is an efficient app that annotates genetic variants of the human genome and provides information about cancer-related variants and genomic regions, allele frequency data, clinical knowledge and insights using ClinVar, OMIM, COSMIC, 1000 Genomes Project allele frequencies, dbSNP and VEP(Variant Effect Predictor) database.
The resulting files will be provided as reports of excel and html type.
· VEP(Variant Effect Predictor) ver.72
http://www.ensembl.org/info/docs/tools/vep
· dbSNP
http://www.ncbi.nlm.nih.gov/SNP/
· ClinVar 20140807GRCh37
http://www.ncbi.nlm.nih.gov/clinvar
· OMIM 20140711
http://www.omim.org
· COSMIC 20140601
http://cancer.sanger.ac.uk
· 1000 Genomes Project
http://www.1000genomes.org
EDGC Annotator is an efficient app that annotates functionally genetic variants from human genome by providing information about cancer related variants, genomic regions, allele frequency data, clinical knowledge and insights using ClinVar, OMIM, COSMIC, 1000 Genomes Project allele frequencies, dbSNP and VEP(Variant Effect Predictor) database. The resulting files will be provided as reports of excel and html type.
| Column Name | Description |
| CHROM | chromosome; VCF field |
| POS | The reference position, with the 1st base having position 1; VCF field |
| ID | dbSNP rs number; VCF field |
| REF | alternate base(s); VCF field |
| QUAL | quality; VCF field |
| FILTER | filter status; VCF field |
| GT_CODE_INFO | genotype code; VEP VCF field |
| GT_INFO | genotype information; VEP VCF field |
| ALLELEFREQ_2010Nov | 1000genomes: allele frequency – 2010Nov |
| ALLELEFREQ_2011May(19/20) | 1000genomes: allele frequency – 2011May |
| ALLELEFREQ_2012April | 1000genomes: allele frequency – 2012Apr |
| CODING_CONSEQUENCE | consequence type of this variation – http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences; VEP VCF field |
| AA_CHANGE | amino acid change; VEP VCF field |
| DNA_CHANGE | dna change; VEP VCF field |
| GENE_HGNC | HGNC Gene Symbol; VEP VCF field |
| SIFT | the SIFT prediction and/or score, with both given as prediction(score); VEP VCF field |
| POLYPHEN | the PolyPhen prediction and/or score; VEP VCF field |
| COSMICID | COSMIC: Gene Id |
| GENE_COSMIC | COSMIC: Gene Name |
| COUNT_COSMIC | COSMIC: Count – How many samples have this mutation |
| INFO_COSMIC | COSMIC: Information |
| GENE_OMIM | OMIM: Gene Symbol(s) |
| GENE_TITLE_OMIM | OMIM: Title |
| MIM_OMIM | OMIM: MIM Number |
| DISORDERS_OMIM | OMIM: Disorders |
| AUTOSOMAL_DOMINANT_CLINVAR | ClinVar: autosomal dominant |
| SIGNIFICANCE_CLINVAR | ClinVar: Variant Clinical Significance, 0 – Uncertain significance, 1 – not provided, 2 – Benign, 3 – Likely benign, 4 – Likely pathogenic, 5 – Pathogenic, 6 – drug response, 7 – histocompatibility, 255 – other |
| CLNDBN_CLINVAR | ClinVar: Variant disease name |
| CLNDSDBID_CLINVAR | ClinVar: Variant disease database ID |
| CLNACC_CLINVAR | ClinVar: Variant Accession and Versions |
| CLNACC_CLINVAR_LINKS | ClinVar: hyperlink(s) for Variant Accession and Versions |
Result from EDGC Annotator do not provide any medical diagnoses. Analyses and reports provided by EDGC Annotator is for informational and research purposes only and are subject to change. Eone-Diagnomics Genome Center is not liable for any result or report generated by Illumina BaseSpace Application.