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Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies
  1. Markus Schueler1,
  2. Jan Halbritter1,2,
  3. Ian G Phelps3,
  4. Daniela A Braun1,
  5. Edgar A Otto4,
  6. Jonathan D Porath1,
  7. Heon Yung Gee1,
  8. Jay Shendure5,
  9. Brian J O'Roak6,
  10. Jennifer A Lawson1,
  11. Marwa M Nabhan7,8,
  12. Neveen A Soliman7,8,
  13. Marwa M Nabhan7,8,
  14. Dan Doherty3,
  15. Friedhelm Hildebrandt1,9
    1. 1Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
    2. 2Divison of Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
    3. 3Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
    4. 4Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
    5. 5University of Washington, Genome Sciences, Seattle, Washington, USA
    6. 6Oregon Health and Science University, Molecular and Medical Genetics, Portland, Oregon, USA
    7. 7Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
    8. 8Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
    9. 9Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
    1. Correspondence to Professor Friedhelm Hildebrandt, Division of Nephrology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; friedhelm.hildebrandt{at}childrens.harvard.edu Dan Doherty MD PhD Associate Professor of Pediatrics, Divisions of Developmental Medicine and Genetic Medicine, University of Washington, Seattle Children's Hospital, Seattle, WA 98195, USA; ddoher@uw.ed

    Abstract

    Background: The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterised by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes.

    Methods: Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe strategy (MIPs) in an international cohort of 384 patients diagnosed with NPHP-RC.

    Results: As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared with the previous approach, MIPs redetected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants.

    Conclusions: In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity.

    • Genetics
    • Diagnostics
    • Molecular genetics
    • Renal Medicine

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