TY - JOUR
T1 - Detection of Circulating Tumor DNA in Patients with Pancreatic Cancer Using Digital Next-Generation Sequencing
AU - Macgregor-Das, Anne
AU - Yu, Jun
AU - Tamura, Koji
AU - Abe, Toshiya
AU - Suenaga, Masaya
AU - Shindo, Koji
AU - Borges, Michael
AU - Koi, Chiho
AU - Kohi, Shiro
AU - Sadakari, Yoshihiko
AU - Dal Molin, Marco
AU - Almario, Jose A.
AU - Ford, Madeline
AU - Chuidian, Miguel
AU - Burkhart, Richard
AU - He, Jin
AU - Hruban, Ralph H.
AU - Eshleman, James R.
AU - Klein, Alison P.
AU - Wolfgang, Christopher L.
AU - Canto, Marcia I.
AU - Goggins, Michael
N1 - Funding Information:
Supported by NIH grants U01210170 (M.G.), CA62924 (M.G. and A.P.K.), and R01CA176828 (M.G.); Susan Wojcicki and Dennis Troper (M.G.); the Rolfe Pancreatic Cancer Foundation (M.G.); and by Stand Up To Cancer–Lustgarten Foundation Pancreatic Cancer Interception Translational Cancer research grant SU2C-AACR-DT25-17 (M.G.). Stand Up To Cancer is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the scientific partner of SU2C. M.G. is the Sol Goldman Professor of Pancreatic Cancer Research.
Funding Information:
Supported by NIH grants U01210170 (M.G.), CA62924 (M.G. and A.P.K.), and R01CA176828 (M.G.); Susan Wojcicki and Dennis Troper (M.G.); the Rolfe Pancreatic Cancer Foundation (M.G.); and by Stand Up To Cancer?Lustgarten Foundation Pancreatic Cancer Interception Translational Cancer research grant SU2C-AACR-DT25-17 (M.G.). Stand Up To Cancer is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the scientific partner of SU2C. M.G. is the Sol Goldman Professor of Pancreatic Cancer Research.
Publisher Copyright:
© 2020 Association for Molecular Pathology and American Society for Investigative Pathology
PY - 2020/6
Y1 - 2020/6
N2 - Circulating tumor DNA (ctDNA) measurements can be used to estimate tumor burden, but avoiding false-positive results is challenging. Herein, digital next-generation sequencing (NGS) is evaluated as a ctDNA detection method. Plasma KRAS and GNAS hotspot mutation levels were measured in 140 subjects, including 67 with pancreatic ductal adenocarcinoma and 73 healthy and disease controls. To limit chemical modifications of DNA that yield false-positive mutation calls, plasma DNA was enzymatically pretreated, after which DNA was aliquoted for digital detection of mutations (up to 384 aliquots/sample) by PCR and NGS. A digital NGS score of two SDs above the mean in controls was considered positive. Thirty-seven percent of patients with pancreatic cancer, including 31% of patients with stages I/II disease, had positive KRAS codon 12 ctDNA scores; only one patient had a positive GNAS mutation score. Two disease control patients had positive ctDNA scores. Low-normal–range digital NGS scores at mutation hotspots were found at similar levels in healthy and disease controls, usually at sites of cytosine deamination, and were likely the result of chemical modification of plasma DNA and NGS error rather than true mutations. Digital NGS detects mutated ctDNA in patients with pancreatic cancer with similar yield to other methods. Detection of low-level, true-positive ctDNA is limited by frequent low-level detection of false-positive mutation calls in plasma DNA from controls.
AB - Circulating tumor DNA (ctDNA) measurements can be used to estimate tumor burden, but avoiding false-positive results is challenging. Herein, digital next-generation sequencing (NGS) is evaluated as a ctDNA detection method. Plasma KRAS and GNAS hotspot mutation levels were measured in 140 subjects, including 67 with pancreatic ductal adenocarcinoma and 73 healthy and disease controls. To limit chemical modifications of DNA that yield false-positive mutation calls, plasma DNA was enzymatically pretreated, after which DNA was aliquoted for digital detection of mutations (up to 384 aliquots/sample) by PCR and NGS. A digital NGS score of two SDs above the mean in controls was considered positive. Thirty-seven percent of patients with pancreatic cancer, including 31% of patients with stages I/II disease, had positive KRAS codon 12 ctDNA scores; only one patient had a positive GNAS mutation score. Two disease control patients had positive ctDNA scores. Low-normal–range digital NGS scores at mutation hotspots were found at similar levels in healthy and disease controls, usually at sites of cytosine deamination, and were likely the result of chemical modification of plasma DNA and NGS error rather than true mutations. Digital NGS detects mutated ctDNA in patients with pancreatic cancer with similar yield to other methods. Detection of low-level, true-positive ctDNA is limited by frequent low-level detection of false-positive mutation calls in plasma DNA from controls.
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U2 - 10.1016/j.jmoldx.2020.02.010
DO - 10.1016/j.jmoldx.2020.02.010
M3 - Article
C2 - 32205290
AN - SCOPUS:85085296570
SN - 1525-1578
VL - 22
SP - 748
EP - 756
JO - Journal of Molecular Diagnostics
JF - Journal of Molecular Diagnostics
IS - 6
ER -