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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Nature Genetics volume 45, pages 299–303 (2013)Cite this article

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Abstract

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (∼1.5–5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.

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Figure 1: Linkage of six families with MCKD1 to chromosome 1.
Figure 2: Discovery of a cytosine insertion in a coding VNTR of MUC1.
Figure 3: Detection of MUC1 cytosine insertion by probe-extension assay.
Figure 4: Immunohistochemical and immunofluorescence studies of the MUC1-fs protein.

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Acknowledgements

We thank T.L. Hatte for reagent use. We thank D. Altshuler, T. Carter and J. Schlondorff for useful discussions and M. Cortes, M. Ilzarbe and M. Betancourt for helpful project management. We also thank F. Letendre, M. Coole, R.P. Frere, C. Bonnet, L. Mulrain, N. Norbui and H. Arachchi for Sanger sequencing. This work was conducted as part of the Slim Initiative for Genomic Medicine, a joint United States–Mexico project funded by the Carlos Slim Health Institute. This research was supported in part by the Intramural Research Program of the US NIH, National Human Genome Research Institute (NHGRI). S.K., H.H., J.S. and V.B. were funded by Charles University programs PRVOUK-P24/LF1/3 and UNCE 204011, and their work was supported by grants LH12015 and NT13116-4/2012 from the Ministry of Education and the Ministry of Health of the Czech Republic. S.L.A. was supported by US NIH grant DK34854 (The Harvard Digestive Diseases Center). N.P. is a Broad Fellow of the Broad Institute and a postdoctoral research fellow of the Fund for Scientific Research–Flanders (FWO Vlaanderen, Belgium). I.G.-V. was supported by the Human Frontier Science Program, Alon, the Israeli Centers of Research Excellence (I-CORE) and the Edmond J. Safra Center for Bioinformatics at Tel Aviv University.

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Author notes

  1. Anthony J Bleyer, Eric S Lander and Mark J Daly: These authors jointly directed this work.

Authors and Affiliations

  1. Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA

    Andrew Kirby, Andreas Gnirke, David B Jaffe, Nathalie Pochet, Brendan Blumenstiel, Chun Ye, Daniel Aird, Christine Stevens, James T Robinson, Moran N Cabili, Irit Gat-Viks, Edward Kelliher, Riza Daza, Matthew DeFelice, Mitchell Guttman, Robert E Handsaker, Danielle Perrin, Scott Steelman, Snaevar Sigurdsson, Carrie Sougnez, Kristian Cibulskis, Melissa Parkin, Todd Green, Elizabeth Rossin, Michael C Zody, Ramnik J Xavier, Kerstin Lindblad-Toh, Stacey Gabriel, Aviv Regev, Chad Nusbaum, Eric S Lander & Mark J Daly

  2. Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA

    Andrew Kirby & Mark J Daly

  3. Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic

    Veronika Barešová, Helena Hůlková, Jana Sovová, Petr Vylet'al & Stanislav Kmoch

  4. Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, VIB, Ghent University, Ghent, Belgium

    Nathalie Pochet

  5. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

    Moran N Cabili

  6. Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel

    Irit Gat-Viks

  7. Institut National de la Santé et de la Recherche Médicale (INSERM) U983, Paris, France

    Corinne Antignac

  8. Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France

    Corinne Antignac

  9. Département de Génétique, Hôpital Necker–Enfants Malades, Assistance Publique–Hôpitaux de Paris, Paris, France

    Corinne Antignac

  10. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

    Robert E Handsaker

  11. The Commonwealth Medical College, Scranton, Pennsylvania, USA

    Steven J Scheinman

  12. Gastrointestinal Unit, Center for the Study of the Inflammatory Bowel Disease and Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA

    Ramnik J Xavier

  13. Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA

    Martin R Pollak & Seth L Alper

  14. Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA

    Martin R Pollak & Seth L Alper

  15. Department of Medical Biochemistry and Microbiology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden

    Kerstin Lindblad-Toh

  16. Office of the Clinical Director, National Human Genome Research Institute, US National Institutes of Health (NIH), Bethesda, Maryland, USA

    P Suzanne Hart

  17. Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA

    Anthony J Bleyer

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  1. Andrew Kirby
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  2. Andreas Gnirke
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Contributions

A.J.B., E.S.L. and M.J.D. jointly supervised the research. R.J.X., M.R.P. and S.L.A. provided study design and interpretation advice. C.A., S.J.S., P.S.H. and A.J.B. performed sample collection. C. Stevens managed the project. C. Sougnez and K.C. provided early genotyping and sequencing support. Linkage analysis was performed by A.K. on the basis of previous work by P.S.H. A.K. and M.J.D. developed variation discovery and analysis methods. A.K., J.T.R. and R.E.H. analyzed structural variation. T.G. performed CNV analysis. S.G. supervised the sequencing. S. Sigurdsson and K.L.-T. designed the custom capture array. M.P. performed direct PCR of the polymorphic VNTR candidates selected by N.P. A.G. and D.A. performed Southern blot and long-range PCR of the MUC1 VNTR. C.N. supervised the MUC1 VNTR sequencing approach. A.G. performed VNTR allele cloning and generation of sequencing libraries. E.K., R.D., D.P. and S. Steelman performed Sanger sequencing. D.B.J. assembled and analyzed VNTR Sanger sequencing. M.G. provided RNA-seq support. S.K. supervised the immunohistochemistry and immunofluorescence work performed by V.B., H.H., J.S. and P.V. A.K., B.B. and M.D. developed the C-insertion genotype assay. M.C.Z. provided informatic and sequencing consultation. A.R. provided informatic and analysis consultation. C.Y., J.T.R., M.N.C., I.G.-V., R.E.H. and E.R. provided informatic support. The manuscript was written primarily by A.K., A.G., A.J.B., E.S.L. and M.J.D. The supplementary information was prepared mainly by A.K., A.G., D.B.J., B.B., R.E.H., S. Sigurdsson, S.K. and A.J.B.

Corresponding authors

Correspondence to Anthony J Bleyer, Eric S Lander or Mark J Daly.

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Competing interests

A.K., A.G., B.B. and M.D. are listed as inventors on the C-insertion genotyping assay under patent review, filed by the Broad Institute. The other authors declare no competing interests.

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Supplementary Note, Supplementary Figures 1–5 and Supplementary Tables 1–3 (PDF 306 kb)

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Kirby, A., Gnirke, A., Jaffe, D. 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). https://doi.org/10.1038/ng.2543

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