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Case Reports
. 2009 Apr;84(4):524-33.
doi: 10.1016/j.ajhg.2009.03.010. Epub 2009 Apr 2.

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

Helen V Firth  1 , Shola M Richards, A Paul Bevan, Stephen Clayton, Manuel Corpas, Diana Rajan, Steven Van Vooren, Yves Moreau, Roger M Pettett, Nigel P Carter
Affiliations
Case Reports

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

Helen V Firth et al. Am J Hum Genet. 2009 Apr.

Abstract

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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Figures

Figure 1
Figure 1
Overview of DECIPHER The DECIPHER database is accessed via the World Wide Web so that patient phenotypic and genomic information can be deposited in a secure and private project areas by consortium members. Interaction with bioinformatic tools allows clinicians and scientists to interpret the genomic information. With informed consent, data become viewable within the Ensembl genome browser so that patients with overlapping copy-number changes can be readily identified.
Figure 2
Figure 2
Searching the Genome by Phenotype Using the phenotype search term “cleft palate” generates an ideogram (below) and list of all the consenting patients that DECIPHER knows to have cleft palate and displays their genomic aberrations. Two clusters, one on 1q and the other on 5q, are seen together.
Figure 3
Figure 3
DECIPHER Syndrome Report for 8p23.1 Deletion Syndrome Detailed information about known syndromes is maintained by expert advisors within DECIPHER. The copy-number change is displayed on a ideogram (1), in a genome browser showing normal copy-number variants (2), and with links to OMIN (3) and Ensembl (4).
Figure 4
Figure 4
Patient Images (A) Case 1. (B) Case 2. (C) Case 3.
Figure 5
Figure 5
International Collaboration through DECIPHER New syndromes defined with the help of DECIPHER: 17q21.3 in 2006, 14q11.2 in 2007, and 19q13.1144 in 2009.
See this image and copyright information in PMC

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