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. a. To add a disease term, type the term (for example, Sarcoma) in the Associated Disease Term(s) field. b. Select the applicable term from the list that displays. c. Make sure that the disease term displays under the field (for example, Sarcoma (SNOMEDCT: 1187396000)). d. To delete a disease term, select the X next to it. e. Select Save to accept any changes.

6. Update the key gene names as follows. a. 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. b. Select Save to accept any changes.

7. Update genome wide thresholds as follows. a. For Genome Wide Thresholds, enter values for the following Tumor Mutational Burden (mut/MB) thresholds:

   • TMB-Low (the range starting point defaults to 0.0)

   • TMB-High

     ❗ If there is a conflict between the low and high values, an error message displays indicating which value needs to be corrected.

   b. Enter values for the following Microsatellite Instability (% unstable sites) thresholds:

   • MS-Stable (the range starting point defaults to 0.0)

   • MSI-High (the range end point defaults to 100)

   c. Enter values for the following Global Instability Score thresholds:

   • GIS-Low (the range starting point defaults to 0.0)

   • GIS-High

   d. 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

Field Name	Description
Cancer Types	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

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.