Compounds

[henrikstranneheim]

1. Use the Compounds column to decide if a variant is a compound or not (="-").
2. Extract compound score from string on format:

chr_start_ref-allel_alt-allel=Compound Score:

for example 17_78184393_C_T=28:17_78187720_A_G=22

[MatsDahlberg]

Jag har lagt till att http://clinical-db:8082/variants/23548020 returnerar alla compounds som hör till varianten.

Är det du menar?

{
    "rating": "", 
    "location_reliability": "", 
    "scaled_c_score_snv": 22.8, 
    "functional_annotation": "nonsynonymous SNV", 
    "stop_bp": 75490896, 
    "dbsnp129": null, 
    "lrt_whole_exome": 2e-06, 
    "omim_morbid_desc": "", 
    "rank_score": 27, 
    "hgnc_synonyms": "", 
    "phast_const_elements": "Score=668;Name=lod=690", 
    "snorna_mirna_annotation": "-", 
    "chr": "chr5", 
    "hgnc_transcript_id": "SV2C:NM_014979:exon3:c.733C>T:p.L245F,", 
    "esp6500": null, 
    "hgnc_symbol": "SV2C", 
    "GT_call_filter": "PASS", 
    "pseudogene": "", 
    "clinical_db_gene_annotation": "NO", 
    "main_location": "", 
    "dbsnp132": null, 
    "disease_group": "", 
    "ref_nt": "C", 
    "mutation_taster": 0.991596, 
    "hgmd_accession": null, 
    "hgmd": "", 
    "gene_annotation": "exonic", 
    "omim_gene_desc": "", 
    "start_bp": 75490896, 
    "hgmd_variant_type": null, 
    "otherVariants": [], 
    "dbsnp": "-", 
    "sift_whole_exome": 0.01, 
    "id": 23548020, 
    "gerp_element": 909.8, 
    "dbsnp_id": "-", 
    "compounds": [
        {
            "alt_nt": "T", 
            "start_bp": 75427518, 
            "chr": "chr5", 
            "variant": 16159878, 
            "ref_nt": "C"
        }, 
        {
            "alt_nt": "A", 
            "start_bp": 75427935, 
            "chr": "chr5", 
            "variant": 16159879, 
            "ref_nt": "G"
        }, 
        {
            "alt_nt": "C", 
            "start_bp": 75470086, 
            "chr": "chr5", 
            "variant": 16159880, 
            "ref_nt": "T"
        }, 
        {
            "alt_nt": "T", 
            "start_bp": 75490892, 
            "chr": "chr5", 
            "variant": 16159881, 
            "ref_nt": "C"
        }
    ], 
    "scaled_c_score_1000g": null, 
    "hgmd_variant_pmid": null, 
    "polyphen_var_human": 0.97, 
    "other_location": "", 
    "disease_gene_model": null, 
    "hbvdb": null, 
    "alt_nt": "T", 
    "unscaled_c_score_1000g": null, 
    "phylop_whole_exome": 2.617, 
    "expression_type": "", 
    "gene_model": "AR_compound:AD_denovo", 
    "variant_count": null, 
    "individual_rank_score": 27, 
    "unscaled_c_score_snv": 4.33376, 
    "thousand_g": null, 
    "ensembl_geneid": "ENSG00000122012;", 
    "hgnc_approved_name": "synaptic vesicle glycoprotein 2C;", 
    "genomic_super_dups": "-", 
    "polyphen_div_human": 0.996, 
    "gerp_whole_exome": 5.27
}

[henrikstranneheim]

Precis.

Sen måste MAXcompound scoren ("=XX") för varje variant lyftas ut från strängen och bli globalt sorterbar så att vi kan göra en filtrering på det bästa High scoring compound pair.

"variant": 16159880, är det ett internt ID?

[MatsDahlberg]

Ja, variant är den interna nyckeln till varianten. Den behövs så att Robin kan göra en länk till varianten.

Jag glömde att ta med combined_score, så här ser compounds entryt ut nu:

    "compounds": [
        {
            "alt_nt": "T", 
            "ref_nt": "C", 
            "variant": 16159881, 
            "combined_score": 42, 
            "chr": "chr5", 
            "start_bp": 75490892
        }, 
        {
            "alt_nt": "A", 
            "ref_nt": "G", 
            "variant": 16159879, 
            "combined_score": 28, 
            "chr": "chr5", 
            "start_bp": 75427935
        }, 
        {
            "alt_nt": "T", 
            "ref_nt": "C", 
            "variant": 16159878, 
            "combined_score": 24, 
            "chr": "chr5", 
            "start_bp": 75427518
        }, 
        {
            "alt_nt": "C", 
            "ref_nt": "T", 
            "variant": 16159880, 
            "combined_score": 24, 
            "chr": "chr5", 
            "start_bp": 75470086
        }
    ], 

[henrikstranneheim]

Kanon!

Gör databas parsern grovjobbet med sortering eller gör front-enden det? dvs ska jag engagera Robin?

[MatsDahlberg]

Databasen levererar compoundsen i en sådan ordning så att den med högst combined_score kommer först.

[MatsDahlberg]

Nu finns en service som ger alla compounds som tillhör en varint: http://clinical-db.scilifelab.se:8082/compounds/39461415

Som ger:

[
    {
        "alt_nt": "A", 
        "ref_nt": "G", 
        "variant": 37432388, 
        "combined_score": 25, 
        "chr": "chr4", 
        "start_bp": 982852
    }, 
    {
        "alt_nt": "A", 
        "ref_nt": "C", 
        "variant": 37432391, 
        "combined_score": 25, 
        "chr": "chr4", 
        "start_bp": 980896
    }, 
    {
        "alt_nt": "A", 
        "ref_nt": "G", 
        "variant": 37432389, 
        "combined_score": 24, 
        "chr": "chr4", 
        "start_bp": 980932
    }, 
    {
        "alt_nt": "C", 
        "ref_nt": "G", 
        "variant": 37432390, 
        "combined_score": 21, 
        "chr": "chr4", 
        "start_bp": 984870
    }
]