> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen/dragen-v4.5/product-guides/dragen-v4.5/germline/mrjd_accuracy.md).

# 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](/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md).

<details>

<summary>hg38 region coordinates covered by MRJD (click to expand)</summary>

| 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           |

</details>

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](/dragen/dragen-v4.5/product-guides/dragen-v4.5/dragen-dna-pipeline/small-variant-calling/multi-region-joint-detection.md#high-sensitivity-mode)

![MRJD Figure 3 performance summary](https://assets.illumina.com/content/dam/illumina-marketing/images/genomics-research/articles/pms2-small-variant-detection/PMS2-small-variant-detection-figure3.png)


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