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:
Example to generate panel of normal
Run the following command on each normal sample to generate .target.counts.gc-corrected.gz
file.
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
LR Output
The output file .cnv.LR.json
contains the breakpoints detected for each specified gene region. The following is an example output file.
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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