The UMCCR germline panel is currently composed only of entries from the PMCC FCC panel with no modifications applied by the curation team. While there is only one source list, the panel creation process is structured similarly to the somatic panel so that additional sources may be added in the future.
- Review literature, community for new sources
- Include new sources in
1_panel_sources/if appropriate with feedback from curation team
- Apply any upstream changes for sources in
1_panel_sources/ - Construct final panel in
2_final_panel/ - Generate panel data files in
3_panel_data/
The following genes are absent from the CPSR superpanel (panel 0) [v20220203;
data/grch38/virtual_panels/cpsr_superpanel.grch38.tsv] and hence do not appear in the CPSR report:
ensembl_gene_symbol ensembl_gene_id hgnc_symbol hgnc_id refseq_gene_symbol ncbi_gene_id
CSDE1 ENSG00000009307.17 CSDE1 HGNC:29905 CSDE1 7812
EGLN1 ENSG00000135766.9 EGLN1 HGNC:1232 EGLN1 54583
EGLN2 ENSG00000269858.6 EGLN2 HGNC:14660 EGLN2 112398
While variants in these genes do not appear in the CPSR report, they are present in the output germline small variant VCF file.