25 October 2021 IMPORTANT NOTICE: On December 19th, the following changes were made to the Dosage Sensitivity FTP download files. The first change slightly altered the Haploinsufficiency and Triplosensitivity Phenotype OMIM IDs columns to support ontologies other than OMIM. Consequently, the column headers were renamed from “Haploinsufficiency Phenotype OMIM ID” to just “Haploinsufficiency Disease ID”, and “Triplosensitivity Phenotype OMIM ID” to just “Triplosensitivity Disease ID.” To distinguish between the multiple ontologies, the ID now include the relative prefix (for example, MONDO:0010758 or OMIM:314580). For backward compatibility, any entries without an ontology prefix can be considered an OMIM ID. For example, an entry of 314580 can be treated equivalent to OMIM:314580. This change only affects the files: Clingen_gene_curation_list_GRCh37.tsv Clingen_gene_curation_list_GRCh38.tsv Clingen_region_curation_list_GRCh37.tsv Clingen_region_curation_list_GRCh38.tsv The second change allowed for full representation of PAR in the FTP files. As you know, PAR genes have genomic coordinates on both the X and Y chromosomes, however, due to a programming error we are only presenting one. The genes currently affected are WASIR1, VAMP7, and CSF2RA. To fully represent both sets of data for PAR genes, two lines are now included within each relevant FTP files for each PAR gene. One line represents the X chromosome data, and one line represents the Y chromosome data. For current consumers of the FTP file data who do not care about full representation of PAR genes, this should have no impact, as the second line will merely overwrite the first on import. For those consumers who are interested in full representation of PAR genes, minimal changes to the import scripts should allow collecting of all data. This change will affect all gene curation files. If you have any questions, please contact us at clingen@clinicalgenome.org. Best Regards, The ClinGen Dosage Sensitivity Team ----------------------------------------------------------------------- This site holds files produced by the Dosage Sensitivity Curation Working Group of the ClinGen Consortium (formerly the ISCA Evidence based review committee). The goal of this group is to curate regions of the genome with respect to their dosage sensitivity. More information about this effort can be found on these sites: https://dosage.clinicalgenome.org/ https://www.clinicalgenome.org/working-groups/dosage-sensitivity-curation/ The files in this directory contain data for genes and regions that have been through the review process. These files are updated daily. Files are available for genes and regions localized on both GRCh37 and GRCh38. tsv files: The tsv files have a header and contain all of the curation information found on the ClinGen Dosage Sensitivity Map web pages: ClinGen_gene_curation_list.tsv: tab separated file for gene curation ClinGen_region_curation_list.tsv: tab separated file for region curation BED files: BED files are available for gene curation. There are separate files for haploinsufficiency and triplosensitivity as the BED file only has one column for 'score'. Because the score column expects a number rather than text, the following scores have been converted to numbers: Dosage sensitivity unlikely: 40 Gene associated with autosomal recessive phenotype: 30 For more information on scoring: https://dosage.clinicalgenome.org/help.shtml ClinGen_haploinsufficiency_gene.bed: BED file with haploinsufficiency scores ClinGen_triplosensitivity_gene.bad: BED file with triplosensitivity scores ClinGen_recurrent_CNV_V1.1.aed - This file contains recurrent copy number variations (CNV) that have been, or are in the process of being, reviewed by the recurrent CNV ClinGen DSC Subgroup. This file is available in genome build hg19 and hg38 and can be opened in ChAS software. The orange bars represent each recurrent region. The black bars represent the segmental duplication clusters/breakpoints. ClinGen_recurrent_CNV_V1.1.bed - This file contains recurrent copy number variations (CNV) that have been, or are in the process of being, reviewed by the recurrent CNV ClinGen DSC Subgroup. This file is available in genome build hg19 and hg38 and can be opened in array analysis software that utilizes .bed files as well as the UCSC genome browser. The orange bars represent each recurrent region. The black bars represent the segmental duplication clusters/breakpoints.