# 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**.