DAC - Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

Nitzan Rosenfeld
nitzan.rosenfeld@cruk.cam.ac.uk

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Dataset ID	Description	Technology	Samples
EGAD00001008589	This study compared different assays for the detection of circulating tumour DNA (ctDNA) in serial plasma from stage IA-IV breast cancer patients, targeting structural variants (SVs), single nucleotide variants (SNVs) and/or somatic copy-number aberrations (SCNAs). SV-multiplex PCR, SNV-/SV-hybrid capture, and different depths of whole-genome sequencing (WGS) were used to evaluate ctDNA levels, demonstrating concordant results. SNV-hybrid capture targeting 1,347-7,491 mutations was the most sensitive assay, detecting 67% (36/54) of samples down to an allele fraction (AF) of 0.00024%. SV-multiplex PCR, targeting 21-47 mutations, detected 63% (34/54) of samples down to 0.00047% AF and has potential as a clinical assay.	HiSeq X Ten Illumina HiSeq 4000 Illumina MiSeq Illumina NovaSeq 6000	1284