DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
Open accessAbstract
Many patients suffering from developmental disorders harbor submicroscopic deletions or duplications that, by affecting the copy number of dosage-sensitive genes or disrupting normal gene expression, lead to disease. However, many aberrations are novel or extremely rare, making clinical interpretation problematic and genotype-phenotype correlations uncertain. Identification of patients sharing a genomic rearrangement and having phenotypic features in common leads to greater certainty in the pathogenic nature of the rearrangement and enables new syndromes to be defined. To facilitate the analysis of these rare events, we have developed an interactive web-based database called DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources) which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance, inversions, and translocations. DECIPHER catalogs common copy-number changes in normal populations and thus, by exclusion, enables changes that are novel and potentially pathogenic to be identified. DECIPHER enhances genetic counseling by retrieving relevant information from a variety of bioinformatics resources. Known and predicted genes within an aberration are listed in the DECIPHER patient report, and genes of recognized clinical importance are highlighted and prioritized. DECIPHER enables clinical scientists worldwide to maintain records of phenotype and chromosome rearrangement for their patients and, with informed consent, share this information with the wider clinical research community through display in the genome browser Ensembl. By sharing cases worldwide, clusters of rare cases having phenotype and structural rearrangement in common can be identified, leading to the delineation of new syndromes and furthering understanding of gene function.
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The human NDR2 gene (STK38l) has been identified as a susceptibility gene for neurodevelopmental disorders, intellectual disability, and autism spectrum disorder.
“The human NDR2 gene (STK38l) has been identified as a susceptibility gene for neurodevelopmental disorders, intellectual disability (Madencioglu et al. 2021; Firth et al. 2009), and autism spectrum disorder (Fromer et al. 2014).”
From The Serine/Threonine Kinase <scp>NDR2</scp> Regulates Integrin Signaling, Synapse Formation, and Synaptic Plasticity in the Hippocampus (2025) · cites this paper as Firth et al. 2009
The Case Studies section (p. 7) links learning disability to a chromosome 14q11.2 deletion and names SUPT16H and CHD8 as candidate genes. Searches for NDR2 and STK38L found no passage identifying that gene as a susceptibility gene for intellectual disability or another neurodevelopmental disorder. The autism claim is cited to a different source. (LLM, conf=0.76)
Experimental — accuracy not yet measuredClinical translation of rare disease technologies has benefited from information resources including open databases of genes, clinically interpreted variants, and patient records.
“Clinical translation of these technologies has benefited from a series of information resources, including open databases of genes associated with rare disorders (for example, OMIM and ORPHANET)21, clinically interpreted variants (for example, ClinVar and ClinGen)22,23 and patient records (for example, DECIPHER and MyGene2 (https://mygene2.org/MyGene2))17.”
From A brief history of human disease genetics (2020) · cites this paper as [17]
The value of sharing genetic and phenotypic data from patients with suspected rare undiagnosed genetic diseases has fostered global collaborative networks designed to match patients with similar variants and/or phenotypes across continents.
“The value of sharing genetic and phenotypic data from those thought to harbour rare undiagnosed genetic diseases has fostered global collaborative networks (for example, Matchmaker Exchange, DECIPHER and GeneMatcher) designed to match patients with similar genetic variants and/or phenotypic manifestations, even across continents17–19.”
From A brief history of human disease genetics (2020) · cites this paper as [17]
In the authors' databases and DECIPHER, five deletions of 313 Kb to 3.31 Mb removing 5 to 23 genes including part or all of ADNP have been described.
“In our own databases and in DECIPHER35, five deletions with sizes 313Kb-3.31Mb, taking away 5-23 genes including (part of) ADNP, have been described.”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [35]
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“These predictions have now been incorporated into the DECIPHER database 19 , assisting clinicians in identifying potential disease mechanisms.”
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- Authors
- Firth, H. V., Richards, S. M., Bevan, A. P., Clayton, S., Corpas, M., Rajan, D., Vooren, S. V., Moreau, Y., Pettett, R. M., & Carter, N. P.
- Affiliations
- University of Cambridge (GB)
- Wellcome Sanger Institute (GB)
- KU Leuven (BE)
- Corresponding author
- Firth, Helen V.
- Carter, Nigel P.
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2009-04
- Volume
- 84
- Issue
- 4
- Pages
- 524-533
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2667985
- OpenAlex
- W2036841261
- Cited by
- 1,990
- References
- 41
- Citations by year
- 2026: 68 · 2025: 132 · 2024: 171 · 2023: 181 · 2022: 211 · 2021: 237 · 2020: 176 · 2019: 144 · 2018: 132 · 2017: 117 · 2016: 64 · 2015: 71 · 2014: 71 · 2013: 65 · 2012: 48
- FWCI
- 28.11
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion, other-oa)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lirias (submittedVersion, other-oa)
- Funders
- Wellcome Trust (WT077008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- DECIPHER, chromosomal imbalances, copy number variation, genotype-phenotype correlation, chromosomal inversions, chromosomal translocation, developmental disorders, genetic counseling, new syndrome
- MeSH terms
- Adult, Child, Child, Preschool, Chromosome Aberrations, Female, Genes, Dominant, Humans, Male, Phenotype, Syndrome, Genome, Human, Gene Dosage, Computational Biology, Internet, Databases, Genetic, Comparative Genomic Hybridization
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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