# 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: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.connected.illumina.com/connected-insights/configure/configuration/c-disease-configuration.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. 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