Circulating cell-free DNA (cfDNA) in the plasma of cancer patients contains cell-free tumour DNA (ctDNA) derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. | Ganesamoorthy et al. BMC Cancer 2022 22 85 https s12885-021-09160-1 RESEARCH ARTICLE Open Access Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content Devika Ganesamoorthy1 2 Alan James Robertson1 Wenhan Chen1 Michael B. Hall1 Minh Duc Cao1 Kaltin Ferguson3 Sunil R. Lakhani3 4 Katia Nones5 Peter T. Simpson3 and Lachlan J. M. Coin1 2 6 7 Abstract Background Circulating cell-free DNA cfDNA in the plasma of cancer patients contains cell-free tumour DNA ctDNA derived from tumour cells and it has been widely recognized as a non-invasive source of tumour DNA for diagnosis and prognosis of cancer. Molecular profiling of ctDNA is often performed using targeted sequencing or low-coverage whole genome sequencing WGS to identify tumour specific somatic mutations or somatic copy num- ber aberrations sCNAs . However these approaches cannot efficiently detect all tumour-derived genomic changes in ctDNA. Methods We performed WGS analysis of cfDNA from 4 breast cancer patients and 2 patients with benign tumours. We sequenced matched germline DNA for all 6 patients and tumour samples from the breast cancer patients. All samples were sequenced on Illumina HiSeqXTen sequencing platform and achieved approximately 30x 60x and 100x coverage on germline tumour and plasma DNA samples respectively. Results The mutational burden of the plasma samples somatic mutations Mb of genome was higher than the matched tumour samples. However 90 of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures. In contrast cfDNA from the di-nucleosome fraction 300 bp 350 bp had much higher proportion 30 of variants shared with tumour. Despite high coverage sequencing we were unable to detect sCNAs in plasma samples. Conclusions Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples which were not
