TY - JOUR
T1 - PACT
T2 - A pipeline for analysis of circulating tumor DNA
AU - Webster, Jace
AU - Dang, Ha
AU - Chauhan, Pradeep S.
AU - Feng, Wenjia
AU - Shiang, Alex
AU - Harris, Peter K.
AU - Pachynski, Russell K.
AU - Chaudhuri, Aadel A.
AU - Maher, Christopher A.
N1 - Funding Information:
This work was supported by the Alvin J. Siteman Cancer Research Fund at Washington University in St. Louis (A.A.C., C.A.M., R.K.P.), the National Cancer Institute of the National Institutes of Health under award number K08CA238711 (A.A.C.), the Cancer Research Foundation Young Investigator Award (A.A.C.), the American Cancer Society Institutional Research Grant: IRG-18-158-61 (H.X.D.), the Prostate Cancer Foundation Young Investigator Award (R.K.P.), the Sidney Kimmel Scholar Award (R.K.P.), the Galen Hoskin and Dina Wolkoff Giving Fund (R.K.P.), and the National Institutes of Health Clinical Center: 1 F31 CA265010-01 (J.W.).
Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press.
PY - 2023/8/1
Y1 - 2023/8/1
N2 - Motivation: Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants. Results: We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments.
AB - Motivation: Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants. Results: We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments.
UR - http://www.scopus.com/inward/record.url?scp=85167842072&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btad489
DO - 10.1093/bioinformatics/btad489
M3 - Article
C2 - 37549060
AN - SCOPUS:85167842072
SN - 1367-4803
VL - 39
JO - Bioinformatics
JF - Bioinformatics
IS - 8
M1 - btad489
ER -