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myCMIE 2.0

2 Genomic profiles

It supports either a single case or a case series.

2.1 Example

The app has two built-in examples, one for “coloreactal cancer” case and the other one for a rare cancer case, “Cholangiocarcinoma”.

2.2 Upload

The app accepts patient genomic profiles in .csv format.

The app also takes table format as an input as introduced below.

2.2.1 A single case

A basic query of a single case study will take a table listing genomic alteration reported. It should include at least four columns:

  • gene: gene symbols reported

  • type: The alteration groups, such as Main and VUS. The app currently supports profiles with 2 groups.

  • alteration: The specific alterations such as mutation sites, amplification, or deletion (allow NA).

  • alt_type: Needs to be one of below: MUT, AMP, DEL

(The column names are required to be identical)

2.2.2 A case series

If there is a case series, the app will take one .csv table file as the input.
Users can concatenate all the profiles in one table and add an Id column specifying the profile names.

Note: The profile names (Id column) can be from patients, cell lines, etc. myCMIE takes genomic alteration profiles from multiple sources as long as they stay in the format we specify above.

2.3 Online Input

For quick query, the app has a editable table for users to input the genomic profile.

You can directly double click cells edit the table. There are pre-set buttons to add rows for mutation/copy number change options.

2.4 Example

Supplement table for easy copy.

Example in table format:

Table.1 Total profile of patient genomic alteration
gene type alteration alt_type
MLH1 VUS E319K MUT
BCL2L1 Main amplification AMP
TP53 Main R248W MUT
ASXL1 VUS amplification AMP
BRCA2 VUS amplification AMP
CDK8 VUS amplification AMP
NBN VUS M152I MUT