Multi-Region Joint Detection

Generated on 2026-05-11

Multi-Region Joint Detection

DRAGEN Multi-region Joint Detection (MRJD) is a de novo germline small variant caller for paralogous regions. In DRAGEN v4.3, MRJD covers regions that include six clinically relevant genes: NEB, TTN, SMN1/2, PMS2, STRC, and IKBKG. MRJD is compatible with hg38, hg19 and GRCh37 reference genome. The table below includes hg38 region coordinates covered by MRJD. For more information, refer to the DRAGEN user guide.

hg38 region coordinates covered by MRJD (click to expand)

Chromosome	Start	End	Description
chr2	151578759	151588523	NEB exon 98-105
chr2	151589318	151599076	NEB exon 90-97
chr2	151599871	151609628	NEB exon 82-89
chr2	178653238	178654995	TTN exon 172-180
chr2	178657498	178659255	TTN exon 181-189
chr2	178661759	178663516	TTN exon 190-198
chr5	70049522	70077596	SMN2
chr5	70924940	70953013	SMN1
chr7	5970924	5980896	PMS2 exon 13-15
chr7	5980968	5987689	PMS2 exon 11-12
chr7	6737007	6743712	PMS2CL exon 2-3
chr7	6743880	6753867	PMS2CL exon 4-6
chr15	43599563	43602630	STRC exon 24-29
chr15	43602982	43611000	STRC exon 14-23
chr15	43611040	43618800	STRC exon 1-13
chr15	43699379	43702452	STRCP1 exon 23-28
chr15	43702488	43710472	STRCP1 exon 13-22
chr15	43710502	43718262	STRCP1 exon 1-12
chrX	154555884	154565047	IKBKG exon 3-10
chrX	154639390	154648553	IKBKGP1

Sample description: 147 cell line samples from the Illumina Polaris 1 diversity panel with orthogonal small variant calls derived from long-range PCR data; RTG Tools ploidy-squash mode was used for benchmarking.

MRJD performance summary

Comparison	SNV recall	INDEL recall	Additional notes
MRJD high sensitivity mode* vs long-range PCR orthogonal truth (Figure 3)	99.7%	97.1%	Aggregated recall in PMS2 high-homology region
MRJD high sensitivity mode* vs long-read-based approach	>99.7%	>99.7%	Independent 147-sample concordance analysis
Spurious call rate analysis	-	-	<0.7% spurious call rate
Non-cell-line validation	Detected all expected clinically relevant small variants	Detected all expected clinically relevant small variants	22 non-cell-line samples (Broad Clinical Labs + Tempus AI)

*For details on MRJD calling in high sensitivity mode refer to DRAGEN user guide

MRJD Figure 3 performance summary