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Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions

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Abstract

Different types of large NF1 deletion are distinguishable by breakpoint location and potentially also by the frequency of mosaicism with normal cells lacking the deletion. However, low-grade mosaicism with fewer than 10% normal cells has not yet been excluded for all NF1 deletion types since it is impossible to assess by the standard techniques used to identify such deletions, including MLPA and array analysis. Here, we used ultra-deep amplicon sequencing to investigate the presence of normal cells in the blood of 20 patients with type-1 NF1 deletions lacking mosaicism according to MLPA. The ultra-deep sequencing entailed the screening of 96 amplicons for heterozygous SNVs located within the NF1 deletion region. DNA samples from three previously identified patients with type-2 NF1 deletions and low-grade mosaicism with normal cells as determined by FISH or microsatellite marker analysis were used to validate our methodology. In these type-2 NF1 deletion samples, proportions of 5.3%, 6.6% and 15.0% normal cells, respectively, were detected by ultra-deep amplicon sequencing. However, using this highly sensitive method, none of the 20 patients with type-1 NF1 deletions included in our analysis exhibited low-grade mosaicism with normal cells in blood, thereby supporting the view that the vast majority of type-1 deletions are germline deletions.

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Acknowledgements

This work has been funded by the Deutsche Forschungsgemeinschaft (DFG) grant KE 724/12-2.

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Authors and Affiliations

  1. Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany

    Anna Summerer, Eleonora Schäfer & Hildegard Kehrer-Sawatzki

  2. Department of Neurology, University Hospital Hamburg Eppendorf, 20246, Hamburg, Germany

    Victor-Felix Mautner

  3. Department of Genetics, University of Alabama at Birmingham, Birmingham, USA

    Ludwine Messiaen

  4. Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK

    David N. Cooper

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  1. Anna Summerer
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  2. Eleonora Schäfer
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  3. Victor-Felix Mautner
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  4. Ludwine Messiaen
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  6. Hildegard Kehrer-Sawatzki
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Correspondence to Hildegard Kehrer-Sawatzki.

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Summerer, A., Schäfer, E., Mautner, VF. et al. Ultra-deep amplicon sequencing indicates absence of low-grade mosaicism with normal cells in patients with type-1 NF1 deletions. Hum Genet 138, 73–81 (2019). https://doi.org/10.1007/s00439-018-1961-5

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