Default region of interest kits

A region of interest (ROI) BED file determines which genomic regions are included in variant analysis. It functions as a preprocessing filter, determining which variants proceed to annotation and interpretation.

Default ROI kits by case type

If no custom ROI BED kit is applied to a case, the system applies a default ROI BED file based on the case type. All default ROI BED files are available for download (see Default ROI kit details).

Case type	Default region of interest BED
Research Genome	None
Whole Genome	Full Genes
Exome	Clinical Regions
Custom Panel	Clinical Regions

Default ROI kit details

Full Genes

A BED file covering a wide range of genomic regions. It contains:

• "RefSeq ALL" transcripts and "GENCODE" full gene regions, with 5 Kbp upstream and 5 Kbp downstream
• Within this range, all “Clinical Regions” are included
• All dosage regions (HI/TS sig level 1, 2, or 3)

Moreover, liftover versions of both reference regions are included for the current and previous range versions.

Sources:

• Liftover is done using CrossMap (v0.5.2), chain hg19ToHg38.over.chain.gz
• NCBI RefSeq regions are based on release 105 (hg19) and release 110 (hg38)
• GENCODE regions are based on release V19 (hg19) and release V41 (hg38)
• All microRNA genes are based on the HGNC miRNA definition from December 2022
• ClinGen dosage regions, December 2022
• Promoters from EPDnew human version V6
• mtDNA CRS
• RNA disease genes based on OMIM and HGNC (Dec 2022): ATXN8OS, TERC, IL12A-AS1, FAAHP1, NUTM2B-AS1, GAS8-AS1, RNU12, MIR204, IGHG2, SLC7A2-IT1, MIR99A, RMRP, XIST, MEG3, DIRC3, MIR17HG, GNAS-AS1, LRTOMT, LINC00299, DUX4L1, MIR137, MIR140, MIR605, SNORD118, RNU4ATAC, HELLPAR, IGHG1, IGHM, MIR19B1, RNU7-1, LINC00237, MIR2861, MIR4718, IGHV3-21, IGHV4-34, IGKC, KCNQ1OT1, MIR184, MIR96, H19, HYMAI, PCDHA9, UGT1A1, AFG3L2P1, DISC2, SNORA31, TRU-TCA1-1, PCDHGA4, TRAC, ECEL1P3, MIAT
• ClinVar variants (ClinVar Dec 2022) with any pathogenic or likely pathogenic significance, and some drug responses associated with pathogenicity
• 50K STR regions based on the DRAGEN 4.0 Specification file

CNV variants are not confined to regions of interest.

Files

Download files used in v100.39.0+

GRC38_full_genes.bed

876KB

Open

GRCh38 Full Genes v100.39.0+

GRC37_full_genes.bed

831KB

Open

GRCh37 Full Genes v100.39.0+

Download files used up to v38.0

GRC38_full_genes (1).bed

887KB

Open

GRCh38 Full Genes ≤v38.0

GRC37_full_genes (1).bed

839KB

Open

GRCh37 Full Genes ≤v38.0

Clinical Regions

This BED file includes regions relevant to disease interpretation, specifically:

• “RefSeq Curated” and “GENCODE” regions with 50 bp flanking regions on each side of all exons, including coding exons and UTRs, for protein-coding genes
• OMIM disease-related RNA genes (flanking 50 bp)
• All ClinVar pathogenic variant regions (flanking 50 bp)
• Promoter regions (EPDnew human version 006, flanking 50 bp)
• Known STR regions (DRAGEN 4.0 specification file)
• All microRNA genes (flanking 50 bp, based on HGNC)
• Full mtDNA region

For consistency, the GRCh38 version includes the lifted-over regions from GRCh37 (using CrossMap for liftover).

CNV variants are not confined to regions of interest.

Files

Download files used in v100.39.0+

GRC38_clinical_regions.bed

6MB

Open

GRCh38 Clinical Regions v100.39.0+

GRC37_clinical_regions.bed

5MB

Open

GRCh37 Clinical Regions v100.39.0+

Download files used up to v38.0

GRC38_clinical_regions (1).bed

5MB

Open

GRCh38 Clinical Regions ≤v38.0

GRC37_clinical_regions (1).bed

5MB

Open

GRCh37 Clinical Regions ≤v38.0