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Clinical-Genomics / scout

VCF visualization interface
https://clinical-genomics.github.io/scout
BSD 3-Clause "New" or "Revised" License
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Export of reduced penetrance file based on gene panels via CLI #1300

Open henrikstranneheim opened 5 years ago

henrikstranneheim commented 5 years ago

We use the this type of file in the analysis together with genmod to modify the inheritance models based on reduced penetrance:

head -n 3 grch37_cust003-cmms-red-pen_-2017-.tsv
#Chromosome Gene_start  Gene_stop   HGNC_symbol Protein_name    Symptoms    Biochemistry    Imaging Disease_trivial_name    Trivial_name_short  Phenotypic_disease_model    OMIM_morbid Gene_locus  UniProt_id  Ensembl_gene_id Ensemble_transcript_ID  Reduced_penetrance  Clinical_db_gene_annotation Disease_associated_transcript   Ensembl_transcript_to_refseq_transcript Gene_description    Genetic_disease_model
8   27317279    27337400    CHRNA2                          CHRNA2:610353>AD    CHRNA2:118502   8p21.2      ENSG00000120903     CHRNA2  FullList,EP CHRNA2:NM_000742.3  CHRNA2:ENST00000240132>NM_001282455/XM_005273396|ENST00000407991>NM_000742/XM_005273397|ENST00000518712|ENST00000520208|ENST00000520600|ENST00000520650|ENST00000520933|ENST00000521921|ENST00000522008|ENST00000523529|ENST00000523695|ENST00000524096 CHRNA2:cholinergic_receptor__nicotinic__alpha_2_(neuronal)
20  61975420    62009753    CHRNA4                          CHRNA4:600513>AD|188890 CHRNA4:118504   20q13.33        ENSG00000101204     CHRNA4  FullList,EP     CHRNA4:ENST00000370263>NM_000744/NM_001256573/XM_005260189/XM_005260191|ENST00000463705|ENST00000467563|ENST00000475033|ENST00000480012|ENST00000498043 CHRNA4:cholinergic_receptor__nicotinic__alpha_4_(neuronal)
moonso commented 4 years ago

Would this be for a specific gene panel? Otherwise it will be tricky... What did you have in mind @henrikstranneheim ?

henrikstranneheim commented 4 years ago

Preferably for all panels (going into an analysis) in one go. Then I do not have to post process the file. But it easy to call the CLI functions in a loop appending to the same file and then making the records unique. However, it should be upstreams of MIP most likely cg - adding to each analysis dynamically by querying Scout.

moonso commented 4 years ago

Ok I think one has to specify the panels on the command line. Something like this:

scout export penetrance --panel IEM --panel OMIM-AUTO
henrikstranneheim commented 4 years ago

Looks great!

dnil commented 4 years ago

It would be great if info like this was available to penetrate the panel boundaries, or end up on a special case/manual annotation gene panel..

While inheritance patterns may sometimes be specific to one gene panel, as with multiple quite different disorders from one gene, most of the time this will be about the same gene and same disorder being on a bunch of different panels. Sometimes someone has annotated it as reduced penetrance, sometimes we don't know - cf OMIM-AUTO.

moonso commented 4 years ago

How would that be done in practice @dnil ?

dnil commented 4 years ago

Not simple with the current concept. Perhaps one could store local/tentative knowledge directly on genes, and make these persistent over gene updates. On panel creation / edit such info could be passed to the panels from the hgnc genes.