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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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question about annotated oncogenes #71

Closed ChongJenniferZhang closed 4 years ago

ChongJenniferZhang commented 4 years ago

Hi， Thanks for this great software. I've noticed that AmpliconArchitect annotates oncogenes in the amplicons. However, when we analyzed data, some tumor suppressor genes like "RB1","APC" etc are also listed in the output file. Does that means AA annotates all genes involved? Could you please tell me what is the gene list used by AA? Thanks a lot.

Best wishes, Jennifer

virajbdeshpande commented 4 years ago

Hello Jennifer,

The genes displayed by AA were downloaded from COSMIC, although since COSMIC is regularly updated there might be some differences w.r.t. the latest version.

On Thu, Jul 16, 2020 at 1:20 PM ChongJenniferZhang notifications@github.com wrote:

Hi， Thanks for this great software. I've noticed that AmpliconArchitect annotates oncogenes in the amplicons. However, when we analyzed data, some tumor suppressor genes like "RB1","APC" etc are also listed in the output file. Does that means AA annotates all genes involved? Could you please tell me what is the gene list used by AA? Thanks a lot.

Best wishes, Jennifer

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Anastasia-pav commented 4 years ago

Hi Viraj,

Could you please tell me the number of genes downloaded from COSMIC that is used in AA?

All the best, Anastasia

jluebeck commented 4 years ago

Hi Anastasia,

In the hg19 oncogene .gff file, there are 490 entries. For GRCh37, there are 464 entries. This information can be found in the $AA_DATA_REPO under the cancer/oncogenes directory for each reference annotated.

Best, Jens

Anastasia-pav commented 4 years ago

Okay great, thanks Jens.