Support ACCESS-HEME gene panel

[n1zea144]

• [ ] Follow up with Aijaz and confirm delivery method
• [ ] If needed, update to include new "standalone" cohort that gets merged in
• [ ] Find and adjust references to P/SID pattern matching in cmo-pipelines

Per Aijaz, the panel will be release within the next month. Below is the gene list, we will need to get additional metadata for the cBioPortal file from Aijaz. We should give external collaborations (AZ, Sophia) a heads up before this goes into production.

ABL1 CD79A H2AC6 MYC SETBP1 AKT1 CD79B HRAS MYD88 SF3B1 ARID1A CD83 ID3 NCOA3 SGK1 ASXL1 CDKN2A IDH1 NF1 SMC1A ASXL2 CEBPA IDH2 NOTCH1 SMC3 ATM CREBBP IGLL5 NOTCH2 SOCS1 B2M CSF3R IKZF1 NPM1 SPEN BACH2 CXCR4 IRF4 NRAS SPRED2 BCL2 DMD JAK1 NT5C2 SRSF2 BCL6 DNMT3A JAK2 PAX5 SRY BCOR DTX1 JAK3 PHF6 ST6GAL1 BCORL1 DUSP2 KDM6A PIM1 STAG2 BIRC3 EP300 KIT PLCG2 STAT6 BRAF ETS1 KMT2A PML TCL1A BTG2 ETV6 KMT2D POU2AF1 TET2 BTK EZH2 KRAS PRDM1 TNFAIP3 CALR FLT3 LRMP PTEN TNFRSF14 CARD11 FOXO1 LTB PTPN11 TP53 CBL GATA1 MAP2K1 RAD21 U2AF1 CBLB GATA2 MEF2B RHOA UBE2J1 CCND1 GNA13 MET RHOH WT1 CD58 GNAS MPL RUNX1 XPO1 CD74 GRHPR MS4A1 SERPINA9 ZRSR2

[averyniceday]

Confirmed introduction of new endpoints from Mihir -- waiting for followup on which datatypes will be included in the endpoint (e.g. support gene panel file creation for SV, CNA, etc.)

Have begun making changes in the cvr codebase - using placeholder endpoint names. Remianing tasks

• [ ] testing (dev server?)
• [ ] evaluate/introduce redcap project inclusion
• [ ] add to overall merge