Diagnostic Value in Discarded Reads: Re-evaluating Multi-Mapping cfDNA Fragmentomics and GC Bias in Early-Stage Cancer.

Background. Low-coverage plasma cell-free DNA (cfDNA) sequencing is an inexpensive substrate for cancer detection. Standard pipelines discard fragments with low mapping quality, which originate mostly from repetitive DNA, although pericentromeric satellite repeats are frequently hypomethylated in cancer. We asked whether the fraction of multi-mapping cfDNA fragments differs between early-stage cancer and matched healthy controls, and how it compares with conventional fragmentomic features under strict control of technical factors. Methods. We analysed public plasma cfDNA whole-genome sequencin

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