bc2575203fb033d240ca8301ccb393f76ce15a1c jnavarr5 Tue Nov 5 16:48:36 2024 -0800 Adding the DECIPHER DDG2P track for hg38 and hg19 on hgwdev, refs #34097 diff --git src/hg/makeDb/trackDb/human/decipherContainer.html src/hg/makeDb/trackDb/human/decipherContainer.html index c9ebf90..1cc2ec8 100644 --- src/hg/makeDb/trackDb/human/decipherContainer.html +++ src/hg/makeDb/trackDb/human/decipherContainer.html @@ -34,36 +34,43 @@ tool, but without verifying the accuracy, clinical validity, or utility of the data. The DECIPHER consortium makes no warranty, express or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.

The DECIPHER database of submicroscopic chromosomal imbalance collects clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map.

-These tracks show genomic regions of reported cases and their +The CNVs and SNVs tracks show genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the -DECIPHER web site. +DECIPHER web site.

+ +

+The DDG2P (Developmental Disorders Genotype-to-Phenotype) track represents a curated +collection of genomic variants associated with developmental disorders. +Each entry in the DDG2P track corresponds to specific genomic regions linked to developmental +disorders, annotated with relevant phenotypic descriptions. +

Display Conventions and Configuration

The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. Mouseover on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant.

For the CNVs track, the entries are colored by the type of variant:

red for loss
blue for gain
grey for amplification

@@ -75,42 +82,85 @@ CNV color code is described here. Items can be filtered according to the size of the variant, variant type, and clinical significance using the track Configure options.

For the SNVs track, the entries are colored according to the estimated clinical significance of the variant:

black for likely or definitely pathogenic
dark grey for uncertain or unknown
light grey for likely or definitely benign

+For the DDG2P track, genomic variants are visually differentiated to facilitate quick and +clear identification. Variants are colored according to their clinical significance and type: +

Red - exclusively deletion site. (deletions)
Blue - exclusively duplication site. (duplication)
Grey - deletions and duplications site. (del/dup)

+ +

+The DDG2P track's mouseover tooltip provides the following information about the data: +

Position: Specifies the chromosomal range of the CNV.
Type of CNV: Indicates if the variation is a loss, gain, or + deletions/duplications(del/dup).
Frequency of CNV: Reflects how often the CNV occurs in the sampled + population.
Number of Observations: The count of times this CNV was observed in the + dataset.
Sample Size of Study: The total number of samples examined.

Method

Data provided by the DECIPHER project group are imported and processed to create a simple BED track to annotate the genomic regions associated with individual patients.

Contact

For more information on DECIPHER, please contact contact@deciphergenomics. org

Data Access

+The DECIPHER project data access and documentation can be found at +DECIPHER Downloads. +

+The raw data can be explored interactively with the +Table Browser or the +Data Integrator. +For automated analysis, the data may be queried from our +REST API +or downloaded from our +Downloads site. Please refer to our + +mailing list archives for questions, or our + +Data Access FAQ for more information. +

References

Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet. 2009 Apr;84(4):524-33. PMID: 19344873; PMC: PMC2667985