> 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-v4.3/product-guide/dragen-v4.3/dragen-dna-pipeline/biomarkers/biomarker-brca-large-rearrangement.md).

# BRCA Large Genomic Rearrangment

Large genomic rearrangements affecting one or more exons account for approximately 5\~10% of all disease-causing mutations in BRCA1 and BRCA2 genes in patients with hereditary breast and ovarian cancer syndrome. DRAGEN LR can detect within gene large genomic rearrangements in tumor-only mode for targeted panels such as TruSight Oncology 500. The performance has been verified for BRCA1/2 with TruSight Oncology 500 Assay.

## Command-Line Options

Use the following command-line options to run large rearrangement detection. The same cmd line options can be tested on other tumor-only pipelines.

`--tso500-solid-brca-lr=true` Set to `true` enable large rearrangement parameters. This is not limited to TruSight Oncology 500 Assay.

`--cnv-normals-list` Specify the panel of normal samples to measure instrinsic biases of the upstream processes to allow for proper normalization. To generate a panel of normals, see the example command line. The panel of normal samples should be well matched to the case sample under analysis.

`--cnv-target-bed` Specify the targeted regions of the panel.

`--cnv-within-gene-lr-bed` Specify the gene regions in BED format to do large rearrangment calling. Example file:

```
chr17	41196312	41277500	BRCA1
chr13	32889617	32973809	BRCA2
```

### Example to generate panel of normal

Run the following command on each normal sample to generate `.target.counts.gc-corrected.gz` file.

```
dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--enable-cnv true \
--cnv-enable-gcbias-correction true \
--cnv-enable-split-intervals true \
--cnv-target-bed <BED> \
--tumor-bam-input <BAM>
```

Put the path to the generated `.target.counts.gc-corrected.gz` files into a txt file. One file per line. This will be the file given to `--cnv-normals-list`.

### Example command lines

```
dragen \
-r <HASHTABLE> \
--output-directory <OUTPUT> \
--output-file-prefix <SAMPLE> \
--tso500-solid-brca-lr true \
--cnv-normals-list <PON> \
--cnv-target-bed <BED> \
--cnv-within-gene-lr-bed <GENE.bed> \
--tumor-bam-input <BAM>
```

## LR Output

The output file `.cnv.LR.json` contains the breakpoints detected for each specified gene region. The following is an example output file.

```
"Breakpoints": {
        "BRCA1": {
            "nSegs": "1",
            "segments": [
                {
                    "id": "BRCA1.1",
                    "chromosome": "chr17",
                    "start": "41197309",
                    "stop": "41276383",
                    "nBin": "95",
                    "segmentMean": "0.77611423479585684",
                    "segmentMeanLog2": "-0.36565907927374325"
                }
            ]
        },
         "BRCA2": {
            "nSegs": "3",
            "segments": [
                {
                    "id": "BRCA2.1",
                    "chromosome": "chr13",
                    "start": "32890596",
                    "stop": "32945239",
                    "nBin": "61",
                    "segmentMean": "0.80852624347115876",
                    "segmentMeanLog2": "-0.3066334928504777"
                },
                {
                    "id": "BRCA2.2",
                    "chromosome": "chr13",
                    "start": "32950805",
                    "stop": "32954284",
                    "nBin": "8",
                    "segmentMean": "0.45378940514841132",
                    "segmentMeanLog2": "-1.1399051688173489"
                },
                {
                    "id": "BRCA2.3",
                    "chromosome": "chr13",
                    "start": "32956413",
                    "stop": "32972909",
                    "nBin": "10",
                    "segmentMean": "0.890907164346186",
                    "segmentMeanLog2": "-0.16665298919550192"
                }
            ]
        }
    }
```

Note that coordinate follows BED format \[start,stop) suggesting:

* start: segment starting coordinate. (0-base inclusive: first base on the chromosome is numbered 0. start coordinate is included in the interval)
* stop: segment stop coordinate. (0-base exclusive: first base on the chromosome is numbered 0. stop coordinate is not included in the interval)


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