus of Drosophila melanogaster . Mol. Gen. Genet. 135, 113–122 (1974). &
- Analysis of the phenotypes exhibited by rudimentary-like mutants of Drosophila melanogaster . Biochem. Genet. 20, 607–619 (1982). &
- Teratogenicity study of the dihydroorotate-dehydrogenase inhibitor and protein tyrosine kinase inhibitor Lefunomide in mice. Reprod. Toxicol. 24, 310–316 (2007). et al.
- Lefunomide protects From T-cell–mediated liver injury in mice through inhibition of nuclear factor κB. Hepatology 40, 1160–1169 (2004). et al.
- Inhibition of NF-κB activity results in disruption of the apical ectodermal ridge and aberrant limb morphogenesis. Nature 392, 615–618 (1998). , &
- TGF alpha deficiency results in hair follicle and eye abnormalities in targeted and waved-1 mice. Cell 73, 263–278 (1993). et al.
- Manifestation of the limb prepattern: limb development in the absence of sonic hedgehog function. Dev. Biol. 236, 421–435 (2001). et al.
- Teratology 57, 51–55 (1978). et al.
- Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008). , &
- Supplementary Text and Figures (820K)
Supplementary Figures 1–3