Bioinformatics

DECIPHER: Shedding Light on Chromosomal Imbalance and Phenotype Interpretation


Presented at the 7th European Cytogenetics Conference, July 4-7 2009, Stockholm, Sweden

Corpas M1, Richards S1, Bevan AP1, Van Vooren S3, Pettett RM1, Firth HV2 ,Carter NP1

1. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SA, UK

2. Cambridge University Dept of Medical Genetics, Addenbrooke’s Hospital, Cambridge CB2 2QQ, UK

3. K.U.Leuven, ESAT/SCD, Kasteelpark Arenberg 10, B-3001 Leuven-Heverlee, Belgium

Availability: https://decipher.sanger.ac.uk

DECIPHER is a web-based database that stores genomic array data and phenotypes from patients world-wide [1]. DECIPHER is a powerful resource for clinical diagnosis and management of patients with congenital abnormalities, providing tools to help in the interpretation of copy number changes in patients with developmental disorders. Enabled by an international collaborative research consortium, DECIPHER hosts data from more than 2200 patients from over 100 centres in more than 20 countries.

In DECIPHER, molecular rearrangements (as defined by genomic array analysis) are mapped on to the reference sequence in Ensembl. Genes within the affected region are identified and prioritised according to phenotype. Clusters of rearrangements within the same region in patients with comparable phenotypes allow new syndromes and genes involved in human development and disease to be defined [2-4]. Of particular importance, DECIPHER utilises a suite of integrated bioinformatics tools to help to distinguish apparently benign copy number variants from those potentially causing disease.

Key features in DECIPHER for aiding in the interpretation of patient data include:

  • Trio analysis tool – A trio of an affected individual and parents are analysed to determine de novo or familial/inherited conditions.

  • Gene prioritisation tool – advanced text mining searches PubMed for associations between highlighted genes and phenotypes.

  • Search tool – a search engine for data (with previous consent from the patient) within DECIPHER to facilitate the identification of rearrangement clusters and links between phenotype and genomic location.

References

  1. Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. Am J Hum Genet. 2009 Apr;84(4):524-33.

  2. Malan V, Raoul O, Firth HV, Royer G, Turleau C, Bernheim A, Willatt L, Munnich A, Vekemans M, Lyonnet S, Cormier-Daire V, Colleaux L, J Med Genet. 2009;. PMID: 19126570 DOI: 10.1136/jmg.2008.062034

  3. Zahir F, Firth HV, Baross A, Delaney AD, Eydoux P, Gibson WT, Langlois S, Martin H, Willatt L, Marra MA, Friedman JM. J Med Genet. 2007;44;556-61. PMID: 17545556 DOI: 10.1136/jmg.2007.050823

  4. Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L, Gribble S, Curley R, Cumming S, Dunn C, Kalaitzopoulos D, Porter K, Prigmore E, Krepischi-Santos AC, Varela MC, Koiffmann CP, Lees AJ, Rosenberg C, Firth HV, de Silva R, Carter NP. Nat Genet. 2006;38;1032-7. PMID: 16906163 DOI: 10.1038/ng1858

Categories: Bioinformatics

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