Meta-Analysis of gross insertions causing human genetic disease: Novel mutational mechanisms and the role of replication slippage

Authors

  • Jian-Min Chen,

    Corresponding author
    1. INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France
    • INSERM U613, Etablissement Français du Sang–Bretagne, 46 rue Félix Le Dantec, 29220 Brest Cedex 2, France
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  • Nadia Chuzhanova,

    1. Biostatistics and Bioinformatics Unit, Cardiff University, Heath Park, Cardiff, United Kingdom
    2. Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, United Kingdom
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  • Peter D. Stenson,

    1. Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, United Kingdom
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  • Claude Férec,

    1. INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France
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  • David N. Cooper

    1. Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, United Kingdom
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Abstract

Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and ∼10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all ≥276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene. Hum Mutat 25:207–221, 2005. © 2005 Wiley-Liss, Inc.

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