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Measurement of uncertainty of CNV breakpoints

The DRAGEN CNV caller algorithm uses deviation in expected read depth in genomic regions (~1000bp windows) to identify gains or losses in genomic content.

Due to the nature of this algorithm, the breakpoints reported by the pipeline are not an accurate representation of exact CNV breakpoints.

Our comparison of DRAGEN CNV breakpoints with the breakpoints obtained from more precise approaches (Manta software, which uses information from split reads and unproperly paired sequencing reads) demonstrated:

  • For CNVs with the breakpoints in well mappable regions (i.e. where sequencing reads can be unambiguously aligned to genome reference), 87.6% of breakpoints determined by DRAGEN CNV are within 1000bp from the breakpoint determined by split or unproperly paired reads, and 98.2% are within 2000bp.

  • For CNVs where the breakpoint falls withing a difficult to map region, e.g. a segmental duplication, the breakpoints cannot be unambiguously determined using short read sequencing technology, and the uncertainty depends on the size of the difficult to map region.