Benchmarking Structural Variant Detection in Whole-Exome Sequencing of 67 Multiple Myeloma Cell Lines

In 67 multiple myeloma cell lines, WGS-derived SV callers on WES showed poor recall of cytogenetically known abnormalities, with no tool exceeding 20% at the coordinate level.

• Why it matters: WGS-optimized SV pipelines are often reused for WES, but cancer-specific and sequencing-context differences may reduce accuracy, leaving uncertainty about which calls are reliable.
• What they did: The study benchmarked seven WGS-derived SV tools (Delly, SvABA, BreakDancer, Smoove, LUMPY, Manta, and Pindel) on WES from 67 MM cell lines, comparing runtime and recall of known SVs by chromosome and genomics coordinate.
• The result: Smoove and Manta ran in under 2 minutes, while SvABA and Pindel required more than 2 hours; SvABA unfiltered captured 78% of known SVs at chromosome level, but all tools recalled less than 10% (and none exceeded 20% at coordinate level), implying WES SV calls need experimental confirmation.

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