Case type and region of interest

Add new case page > Case info screen > Select case type

Select the case type in order to define the proper analysis of your case.

Select the region of interest in order to filter-in only variants located within the proper regions.

Regional information is used to process genomic data in a variety of ways. Regional information influences the variants presented in gene panels, exomes, and genomes, variant quality and variant annotations.

Regardless of the case type, you can select any region of interest.

When selecting a Custom BED as you region of interest, you must select a specific BED file that is configured in your organization.

Case type table:

Case Type	Default Region of Interest BED
Research Genome	None
Whole Genome	Full Genes
Exome	Clinical Regions
Custom Panel	Clinical Regions

Case type + regions of interest BEDs are applied as follows:

1. Research Genome + No Region of interest: There is no intersection and all variants are viewable (Note: data pipeline time will increase, and intergenic variants have very limited annotations).

2. Whole Genome + Full genes: A wide range of genomic regions BED file. It contains:

   • "RefSeq ALL" transcripts and "GENCODE" full genes regions with 5Kbp upstream and 5Kbp downstream

   • Within this range, all “Clinical Regions” are included

   • All dosage regions (HI/TS sig level 1, 2 or 3)

3. Exome + Clinical regions: A comprehensive bed file that includes every clinically relevant region. The following are included:

   • “RefSeq Curated” and “GENCODE” regions with flanking areas of 50bp from each side 5UTR and 3UTR region for protein coding genes (based on RefSeq)

   • OMIM disease-related RNA genes (50bp flanking)

   • All Clinvar Pathogenic variants regions (flanking 50bp)

   • Promoters region (EPDnew human version 006, flanking 50bp)

   • Known STR regions (Dragen 4.0 specification file)

   • All microRNA genes (flanking 50bp based on HGNC)

   • Full mtDNA region

4. Custom Panel+ Custom BED: You can select any existing BED file configured in your organization to restrict according to it's regions.

BED files

2MB

GRCh37_clinical_regions.bed.gz

GRCh37 Clinical Regions BED

2MB

GRCh38_clinical_regions.bed.gz

GRCh38 Clinical Regions BED

294KB

GRCh37_full_genes.bed.gz

GRCh37 Full Genes BED

311KB

GRCh38_full_genes.bed.gz

GRCh38 Full Genes BED

1MB

GRCh37_coding_regions.bed.gz

GRCh37 Coding Regions BED

2MB

GRCh38_coding_regions.bed.gz

GRCh38 Coding Regions BED