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Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer

Charlotte Derpoorter (UGent) , Ruben Van Paemel (UGent) , Katrien Vandemeulebroecke (UGent) , Jolien Vanhooren (UGent) , Bram De Wilde (UGent) , Genevieve Laureys (UGent) and Tim Lammens (UGent)
(2023) PEDIATRIC HEMATOLOGY AND ONCOLOGY. 40(4). p.326-340
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Abstract
Survival rates for pediatric cancer have significantly increased the past decades, now exceeding 70-80% for most cancer types. The cause of cancer in children and adolescents remains largely unknown and a genetic susceptibility is considered in up to 10% of the cases, but most likely this is an underestimation. Families with multiple pediatric cancer patients are rare and strongly suggestive for an underlying predisposition to cancer. The absence of identifiable mutations in known cancer predisposing genes in such families could indicate undiscovered heritability. To discover candidate susceptibility variants, whole genome sequencing was performed on germline DNA of a family with two children affected by Burkitt lymphoma. Using an inheritance-based filtering approach, 18 correctly segregating coding variants were prioritized without a biased focus on specific genes or variants. Two variants in FAT4 and DCHS2 were highlighted, both involved in the Hippo signaling pathway, which controls tissue growth and stem cell activity. Similarly, a set of nine non-coding variants was prioritized, which might contribute, in differing degrees, to the increased cancer risk within this family. In conclusion, inheritance-based whole genome sequencing in selected families or cases is a valuable approach to prioritize variants and, thus, to further unravel genetic predisposition in childhood cancer.
Keywords
Oncology, Hematology, Pediatrics, Perinatology and Child Health, Familial, germline predisposition, missing heritability, pediatric cancer, whole genome sequencing, FAMILIAL BURKITTS-LYMPHOMA, TUMOR-SUPPRESSOR, GASTRIC-CANCER, PREDISPOSITION, FAT4, MUTATIONS, RESTRICT, ACTS

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Citation

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MLA
Derpoorter, Charlotte, et al. “Whole Genome Sequencing and Inheritance-Based Variant Filtering as a Tool for Unraveling Missing Heritability in Pediatric Cancer.” PEDIATRIC HEMATOLOGY AND ONCOLOGY, vol. 40, no. 4, 2023, pp. 326–40, doi:10.1080/08880018.2022.2101723.
APA
Derpoorter, C., Van Paemel, R., Vandemeulebroecke, K., Vanhooren, J., De Wilde, B., Laureys, G., & Lammens, T. (2023). Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer. PEDIATRIC HEMATOLOGY AND ONCOLOGY, 40(4), 326–340. https://doi.org/10.1080/08880018.2022.2101723
Chicago author-date
Derpoorter, Charlotte, Ruben Van Paemel, Katrien Vandemeulebroecke, Jolien Vanhooren, Bram De Wilde, Genevieve Laureys, and Tim Lammens. 2023. “Whole Genome Sequencing and Inheritance-Based Variant Filtering as a Tool for Unraveling Missing Heritability in Pediatric Cancer.” PEDIATRIC HEMATOLOGY AND ONCOLOGY 40 (4): 326–40. https://doi.org/10.1080/08880018.2022.2101723.
Chicago author-date (all authors)
Derpoorter, Charlotte, Ruben Van Paemel, Katrien Vandemeulebroecke, Jolien Vanhooren, Bram De Wilde, Genevieve Laureys, and Tim Lammens. 2023. “Whole Genome Sequencing and Inheritance-Based Variant Filtering as a Tool for Unraveling Missing Heritability in Pediatric Cancer.” PEDIATRIC HEMATOLOGY AND ONCOLOGY 40 (4): 326–340. doi:10.1080/08880018.2022.2101723.
Vancouver
1.
Derpoorter C, Van Paemel R, Vandemeulebroecke K, Vanhooren J, De Wilde B, Laureys G, et al. Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer. PEDIATRIC HEMATOLOGY AND ONCOLOGY. 2023;40(4):326–40.
IEEE
[1]
C. Derpoorter et al., “Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer,” PEDIATRIC HEMATOLOGY AND ONCOLOGY, vol. 40, no. 4, pp. 326–340, 2023.
@article{8768224,
  abstract     = {{Survival rates for pediatric cancer have significantly increased the past decades, now exceeding 70-80% for most cancer types. The cause of cancer in children and adolescents remains largely unknown and a genetic susceptibility is considered in up to 10% of the cases, but most likely this is an underestimation. Families with multiple pediatric cancer patients are rare and strongly suggestive for an underlying predisposition to cancer. The absence of identifiable mutations in known cancer predisposing genes in such families could indicate undiscovered heritability. To discover candidate susceptibility variants, whole genome sequencing was performed on germline DNA of a family with two children affected by Burkitt lymphoma. Using an inheritance-based filtering approach, 18 correctly segregating coding variants were prioritized without a biased focus on specific genes or variants. Two variants in FAT4 and DCHS2 were highlighted, both involved in the Hippo signaling pathway, which controls tissue growth and stem cell activity. Similarly, a set of nine non-coding variants was prioritized, which might contribute, in differing degrees, to the increased cancer risk within this family. In conclusion, inheritance-based whole genome sequencing in selected families or cases is a valuable approach to prioritize variants and, thus, to further unravel genetic predisposition in childhood cancer.}},
  author       = {{Derpoorter, Charlotte and Van Paemel, Ruben and Vandemeulebroecke, Katrien and Vanhooren, Jolien and De Wilde, Bram and Laureys, Genevieve and Lammens, Tim}},
  issn         = {{0888-0018}},
  journal      = {{PEDIATRIC HEMATOLOGY AND ONCOLOGY}},
  keywords     = {{Oncology,Hematology,Pediatrics,Perinatology and Child Health,Familial,germline predisposition,missing heritability,pediatric cancer,whole genome sequencing,FAMILIAL BURKITTS-LYMPHOMA,TUMOR-SUPPRESSOR,GASTRIC-CANCER,PREDISPOSITION,FAT4,MUTATIONS,RESTRICT,ACTS}},
  language     = {{eng}},
  number       = {{4}},
  pages        = {{326--340}},
  title        = {{Whole genome sequencing and inheritance-based variant filtering as a tool for unraveling missing heritability in pediatric cancer}},
  url          = {{http://doi.org/10.1080/08880018.2022.2101723}},
  volume       = {{40}},
  year         = {{2023}},
}
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