> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/connected-insights/configure/configuration/c-disease-configuration.md). # Disease Configuration The Disease Configuration section can be used to view, add, and edit the key genes associated with disease terms. ## Add a New Disease Configuration 1. On the Configuration page, select the **General** tab. 2. Select **Disease Configuration**. 3. Select **+New** on the right side of the pane. 4. In the Disease Name field, type the disease name. This name can be based on a group of diseases or cancer types (for example, Bone). 5. In the Associated Disease Term(s) field, type a term (for example, Sarcoma). 6. Select the applicable term from the list that displays. 7. Make sure that the disease term displays under the field (for example, Sarcoma (SNOMEDCT: 1187396000)). 8. Under Key Genes, type a gene name in the field. You can enter one gene name per line, or multiple gene names separated by commas. A maximum of 250 names can be entered. The names are case-sensitive. 9. Select **Save**. ## Update Disease Configuration 1. On the Configuration page, select the **General** tab. 2. Select **Disease Configuration** to expand the list of disease categories. 3. Select a disease (for example, Bone). 4. On the right side of the screen, select **Edit**. 5. Update the disease terms as follows. 1. To add a disease term, type the term (for example, Sarcoma) in the Associated Disease Term(s) field. 2. Select the applicable term from the list that displays (e.g., Sarcoma (SNOMEDCT: 1187396000)) 3. To delete a disease term, select the X next to it. 4. Select **Save** to accept any changes. 6. Update the key gene names as follows. 1. For Key Genes, enter a gene name in the field.\ You can enter one gene symbol per line, or multiple gene names separated by commas. A maximum of 250 names can be entered. The names are case-sensitive. 2. Select **Save** to accept any changes. 7. Update genome wide thresholds as follows. 1. For Genome Wide Thresholds, enter values for the following Tumor Mutational Burden (mut/MB) thresholds: 1. TMB-Low 2. TMB-High 2. Enter values for the following Microsatellite Instability thresholds, depending on the measurement used (i.e., % unstable sites or sumJSD): 1. MS-Stable 2. MSI-High 3. Enter values for the following Global Instability Score thresholds, depending on the algorithm used (i.e., Myriad or DRAGEN): 1. GIS-Low 2. GIS-High 4. Select **Save** to accept any changes. ## Cancer Types with Key Genes The following table shows the default key genes for select cancer types based on data provided by the Illumina Medical Affairs team. ### Default Key Genes for Select Cancer Types | Cancer Type | Key Genes | | ---------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Melanoma | BRAF, KIT, NRAS, NTRK1, NTRK2, NTRK3, TERT, GNAQ, GNA11, BAP1, SF3B1, EIF1AX, CDKN2A, BRCA2, PALB2, NF1, PTEN, CDK4, MC1R, MITF, MBD4 | | Prostate | ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK2, FANCL, FGFR2, FGFR3, PALB2, PPP2R2A, RAD51B, RAD51C, RAD51D, RAD54L, NTRK1, NTRK2, NTRK3, ATR, EPCAM, ABRAXAS1, FANCA, GEN1, MLH1, MRE11, MSH2, MSH6, MUTYH, NBN, PMS2 | | Uterine and Cervical | ERBB2, ESR1, FOXO1, NCOA3, PAX3, PAX7, SMARCA4, SUZ12, NTRK1, NTRK2, NTRK3, ALK, ATRX, BCOR, CDK4, DICER1, FGFR2, GREB1, KMT2C, MDM2, MYBL1, NCOA2, CD274, PGR, PHF1, PIK3CA, PLAG1, RAD51B, RB1, TERT, TFE3, TP53, YWHAE, PTEN, POLE, MLH1, MSH2, MSH6, PMS2 | | Lung | ALK, BRAF, EGFR, ERBB2, KRAS, MET, NUTM1, RET, ROS1, NTRK1, NTRK2, NTRK3, CD274 | | Breast | BRCA1, BRCA2, ERBB2, ESR1, PIK3CA, NTRK1, NTRK2, NTRK3, CD274, PALB2, RAD51D, RAD51C, ATM, STK11, TP53, NF1, NBN, PTEN | | Thyroid | BRAF, HRAS, KRAS, NRAS, RET, TERT, NTRK1, NTRK2, NTRK3, PAX8, PPARG, PTEN | | Ovarian | BRCA1, BRCA2, FOXL2, NTRK1, NTRK2, NTRK3, ATM, BRIP1, MLH1, MSH2, PALB2, RAD51C, RAD51D, NBN, STK11 | | Colorectal | BRAF, ERBB2, KRAS, NRAS, NTRK1, NTRK2, NTRK3, MLH1, MSH2, MSH6, PMS2 | | CNS | ATRX, BRAF, EGFR, H3F3A, HIST1H3B, IDH1, IDH2, PTCH1, TERT, TP53, NTRK1, NTRK2, NTRK3, MGMT, PTEN | | Bone | EWSR1, EGFR, ERG, ETV1, ETV4, FLI1, IDH1, NTRK1, NTRK2, NTRK3, FEV, IDH2, FUS | | Other Solid (as a default for any other cancertypes) | ALK, APC, BCOR, BRAF, BRCA1, BRCA2, CDK4, CIC, CTNNB1, DNAJB1, ERBB2, EPCAM, ERG, ETV1, ETV4, ETV6, EWSR1, FGFR2, FGFR3, FOXO3, GLI1, IDH1, KIT, KRAS, MDM2, MLH1, MSH2, MSH6, MYOD1, NAB2, NTRK1, NTRK2, NTRK3, PAX3, PAX7, PDGFRA, PMS2, RANBP2, SDHB, SMARCB1, TFE3, WT1, YAP1, RET, ROS1, MET, IDH2 | The following resources can be used to identify other actionable genes to expand your key genes with: * [OncoKB Gene List](https://www.oncokb.org/actionable-genes) * [CKB Gene List](https://ckbhome.genomenon.com/gene/grid) * [CIViC Gene List](https://civicdb.org/features/home) ## Restore Disease Configuration to Default Settings 1. On the Configuration page, select the **General** tab. 2. Select **Disease Configuration**. 3. Select .... 4. Select **Restore to Default**. 5. To confirm the action, select **Yes,Restore to Default**. 6. To confirm the action, select **Yes, Delete**. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation by asking a question. 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