Portal de Periódicos da CAPES

1. Clinical validation of plasma whole genome sequencing for detection of minimal residual disease from solid tumours

2023; Elsevier BV; Volume: 278-279; Linguagem: Inglês

10.1016/j.cancergen.2023.08.009

2210-7770

Felix E.G. Beaudry, Lubaina Kothari, Savo Lazic, Kristie Ng, Sharanjit Singh, Theodore Chan, Faridah Mbabaali, Andrea Bevan, Samy Danial, Sarah Donald, Austin Devries, Alexander Fortuna, Iain Bancarz, Ilinca M. Lungu, Madhuran Thiagarajah, Jessica K. Miller, Carolyn Ptak, Bernard Lam, Morgan L. Taschuk, Trevor J. Pugh,

Genetic factors in colorectal cancer

Plasma whole genome sequencing of peripheral blood cell-free DNA (cfDNA) can sample the mutational spectrum of a tumour to enable minimal residual disease (MRD) detection without serial, invasive tissue collections. We validated the use of plasma WGS for detection of MRD in a CAP/CLIA/ACD-accredited laboratory using the MRDetect algorithm. We prepared libraries using automated and manual workflows across cfDNA inputs from 1-50 ng. We determined that cfDNA input levels down to 10 ng, using both automated (88 samples/run) and manual (14 samples/run) workflows, yielded comparable and reproducible duplication rates 0.2 reads / GB), and median fragment insert sizes of 165 bp. Using dilution series ranging from 100% to 0.001% of a commercial control and clinical samples with known mutation variant allele frequencies, we established a lower limit of detection of 0.05% circulating tumour DNA (ctDNA). To establish clinical sensitivity, we tested cfDNA samples from patients with a range of metastatic solid tumours (13 ovarian, 5 melanoma, 5 pancreatic, and 11 other cancers). From these patients, we classified plasmas as 18 ctDNA positive and 16 negative based on detection of mutations in a cancer gene annotated by OncoKB known from matching tissue WGS. With this dataset, we established 100% sensitivity and 88% specificity. This test provides a limit of detection nearly two orders of magnitude lower than our previous panel test while maintaining high sensitivity and specificity across multiple cancer types to enable innovative new clinical MRD studies. Plasma whole genome sequencing of peripheral blood cell-free DNA (cfDNA) can sample the mutational spectrum of a tumour to enable minimal residual disease (MRD) detection without serial, invasive tissue collections. We validated the use of plasma WGS for detection of MRD in a CAP/CLIA/ACD-accredited laboratory using the MRDetect algorithm. We prepared libraries using automated and manual workflows across cfDNA inputs from 1-50 ng. We determined that cfDNA input levels down to 10 ng, using both automated (88 samples/run) and manual (14 samples/run) workflows, yielded comparable and reproducible duplication rates 0.2 reads / GB), and median fragment insert sizes of 165 bp. Using dilution series ranging from 100% to 0.001% of a commercial control and clinical samples with known mutation variant allele frequencies, we established a lower limit of detection of 0.05% circulating tumour DNA (ctDNA). To establish clinical sensitivity, we tested cfDNA samples from patients with a range of metastatic solid tumours (13 ovarian, 5 melanoma, 5 pancreatic, and 11 other cancers). From these patients, we classified plasmas as 18 ctDNA positive and 16 negative based on detection of mutations in a cancer gene annotated by OncoKB known from matching tissue WGS. With this dataset, we established 100% sensitivity and 88% specificity. This test provides a limit of detection nearly two orders of magnitude lower than our previous panel test while maintaining high sensitivity and specificity across multiple cancer types to enable innovative new clinical MRD studies.