Editors' ChoiceGenetics

Deep Sequencing

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Science Translational Medicine  25 Nov 2009:
Vol. 1, Issue 8, pp. 8ec29
DOI: 10.1126/scitranslmed.3000638

Although whole genome sequencing is becoming more practical, high-throughput technologies for deep resequencing of just the protein-coding regions of the genome—the exome—are accelerating the discovery of the genetic bases of rare diseases at considerably lower cost. Exome resquencing, plus appropriate filtering against public single nucleotide polymorphism databases (dbSNP) and HapMap exomes, offers investigators a rapid approach to identify causal culprits for Mendelian conditions. Now, Ng and colleagues demonstrate the utility of this technical approach by determining the gene responsible for Miller syndrome, a rare disorder that causes malformation of multiple body parts, the cause of which has defied current methods of discovery. To identify pathogenic mutations from normal variants, the authors sequenced the exomes of four affected individuals (two of which were siblings) in three independent kindreds and focused only on previously unidentified nonsynonymous variants (NS), splice acceptor and donor site mutations (SS), and short coding insertions or deletions (indels). Of the two siblings in kindred 1, each was found to have at least a single NS/SS/I variant in ~4600 genes (dominant model) and two or more NS/SS/I variants in ~2800 genes (recessive model). Filtering these genes against dbSNP and HapMap databases reduced the candidate gene pool to 228 for the dominant model and 9 for the recessive model. These candidate gene pools were further reduced when compared to results from unrelated individuals in kindreds 2 and 3, yielding 8 for the dominant model and only a single shared gene, DHODH, encoding the enzyme dihydroorotate dehydrogenase, for the recessive model. After the implicated gene was sequenced by the Sanger method, a grand total of 11 different mutations were identified in 6 families with Miller syndrome, and none of these mutations were found in 200 control genotyped chromosomes from unaffected individuals of matched geographical ancestry. The mechanism by which these mutations in DHODH cause Miller syndrome remains to be explored. Nevertheless, this powerful, efficient, and cost-effective strategy to identify causal mutations in unique genes underlying rare Mendelian disorders may guide the evolving platform by which rare variants influencing common diseases are uncovered.

S. B. Ng et al., Exome sequencing identifies the cause of a mendelian disorder. Nat. Gen. 13 November 2009 (10.1038/ng.499) [Abstract]

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