High-sensitivity sequencing reveals multi-organ somatic mosaicism causing DICER1 syndrome

Leanne de Kock, Yu Chang Wang, Timothée Revil, Dunarel Badescu, Barbara Rivera, Nelly Sabbaghian, Mona Wu, Evan Weber, Claudio Sandoval, Saskia M J Hopman, Johannes H M Merks, Johanna M van Hagen, Antonia H M Bouts, David A Plager, Aparna Ramasubramanian, Linus Forsmark, Kristine L Doyle, Tonja Toler, Janine Callahan, Charlotte EngelenbergDorothée Bouron-Dal Soglio, John R Priest, Jiannis Ragoussis, William D Foulkes

Research output: Contribution to journalArticlepeer-review

57 Citations (Scopus)

Abstract

BACKGROUND: Somatic mosaicism is being increasingly recognised as an important cause of non-Mendelian presentations of hereditary syndromes. A previous whole-exome sequencing study using DNA derived from peripheral blood identified mosaic mutations in DICER1 in two children with overgrowth and developmental delay as well as more typical phenotypes of germline DICER1 mutation. However, very-low-frequency mosaicism is difficult to detect, and thus, causal mutations can go unnoticed. Highly sensitive, cost-effective approaches are needed to molecularly diagnose these persons. We studied four children with multiple primary tumours known to be associated with the DICER1 syndrome, but in whom germline DICER1 mutations were not detected by conventional mutation detection techniques.

METHODS AND RESULTS: We observed the same missense mutation within the DICER1 RNase IIIb domain in multiple tumours from different sites in each patient, raising suspicion of somatic mosaicism. We implemented three different targeted-capture technologies, including the novel HaloPlex(HS) (Agilent Technologies), followed by deep sequencing, and confirmed that the identified mutations are mosaic in origin in three patients, detectable in 0.24-31% of sequencing reads in constitutional DNA. The mosaic origin of patient 4's mutation remains to be unequivocally established. We also discovered likely pathogenic second somatic mutations or loss of heterozygosity (LOH) in tumours from all four patients.

CONCLUSIONS: Mosaic DICER1 mutations are an important cause of the DICER1 syndrome in patients with severe phenotypes and often appear to be accompanied by second somatic truncating mutations or LOH in the associated tumours. Furthermore, the molecular barcode-containing HaloPlex(HS) provides the sensitivity required for detection of such low-level mosaic mutations and could have general applicability.

Original languageEnglish
Pages (from-to)43-52
Number of pages10
JournalJournal of medical genetics
Volume53
Issue number1
DOIs
Publication statusPublished - Oct 2015
Externally publishedYes

Keywords

  • Child
  • Child, Preschool
  • Computational Biology/methods
  • DEAD-box RNA Helicases/genetics
  • DNA Mutational Analysis
  • Female
  • Genetic Association Studies
  • High-Throughput Nucleotide Sequencing/methods
  • Humans
  • Loss of Heterozygosity
  • Male
  • Mosaicism
  • Mutation
  • Neoplasms, Multiple Primary/diagnosis
  • Phenotype
  • Ribonuclease III/genetics
  • Sensitivity and Specificity
  • Syndrome

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