@article{134ad1ea3d2b4f868ee45a7d1c7e064f,
title = "MPAPASS software enables stitched multiplex, multidimensional EV repertoire analysis and a standard framework for reporting bead-based assays",
abstract = "Extracellular vesicles (EVs) of various types are released or shed from all cells. EVs carry proteins and contain additional protein and nucleic acid cargo that relates to their biogenesis and cell of origin. EV cargo in liquid biopsies is of widespread interest owing to its ability to provide a retrospective snapshot of cell state at the time of EV release. For the purposes of EV cargo analysis and repertoire profiling, multiplex assays are an essential tool in multiparametric analyte studies but are still being developed for high-parameter EV protein detection. Although bead-based EV multiplex analyses offer EV profiling capabilities with conventional flow cytometers, the utilization of EV multiplex assays has been limited by the lack of software analysis tools for such assays. To facilitate robust EV repertoire studies, we developed multiplex analysis post-acquisition analysis (MPAPASS) open-source software for stitched multiplex analysis, EV database-compatible reporting, and visualization of EV repertoires.",
keywords = "EV flow cytometry, atlas, liquid biopsy methods, multiplex, standardization",
author = "Welsh, {Joshua A.} and Bryce Killingsworth and Julia Kepley and Tim Traynor and Sean Cook and Jason Savage and Jenn Marte and Lee, {Min Jung} and Maeng, {Hoyoung M.} and Pleet, {Michelle L.} and Setty Magana and Andr{\'e} Gorgens and Maire, {Cecile L.} and Katrin Lamszus and Ricklefs, {Franz L.} and Merino, {Maria J.} and Linehan, {W. Marston} and Tim Greten and Tomer Cooks and Harris, {Curtis C.} and Andrea Apolo and Asim Abdel-Mageed and Ivanov, {Alexander R.} and Trepel, {Jane B.} and Matthew Roth and Mercedes Tkach and Aleksandar Milosavljevic and Clotilde Th{\'e}ry and Amy LeBlanc and Berzofsky, {Jay A.} and Eytan Ruppin and Kenneth Aldape and Kevin Camphausen and Gulley, {James L.} and Ionita Ghiran and Steve Jacobson and Jones, {Jennifer C.}",
note = "Funding Information: We thank the translational clinical programs and staff at the United States National Institutes of Health (NIH) National Cancer Institute (NCI) and the National Institute of Neurological Disorders and Stroke (NINDS) Clinics. J.W. T.T. B.K. J.K. J.S. J.L.G. J.B.T. M.M. T.G, T.C. C.H. A.A. H.M. M.L, K.C. J.G, A.L. J.B. E.R. K.A. and J.J. were supported by the Intramural Research Program of the NIH, NCI, Center for Cancer Research. S.J. S.M. and M.P. were supported by the intramural NIH, NINDS program. I.G. A.M. A.A-M. and J.J. were supported by the NIH Common Fund. J.J. specifically acknowledges NIH ZIA BC011502, ZIA BC011503, U01 HL126497, and UG3 TR002881, the Prostate Cancer Foundation, and the NCI-Curie Partnership Program (J.J. and C.T.). A.L. acknowledges NIH Z01-BC006161. F.R. was funded by the Deutsche Forschungsgemeinschaft (RI2616/3-1). A.I. acknowledges support by NIH 1R01GM120272 (A.I.) and R01CA218500 (A.I. I.G. and J.J.). J.W. is an International Society for Advancement of Cytometry (ISAC) Marylou Ingram Scholar (2019-2023). J.A.W. and J.C.J. conceived this research and designed the experiments. All authors participated in sample and data acquisition, data analysis, and editing of the manuscript. A.G. has an affiliation with Evox Therapeutics, Ltd. All other authors declare no competing interests. Funding Information: We thank the translational clinical programs and staff at the United States National Institutes of Health (NIH) National Cancer Institute (NCI) and the National Institute of Neurological Disorders and Stroke (NINDS) Clinics. J.W., T.T., B.K., J.K., J.S., J.L.G., J.B.T., M.M., T.G, T.C., C.H., A.A., H.M., M.L, K.C., J.G, A.L., J.B., E.R., K.A., and J.J. were supported by the Intramural Research Program of the NIH, NCI, Center for Cancer Research. S.J., S.M., and M.P. were supported by the intramural NIH, NINDS program. I.G., A.M., A.A-M., and J.J. were supported by the NIH Common Fund. J.J. specifically acknowledges NIH ZIA BC011502 , ZIA BC011503 , U01 HL126497 , and UG3 TR002881, the Prostate Cancer Foundation, and the NCI-Curie Partnership Program (J.J. and C.T.). A.L. acknowledges NIH Z01-BC006161 . F.R. was funded by the Deutsche Forschungsgemeinschaft ( RI2616/3-1 ). A.I. acknowledges support by NIH 1R01GM120272 (A.I.) and R01CA218500 (A.I., I.G., and J.J.). J.W. is an International Society for Advancement of Cytometry (ISAC) Marylou Ingram Scholar (2019-2023). Publisher Copyright: {\textcopyright} 2022",
year = "2022",
month = jan,
day = "24",
doi = "https://doi.org/10.1016/j.crmeth.2021.100136",
language = "English",
volume = "2",
journal = "Cell Reports Methods",
issn = "2667-2375",
publisher = "Cell Press",
number = "1",
}