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| DECIPHER | |
|---|---|
| Name | DECIPHER |
| Type | genetic variation database |
| Established | 2004 |
| Country | United Kingdom |
| Institution | Wellcome Sanger Institute |
DECIPHER DECIPHER is a curated clinical genomics database and platform used to interpret rare chromosomal and sequence variants in human patients. It integrates genotype and phenotype data to support diagnosis, research, and variant classification across clinical genetics services, academic hospitals, research institutes, and consortia. The resource connects clinicians, geneticists, and researchers via shared case-level data to facilitate discovery similar to networks like ClinVar, dbSNP, OMIM, Human Genome Project, and UK Biobank.
DECIPHER aggregates anonymized patient-level variant calls, chromosomal copy-number variants, and associated phenotypes using structured vocabularies such as Human Phenotype Ontology, linking to reference resources including Ensembl, UCSC Genome Browser, RefSeq, GENCODE, and Genome Reference Consortium. The platform supports visualization akin to tools from Broad Institute, European Bioinformatics Institute, National Institutes of Health, Wellcome Trust Sanger Institute, and Genomics England while enabling case matching comparable to Matchmaker Exchange and cohort analyses like those performed with 1000 Genomes Project. Contributors include clinical services at institutions such as Great Ormond Street Hospital, Addenbrooke's Hospital, Great Ormond Street Hospital for Children NHS Foundation Trust, Royal Manchester Children’s Hospital, and research centers like Cambridge University and University of Oxford.
Founded in 2004 at the Wellcome Sanger Institute with funding from entities including the Wellcome Trust and collaborations involving the European Molecular Biology Laboratory and Medical Research Council, the resource evolved alongside projects such as the Deciphering Developmental Disorders study and national initiatives like Genomics England 100,000 Genomes Project. Software and data standards were influenced by initiatives at European Bioinformatics Institute, National Human Genome Research Institute, and coordination with registries like DECIPHER-adjacent clinical networks and academic consortia including Human Variome Project and International Rare Diseases Research Consortium. Technical development tracked advances from platforms developed at Broad Institute, Google Genomics, and tools used in Cancer Genome Atlas analyses.
DECIPHER ingests array comparative genomic hybridization, single-nucleotide variant calls from exome and genome sequencing, and structural variant calls using pipelines similar to those at Illumina, Thermo Fisher Scientific, GATK, and algorithms developed in groups at Wellcome Sanger Institute and Broad Institute. Variant annotation references databases like ClinVar, dbVar, gnomAD, ExAC, OMIM, and integrates phenotype terms from Human Phenotype Ontology and patient metadata standards promoted by Global Alliance for Genomics and Health. Visualization leverages genome browsers such as Ensembl and UCSC Genome Browser, and matching algorithms are conceptually related to services in Matchmaker Exchange and European Genome-phenome Archive workflows.
Clinicians at centers including Great Ormond Street Hospital, Addenbrooke's Hospital, and laboratories associated with NHS England use the platform to interpret variants for patients with developmental disorders, congenital anomalies, and neurodevelopmental conditions similar to cohorts studied in the Deciphering Developmental Disorders project and UK10K program. Researchers from University College London, University of Cambridge, University of Oxford, and international partners use aggregated DECIPHER data to discover novel disease genes, validate pathogenicity alongside resources like ClinGen and GeneMatcher, and to support publications in journals connected to groups at Nature Publishing Group, The Lancet, and American Journal of Human Genetics.
Governance involves institutions such as the Wellcome Sanger Institute, collaborating clinical genetics services at NHS England hospitals, funding bodies like the Wellcome Trust, and data-sharing frameworks from the Global Alliance for Genomics and Health and European Society of Human Genetics. Collaborative projects have linked DECIPHER to consortia including Deciphering Developmental Disorders, Genomics England, Matchmaker Exchange, and multinational rare-disease networks at universities such as Harvard University, Massachusetts General Hospital, Karolinska Institutet, and McGill University.
Data deposition and access operate under governance frameworks aligned with policies from General Data Protection Regulation, institutional review boards at centers like Wellcome Sanger Institute and NHS Research Ethics Committee, and consent practices consistent with documents from UK Biobank and Genomics England. Anonymization, controlled access, and data use agreements reflect standards advocated by Global Alliance for Genomics and Health and ethics committees at institutions such as University of Oxford and University of Cambridge to balance research utility with participant privacy.
DECIPHER-supported analyses contributed to gene-disease associations reported in studies from the Deciphering Developmental Disorders project, influenced diagnostic practice at centers including Great Ormond Street Hospital and Addenbrooke's Hospital, and enabled discoveries published in journals associated with Nature, The Lancet, and American Journal of Human Genetics. The platform has facilitated identification of pathogenic copy-number variants and novel Mendelian genes in cohorts linked to initiatives like 100,000 Genomes Project and UK10K, and supported collaboration across clinical and research institutions including Wellcome Sanger Institute, Genomics England, ClinVar, and Matchmaker Exchange.
Category:Genetics databases