Editors' ChoiceHuman Genetics

Accessing the Inaccessible Genome

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Science Translational Medicine  03 Apr 2013:
Vol. 5, Issue 179, pp. 179ec58
DOI: 10.1126/scitranslmed.3006206

Next-generation sequencing in families with rare autosomal dominant disorders can identify candidate genes that are mutated in affected individuals but not in healthy controls. But what happens when careful analysis fails to identify a mutation that perfectly segregates with disease, which is expected for a high-penetrance allele? Kirby et al. report such a scenario for medullary cystic kidney disease type 1 (MCKD1).

MCKD1 is a rare Mendelian disorder characterized by a chronic, progressive kidney disease that eventually leads to end-stage renal failure. The disease has been consistently mapped to a single autosomal locus; however, sequencing and careful analysis revealed no coding, noncoding, or copy-number polymorphisms that segregated specifically in affected individuals. Given the strong linkage evidence, Kirby et al. surmised that mutations must exist in this region that had somehow been missed in the sequencing effort. Certain kinds of sequences are troublemakers when it comes to variant detection, especially regions that include variable repeats (VNTRs). Therefore, the authors focused on one gene in the region of interest that contained a polymorphic VNTR: mucin 1 (MUC1). MUC1 is specifically expressed in the kidney, making it an even more intriguing candidate. First, Kirby et al. excluded VNTR length itself as causal for MCKD1. Then after cloning, subcloning, Sanger sequencing, and constructing de novo assemblies for affected individuals, the authors identified a single–base pair insertion within the MUC1 VNTR. The insertion, perfectly segregating within all six families, appears to have arisen independently in each family and introduces a premature stop codon, producing a protein lacking key functional elements. This mutational mechanism was found in more than 60% of families with MCKD1-like symptoms, pointing to a substantial role for MUC1 in this disorder.

This report by Kirby et al. provides a good lesson, worth remembering: Think carefully about the results returned by sequencing studies. These data sets are huge and relatively quick to generate, but are likely incomplete. It’s always important to consider what might be missing. The answers are there, under our noses, and might simply require a bit of extra grit to access.

A. Kirby et al., Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat. Genet. 45, 299–303 (2013). [Abstract]

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