Essa base de dados permite identificar uma variante dentro do arquivo VCF de um paciente e gerar um reporte sobre o diagnóstico molecular do paciente com ATTR indicando o grau de comprometimento do gene.
T1 2020 - Pós-Graduação em Bioinformática aplicada a Genômica Médica - Albert Einstein.
Site do Projeto
Grupo
- Anelisie Santos
- Bruno Martinucci
- Carlos Eugênio
- Kelin Chen
- Rocío Cuaspa
O Docker Engine está disponível em diversas de plataformas Linux, macOS e Windows 10 por meio do Docker Desktop. Encontre seu sistema operacional preferido abaixo.
Nota: Para executar o Docker sem privilégios de root, consulte Executar o daemon do Docker como um usuário não root (modo Rootless).
Crie o grupo docker.
sudo groupadd dockerAdicione seu usuário ao grupo docker.
sudo usermod -aG docker $USER- Baixar a image do ensembl-vep (caso não tenha)
- Clonar o git ttr-database
- Executar o ensembl-vep com as opções:
--id "18 29172865 29172865 G/A 1"--species homo_sapiens--force--database--assembly GRCh37--refseq--tabe--custom /data/TTRdb_cureted.sort.vcf.gz,TTRdb,vcf,exact,0,REVEL,REVEL_TTMDB,REVEL_RISK
docker pull ensemblorg/ensembl-vepgit clone https://github.com/projetottr/ttr-database.gitou
Neste exemplo vamos anotar a variante 18 29172865 29172865 G/A 1, o resultado será salvo no arquivo TTRdb_output.txt.
- No terminal, entre no diretório
ttr-database - Execute o
docker run(comando completo abaixo)
docker run -it -v $(pwd):/data ensemblorg/ensembl-vep ./vep --id "18 29172865 29172865 G/A 1" --species homo_sapiens --force --database --assembly GRCh37 --refseq --tab --custom /data/TTRdb_curated.vcf.gz,TTRdb,vcf,exact,0,REVEL,REVEL_TTMDB,REVEL_RISK -o /data/TTRdb_output.txtAs últimas colunas da tabela: REVEL, REVEL_TTMDB e REVEL_RISK.
## ENSEMBL VARIANT EFFECT PREDICTOR v104.3
## Output produced at 2021-08-19 01:44:03
## Connected to homo_sapiens_core_104_37 on ensembldb.ensembl.org
## Using API version 104, DB version 104
## ensembl-variation version 104.6154f8b
## ensembl version 104.1af1dce
## ensembl-funcgen version 104.59ae779
## ensembl-io version 104.1d3bb6e
## refseq version 2020-10-26 17:03:42 - GCF_000001405.25_GRCh37.p13_genomic.gff
## gencode version GENCODE 19
## assembly version GRCh37.p13
## genebuild version 2011-04
## Column descriptions:
## Uploaded_variation : Identifier of uploaded variant
## Location : Location of variant in standard coordinate format (chr:start or chr:start-end)
## Allele : The variant allele used to calculate the consequence
## Gene : Stable ID of affected gene
## Feature : Stable ID of feature
## Feature_type : Type of feature - Transcript, RegulatoryFeature or MotifFeature
## Consequence : Consequence type
## cDNA_position : Relative position of base pair in cDNA sequence
## CDS_position : Relative position of base pair in coding sequence
## Protein_position : Relative position of amino acid in protein
## Amino_acids : Reference and variant amino acids
## Codons : Reference and variant codon sequence
## Existing_variation : Identifier(s) of co-located known variants
## IMPACT : Subjective impact classification of consequence type
## DISTANCE : Shortest distance from variant to transcript
## STRAND : Strand of the feature (1/-1)
## FLAGS : Transcript quality flags
## REFSEQ_MATCH : RefSeq transcript match status
## REFSEQ_OFFSET : HGVS adjustment length required due to mismatch between RefSeq transcript and the reference genome
## SOURCE : Source of transcript
## TTRdb : /data/TTRdb_curated.vcf.gz (exact)
## TTRdb_REVEL : REVEL field from /data/TTRdb_curated.vcf.gz
## TTRdb_REVEL_TTMDB : REVEL_TTMDB field from /data/TTRdb_curated.vcf.gz
## TTRdb_REVEL_RISK : REVEL_RISK field from /data/TTRdb_curated.vcf.gz
#Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation IMPACT DISTANCE STRAND FLAGS REFSEQ_MATCH REFSEQ_OFFSET SOURCE TTRdb TTRdb_REVEL TTRdb_REVEL_TTMDB TTRdb_REVEL_RISK
18_29172865_G/A 18:29172865 A 7276 NM_000371.4 Transcript missense_variant 102 726 G/S Ggt/Agt - MODERATE - 1 - - - - NM_000371.4:c.76G>A BENIGN 0.174 VERY LOW
| Campos | Valores |
|---|---|
| #Uploaded_variation | 18_29172865_G/A |
| Location | 18:29172865 |
| Allele | A |
| Gene | 7276 |
| Feature | NM_000371.4 |
| Feature_type | Transcript |
| Consequence | missense_variant |
| cDNA_position | 102 |
| CDS_position | 76 |
| Protein_position | 26 |
| Amino_acids | G/S |
| Codons | Ggt/Agt |
| Existing_variation | - |
| IMPACT | MODERATE |
| DISTANCE | - |
| STRAND | 1 |
| FLAGS | - |
| REFSEQ_MATCH | - |
| REFSEQ_OFFSET | - |
| SOURCE | - |
| TTRdb | NM_000371.4:c.76G>A |
| TTRdb_REVEL | BENIGN |
| TTRdb_REVEL_TTMDB | 0.174 |
| TTRdb_REVEL_RISK | VERY LOW |
| RISK (valores) | RISK (descrição) |
|---|---|
| <=0.559 | VERY LOW |
| 0.559 | LOW |
| >=0.711 | MODERATE |
| >=0.929 | HIGH |
| Colunas | Valores |
|---|---|
| CHROM | 18 |
| POS | 29172877 |
| ID | NM_000371.4:c.88T>C |
| REF | T |
| ALT | C |
| HGVSC | NM_000371.4:c.88T>C |
| HGVSP | NP_000362.1:p.Cys30Arg |
| AACHANGE | Cys10Arg (p.Cys30Arg) |
| VARIANT | c.88T>C |
| EXON | Exon 2 |
| PHENOTYPE | AN, E, H, PN |
| ETHNIC GROUP | American (Hungarian) |
| REFERENCE | Uemichi (1992) J Med Genet 29, 888 |
| IMUTANT3 | Destabilizing |
| STRUM | Destabilizing |
| ISTABLE | Destabilizing |
| PROVEAN | Deleterious |
| PREDICTSNP | Deleterious |
| PHD-SNP | Deleterious |
| POLYPHEN-2 | Deleterious |
| SIFT | Deleterious |
| FATHMM | Damaging |
| MCSM | Stabilizing |
| SDM | Destabilizing |
| DUET | Stabilizing |
| DYNAMUT | Destabilizing |
| CUPSAT | Destabilizing |
| ENCOM | Destabilizing |
| FOLDX_PROTEIN_STABILITY | No effect |
| TANGO_AGGREGATION_TENDENCY | No effect |
| WALTZ_AMYLOID_PROPENSITY | No effect |
| LIMBO_CHAPERONE_BINDING_TENDENCY | No effect |
| REVEL | PATHOGENIC |
| CLINVAR | Pathogenic/Likely pathogenic/Uncertain Significance |
| SEQUENCE_DESTABILIZING | 3 |
| SEQUENCE_DELETERIOUS | 6 |
| STRUCTURE | 4 |
| AGGREGATION | 0 |
| SCORE_RISK_TTMDB | MODERATE |
| REVEL_TTMDB | 0.898 |
| START_SYMPTOMS_MIN | 63 |
| START_SYMPTOMS_MAX | 68 |
| REVEL_RISK | MODERATE |
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