The cancer predisposition report can show variants found in a number of well-known cancer predisposition genes, and the specific set of genes can be customized by the user by choosing any of the following virtual gene panels (0 - 43):
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Panel 0 is a non-conservative, research-based superpanel assembled through multiple sources on cancer predisposition genes:
- A list of 151 genes that were curated and established within TCGA’s pan-cancer study (Huang et al., Cell, 2018).
- A list of 112 protein-coding genes that has been curated in the CanVar-UK resource on cancer predisposition genes
- Genes from all Genomics England PanelApp panels for inherited cancers and tumor syndromes, as well as DNA repair genes (detailed below)
- Additional genes deemed relevant for cancer predisposition (i.e. contributed by CPSR users etc.)
- IMPORTANT: Note that mutations in many of the genes in panel 0 are not directly linked to risk of tumor development, but are rather associated with other genetic diseases. There is however evidence from the literature that these diseases may carry secondary, context-dependent cancer risks (e.g. ABCB11, COL7A1, HNF1A, PAH)
The combination of the above sources resulted in a non-redundant set of n = 555 genes of relevance for cancer predisposition (see complete details below)
Data with respect to mechanisms of inheritance (MoI - autosomal recessive (AR) vs. autosomal dominant (AD) etc.) and whether mechanisms of disease are associated with loss-of-function (LoF) or gain-of-function (GoF) were primarily retrieved from Maxwell et al., Am J Hum Genet, 2016, and Genomics England PanelApp. We want to make it explicit that this list is by no means regarded as an international consensus, but should rather be subject to continuous update by the international community that carry expertise on genetic risk factors for cancer. Do you miss other genes of relevance for cancer predisposition/inherited tumor syndromes? Please forward a list of gene identifiers, preferably also with mode of inheritance and literature support to sigven AT ifi.uio.no, so we can include them in Panel 0.
Panels 1 - 43 are panels for inherited cancers and tumor syndromes assembled within the Genomics England PanelApp: