DECIPHER

Overview

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants.

DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient. The patient's variant is displayed in the context of both normal variation and pathogenic variation reported at that locus thereby facilitating interpretation.

Publication

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth, H.V. et al., 2009. Am.J.Hum.Genet 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)

TSV Extraction

#population_cnv_id	chr	start	end	deletion_observations	deletion_frequency	deletion_standard_error	duplication_observations	duplication_frequency	duplication_standard_error	observations	frequency	standard_error	type	sample_size	study
1	1	10529	177368	0	0	1	3	0.075	0.555277708	3	0.075	0.555277708	1	40	42M calls
2	1	13516	91073	0	0	1	27	0.675	0.109713431	27	0.675	0.109713431	1	40	42M calls
3	1	18888	35451	0	0	1	2	0.002366864	0.706269473	2	0.002366864	0.706269473	1	845	DDD

Parsing

We parse the DECIPHER tsv file and extract the following columns:

• chr
• start
• end
• deletion_observations
• deletion_frequency
• duplication_observations
• duplication_frequency
• sample_size

Download URL

https://www.deciphergenomics.org/files/downloads/population_cnv_grch38.txt.gz https://www.deciphergenomics.org/files/downloads/population_cnv_grch37.txt.gz

JSON output

"decipher":[
  {
    "chromosome":"1",
    "begin":13516,
    "end":91073,
    "numDeletions":27,
    "deletionFrequency":0.675,
    "numDuplications":27,
    "duplicationFrequency":0.675,
    "sampleSize":40,
    "reciprocalOverlap": 0.27555,
    "annotationOverlap": 0.5901
  }
],

Field	Type	Notes
chromosome	int	Ensembl-style chromosome names
begin	int	1-based position
end	int	1-based position
numDeletions	int	# of observed deletions
deletionFrequency	float	deletion frequency
numDuplications	int	# of observed duplications
duplicationFrequency	float	duplication frequency
sampleSize	int	total # of samples
reciprocalOverlap	float	Range: 0 - 1. E.g. 0.57 would indicate a 57% reciprocal overlap
annotationOverlap	float	Range: 0 - 1. E.g. 0.57 would indicate a 57% annotation overlap