Inquiry Regarding Mutation Types in cBioPortal

[Larissa Artiles]

Dear developers,
Good afternoon. My name is Larissa, and I am currently in the final stages of completing my biology degree. Throughout my academic journey, I have extensively utilized cBioPortal for my research endeavors.
Recently, my adviser tasked me with gathering specific information regarding mutation types, namely Splice, Inframe, Missense, Gain, Shallow Depletion, Deep Deletion, and amplification. Despite my efforts, I have been unable to find detailed explanations for each of these categories within the cBioPortal platform.
Could you please provide me with comprehensive definitions and explanations for the aforementioned mutation types? Your assistance in clarifying these details would be immensely valuable for my research.
Thank you very much for your time and consideration.
Best regards, Larissa

[JJ Gao]

Dear Larissa,

Thanks for reaching out to us. Great to hear that cBioPortal has been helpful for your research endeavors!

For the copy number alteration definition, you can find them here: https://docs.cbioportal.org/user-guide/faq/#what-do-amplification-gain-deep-deletion-shallow-deletion-and--2--1-0-1-and-2-mean-in-the-copy-number-data

For mutations, we follow the Mutation Annotation Format (MAF). Here are the ones we use.

1. Frame_Shift_Del: A deletion that shifts the reading frame of the gene.

2. Frame_Shift_Ins: An insertion that shifts the reading frame.

3. In_Frame_Del: An in-frame deletion that does not disrupt the reading frame.

4. In_Frame_Ins: An in-frame insertion that preserves the reading frame.

5. Missense_Mutation: A nucleotide change that results in a different amino acid in the protein.

6. Nonsense_Mutation: A mutation that introduces a premature stop codon, truncating the protein.

7. Splice_Site: A mutation near a splice site, potentially affecting splicing of the transcript.
   

8. Translation_Start_Site: A mutation at the start codon which could impact translation.

9. Nonstop_Mutation: A mutation that changes a stop codon into one that codes for an amino acid, resulting in elongation of the protein.

10. De_novo_Start_InFrame: A mutation that creates a new start codon in frame with the original one.
    

11. De_novo_Start_OutOfFrame: A new start codon is created out of frame with the original.

12. Splice_Region: A mutation in a splice region but not directly in a splice junction.

Just to complete, here are mutation types that are in the MAF but not imported into cBioPortal (non-coding mutations).

1. Silent: A change in DNA sequence that does not result in an amino acid change (synonymous mutation).
   

2. 3'UTR: A mutation in the 3' untranslated region of a gene.
   

3. 5'UTR: A mutation in the 5' untranslated region.

4. 5'Flank: A mutation in the 5' flanking region, which is upstream of the transcription start site.

5. 3'Flank: A mutation in the 3' flanking region, downstream of the coding sequence.

6. Intron: A mutation occurring in the intronic region (between exons).

7. RNA: Mutations in genes that are not translated into proteins.

8. Targeted_Region: This category is used in targeted sequencing and refers to a mutation found in a region of interest.

9. IGR: Stands for intergenic region, indicating a mutation occurring between genes.

10. 
    

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