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Targeted Sequencing of a Pediatric Metabolic Bone Gene Panel Using a Desktop Semiconductor Next-Generation Sequencer

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Abstract

Metabolic bone disorders in children frequently are heritable, but the expanding number of genes associated with these conditions makes it difficult to perform molecular diagnosis. In the present study, we therefore evaluated a semiconductor (SC)-based sequencing system for this purpose. A total of 65 DNA samples were analyzed comprising 24 samples from patients with 27 known pathogenic mutations, 6 samples from patients with prior negative Sanger sequencing, and 35 consecutive samples from patients with suspected heritable metabolic bone disorders who had not had prior molecular diagnosis. In the samples with known pathogenic mutations, 26 of 27 mutations were identified by SC sequencing. All single nucleotide variants were correctly identified, but a 7-nucleotide duplication in CYP27B1 was not detected. SC sequencing revealed two pathogenic mutations in the six samples where prior Sanger sequencing had failed to identify a mutation. Finally, pathogenic mutations were found in 27 samples of patients with unknown mutation status (15 in COL1A1, 9 in COL1A2, 1 in LEPRE1, 1 in LRP5, 1 in PHEX). Subsequent Sanger sequencing confirmed the mutations in all 27 samples. In conclusion, we found that SC sequencing is suitable for the diagnosis of heritable metabolic bone disorders in children.

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Acknowledgments

We thank Ghalib Bardai for assistance with sequencing data analysis and Mark Lepik for preparation of the figures. This study was supported by the Shriners of North America and the Fonds de recherche Québec - Santé.

Conflict of interests

Frank Rauch received support from the Chercheur-Boursier Clinicien program of the Fonds de Recherche du Québec – Santé and has received consultancy fees from Genzyme Inc and Alexion Inc. Francis H Glorieux has received consultancy fees from Novartis Inc., Amgen Inc. and Alexion Inc. Liljana Lalic, Pierre Moffatt, and Peter Roughley declare no conflict of interest.

Human and Animal Rights and Informed Consent

All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000. Informed consent was obtained from study participants or the legal guardians.

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Authors and Affiliations

  1. Shriners Hospital for Children and McGill University, 1529 Cedar Avenue, Montreal, QC, H3G 1A6, Canada

    Frank Rauch, Liljana Lalic, Francis H. Glorieux, Pierre Moffatt & Peter Roughley

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  1. Frank Rauch
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  2. Liljana Lalic
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  3. Francis H. Glorieux
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Correspondence to Frank Rauch.

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Rauch, F., Lalic, L., Glorieux, F.H. et al. Targeted Sequencing of a Pediatric Metabolic Bone Gene Panel Using a Desktop Semiconductor Next-Generation Sequencer. Calcif Tissue Int 95, 323–331 (2014). https://doi.org/10.1007/s00223-014-9897-9

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  • DOI: https://doi.org/10.1007/s00223-014-9897-9

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