Default region of interest kits

A region of interest (ROI) BED file determines which genomic regions will be included in the 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 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)

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

Sources:

• Liftover done using CrossMap (v0.5.2), chain hg19ToHg38.over.chain.gz

• NCBI RefSeq regions are based on the release 105 (hg19) and 110 (hg38)

• Gencode regions are based on the release V19 (hg19) and V41 (hg38)

• All microRNA genes based on HGNC miRNA definition December 2022

• ClinGen Dosage region Dec 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 that are affiliated 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+

876KB

GRC38_full_genes.bed

Open

GRCh38 Full Genes v100.39.0+

831KB

GRC37_full_genes.bed

Open

GRCh37 Full Genes v100.39.0+

Download files used up to v38.0

887KB

GRC38_full_genes (1).bed

Open

GRCh38 Full Genes ≤v38.0

839KB

GRC37_full_genes (1).bed

Open

GRCh37 Full Genes ≤v38.0

Clinical Regions

This is a 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 (flanking 50bp)

• 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

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

CNV variants are not confined to regions of interest.

Files

Download files used in v100.39.0+

6MB

GRC38_clinical_regions.bed

Open

GRCh38 Clinical Regions v100.39.0+

5MB

GRC37_clinical_regions.bed

Open

GRCh37 Clinical Regions v100.39.0+

Download files used up to v38.0

5MB

GRC38_clinical_regions (1).bed

Open

GRCh38 Clinical Regions ≤v38.0

5MB

GRC37_clinical_regions (1).bed

Open

GRCh37 Clinical Regions ≤v38.0