Protein Prediction from cancer

Question

[deepakkumarbt]

How I can predict all the possible proteins from a cancer genome ??

Please suggest me the way how it can be done.

Cancer Genome (fastq file) -- > preprocessing --> denovo genome assembly -- > protein prediction from assembled genome. ??

Answer 1

[Satyajeet Khare]

Protein prediction from cancer genome is difficult. You may need transcriptome (RNA-Seq) for that. From genome, you can get mutations, insertion, deletions and translocations. You may not need de-novo assembly for that. Alignment to existing genome should be sufficient.

Answer 2

[Nicolas Rosewick]

One thing you could do is to infer a list of proteins that are modified in cancer genome due to specific mutations leading to modifications in the CDS of transcripts (premature polyA, frameshifts, etc...)

[deepakkumarbt]

Dear Satya & NicoBxl,

Thanks for your response.

I think my question is not clear. Please let me know whether this procedure can be followed or not.

Denovo Assembled Cancer Genome -- > ORF Finders -- > Protein prediction.

I dont want to miss any single protein that can be translated from a cancer genome. My interest is sometimes these proteins may not be of human origin.

Please update me what can be done further.

[Satyajeet Khare]

If your ORF finder accurately predicts splicing, you may be able to predict proteins. But its difficult not to "miss any single protein". Since expression of non-canonical ORFs and alternative isoforms is condition specific and may not be predictable from genome sequence.

Answer 3

[deepakkumarbt]

Dear Satya & NicoBxl,

Thanks for your response.

I think my question is not clear. Please let me know whether this procedure can be followed or not.

Denovo Assembled Cancer Genome -- > ORF Finders -- > Protein prediction.

I dont want to miss any single protein that can be translated from a cancer genome. My interest is sometimes these proteins may not be of human origin.

Please update me waht can be done further.