1
|
Keloth VK, Banda JM, Gurley M, Heider PM, Kennedy G, Liu H, Liu F, Miller T, Natarajan K, V Patterson O, Peng Y, Raja K, Reeves RM, Rouhizadeh M, Shi J, Wang X, Wang Y, Wei WQ, Williams AE, Zhang R, Belenkaya R, Reich C, Blacketer C, Ryan P, Hripcsak G, Elhadad N, Xu H. Representing and utilizing clinical textual data for real world studies: An OHDSI approach. J Biomed Inform 2023; 142:104343. [PMID: 36935011 PMCID: PMC10428170 DOI: 10.1016/j.jbi.2023.104343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Clinical documentation in electronic health records contains crucial narratives and details about patients and their care. Natural language processing (NLP) can unlock the information conveyed in clinical notes and reports, and thus plays a critical role in real-world studies. The NLP Working Group at the Observational Health Data Sciences and Informatics (OHDSI) consortium was established to develop methods and tools to promote the use of textual data and NLP in real-world observational studies. In this paper, we describe a framework for representing and utilizing textual data in real-world evidence generation, including representations of information from clinical text in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM), the workflow and tools that were developed to extract, transform and load (ETL) data from clinical notes into tables in OMOP CDM, as well as current applications and specific use cases of the proposed OHDSI NLP solution at large consortia and individual institutions with English textual data. Challenges faced and lessons learned during the process are also discussed to provide valuable insights for researchers who are planning to implement NLP solutions in real-world studies.
Collapse
Affiliation(s)
- Vipina K Keloth
- Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Juan M Banda
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Michael Gurley
- Lurie Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Paul M Heider
- Biomedical Informatics Center, Medical University of South Carolina, Charleston, SC, USA
| | - Georgina Kennedy
- Ingham Institute for Applied Medical Research, Sydney, Australia
| | - Hongfang Liu
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Feifan Liu
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Timothy Miller
- Computational Health Informatics Program, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Olga V Patterson
- VA Informatics and Computing Infrastructure, Department of Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA; Division of Epidemiology, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah, USA; Verily Life Sciences, Mountain View, CA, USA
| | - Yifan Peng
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Kalpana Raja
- Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Ruth M Reeves
- TN Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Masoud Rouhizadeh
- Department of Pharmaceutical Outcomes & Policy, University of Florida, Gainesville, FL, USA; Biomedical Informatics and Data Science, Johns Hopkins University, Baltimore, MD, USA
| | - Jianlin Shi
- VA Informatics and Computing Infrastructure, Department of Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah, USA; Division of Epidemiology, Department of Internal Medicine, School of Medicine, University of Utah, Salt Lake City, Utah, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, USA
| | - Xiaoyan Wang
- Sema4 Mount Sinai Genomics Incorporation, Stamford, CT, USA
| | - Yanshan Wang
- Department of Health Information Management, Department of Biomedical Informatics, and Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Rui Zhang
- Institute for Health Informatics, and Department of Pharmaceutical Care & Health Systems, University of Minnesota, Minneapolis, MN, USA
| | | | | | - Clair Blacketer
- Janssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA; Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Patrick Ryan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA; Janssen Pharmaceutical Research and Development LLC, Titusville, NJ, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Noémie Elhadad
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Hua Xu
- Section of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, CT, USA.
| |
Collapse
|
2
|
Bakouny Z, Labaki C, Grover P, Awosika J, Gulati S, Hsu CY, Alimohamed SI, Bashir B, Berg S, Bilen MA, Bowles D, Castellano C, Desai A, Elkrief A, Eton OE, Fecher LA, Flora D, Galsky MD, Gatti-Mays ME, Gesenhues A, Glover MJ, Gopalakrishnan D, Gupta S, Halfdanarson TR, Hayes-Lattin B, Hendawi M, Hsu E, Hwang C, Jandarov R, Jani C, Johnson DB, Joshi M, Khan H, Khan SA, Knox N, Koshkin VS, Kulkarni AA, Kwon DH, Matar S, McKay RR, Mishra S, Moria FA, Nizam A, Nock NL, Nonato TK, Panasci J, Pomerantz L, Portuguese AJ, Provenzano D, Puc M, Rao YJ, Rhodes TD, Riely GJ, Ripp JJ, Rivera AV, Ruiz-Garcia E, Schmidt AL, Schoenfeld AJ, Schwartz GK, Shah SA, Shaya J, Subbiah S, Tachiki LM, Tucker MD, Valdez-Reyes M, Weissmann LB, Wotman MT, Wulff-Burchfield EM, Xie Z, Yang YJ, Thompson MA, Shah DP, Warner JL, Shyr Y, Choueiri TK, Wise-Draper TM, Gandhi R, Gartrell BA, Goel S, Halmos B, Makower DF, O' Sullivan D, Ohri N, Portes M, Shapiro LC, Shastri A, Sica RA, Verma AK, Butt O, Campian JL, Fiala MA, Henderson JP, Monahan RS, Stockerl-Goldstein KE, Zhou AY, Bitran JD, Hallmeyer S, Mundt D, Pandravada S, Papaioannou PV, Patel M, Streckfuss M, Tadesse E, Gatson NTN, Kundranda MN, Lammers PE, Loree JM, Yu IS, Bindal P, Lam B, Peters MLB, Piper-Vallillo AJ, Egan PC, Farmakiotis D, Arvanitis P, Klein EJ, Olszewski AJ, Vieira K, Angevine AH, Bar MH, Del Prete SA, Fiebach MZ, Gulati AP, Hatton E, Houston K, Rose SJ, Steve Lo KM, Stratton J, Weinstein PL, Garcia JA, Routy B, Hoyo-Ulloa I, Dawsey SJ, Lemmon CA, Pennell NA, Sharifi N, Painter CA, Granada C, Hoppenot C, Li A, Bitterman DS, Connors JM, Demetri GD, Florez (Duma) N, Freeman DA, Giordano A, Morgans AK, Nohria A, Saliby RM, Tolaney SM, Van Allen EM, Xu WV, Zon RL, Halabi S, Zhang T, Dzimitrowicz H, Leighton JC, Graber JJ, Grivas P, Hawley JE, Loggers ET, Lyman GH, Lynch RC, Nakasone ES, Schweizer MT, Vinayak S, Wagner MJ, Yeh A, Dansoa Y, Makary M, Manikowski JJ, Vadakara J, Yossef K, Beckerman J, Goyal S, Messing I, Rosenstein LJ, Steffes DR, Alsamarai S, Clement JM, Cosin JA, Daher A, Dailey ME, Elias R, Fein JA, Hosmer W, Jayaraj A, Mather J, Menendez AG, Nadkarni R, Serrano OK, Yu PP, Balanchivadze N, Gadgeel SM, Accordino MK, Bhutani D, Bodin BE, Hershman DL, Masson C, Alexander M, Mushtaq S, Reuben DY, Bernicker EH, Deeken JF, Jeffords KJ, Shafer D, Cárdenas AI, Cuervo Campos R, De-la-Rosa-Martinez D, Ramirez A, Vilar-Compte D, Gill DM, Lewis MA, Low CA, Jones MM, Mansoor AH, Mashru SH, Werner MA, Cohen AM, McWeeney S, Nemecek ER, Williamson SP, Peters S, Smith SJ, Lewis GC, Zaren HA, Akhtari M, Castillo DR, Cortez K, Lau E, Nagaraj G, Park K, Reeves ME, O'Connor TE, Altman J, Gurley M, Mulcahy MF, Wehbe FH, Durbin EB, Nelson HH, Ramesh V, Sachs Z, Wilson G, Bardia A, Boland G, Gainor JF, Peppercorn J, Reynolds KL, Rosovsky RP, Zubiri L, Bekaii-Saab TS, Joyner MJ, Riaz IB, Senefeld JW, Shah S, Ayre SK, Bonnen M, Mahadevan D, McKeown C, Mesa RA, Ramirez AG, Salazar M, Shah PK, Wang CP, Bouganim N, Papenburg J, Sabbah A, Tagalakis V, Vinh DC, Nanchal R, Singh H, Bahadur N, Bao T, Belenkaya R, Nambiar PH, O’Cearbhaill RE, Papadopoulos EB, Philip J, Robson M, Rosenberg JE, Wilkins CR, Tamimi R, Cerrone K, Dill J, Faller BA, Alomar ME, Chandrasekhar SA, Hume EC, Islam JY, Ajmera A, Brouha SS, Cabal A, Choi S, Hsiao A, Jiang JY, Kligerman S, Park J, Razavi P, Reid EG, Bhatt PS, Mariano MG, Thomson CC, Glace M(G, Knoble JL, Rink C, Zacks R, Blau SH, Brown C, Cantrell AS, Namburi S, Polimera HV, Rovito MA, Edwin N, Herz K, Kennecke HF, Monfared A, Sautter RR, Cronin T, Elshoury A, Fleissner B, Griffiths EA, Hernandez-Ilizaliturri F, Jain P, Kariapper A, Levine E, Moffitt M, O'Connor TL, Smith LJ, Wicher CP, Zsiros E, Jabbour SK, Misdary CF, Shah MR, Batist G, Cook E, Ferrario C, Lau S, Miller WH, Rudski L, Santos Dutra M, Wilchesky M, Mahmood SZ, McNair C, Mico V, Dixon B, Kloecker G, Logan BB, Mandapakala C, Cabebe EC, Jha A, Khaki AR, Nagpal S, Schapira L, Wu JTY, Whaley D, Lopes GDL, de Cardenas K, Russell K, Stith B, Taylor S, Klamerus JF, Revankar SG, Addison D, Chen JL, Haynam M, Jhawar SR, Karivedu V, Palmer JD, Pillainayagam C, Stover DG, Wall S, Williams NO, Abbasi SH, Annis S, Balmaceda NB, Greenland S, Kasi A, Rock CD, Luders M, Smits M, Weiss M, Chism DD, Owenby S, Ang C, Doroshow DB, Metzger M, Berenberg J, Uyehara C, Fazio A, Huber KE, Lashley LN, Sueyoshi MH, Patel KG, Riess J, Borno HT, Small EJ, Zhang S, Andermann TM, Jensen CE, Rubinstein SM, Wood WA, Ahmad SA, Brownfield L, Heilman H, Kharofa J, Latif T, Marcum M, Shaikh HG, Sohal DPS, Abidi M, Geiger CL, Markham MJ, Russ AD, Saker H, Acoba JD, Choi H, Rho YS, Feldman LE, Gantt G, Hoskins KF, Khan M, Liu LC, Nguyen RH, Pasquinelli MM, Schwartz C, Venepalli NK, Vikas P, Zakharia Y, Friese CR, Boldt A, Gonzalez CJ, Su C, Su CT, Yoon JJ, Bijjula R, Mavromatis BH, Seletyn ME, Wood BR, Zaman QU, Kaklamani V, Beeghly A, Brown AJ, Charles LJ, Cheng A, Crispens MA, Croessmann S, Davis EJ, Ding T, Duda SN, Enriquez KT, French B, Gillaspie EA, Hausrath DJ, Hennessy C, Lewis JT, Li X(L, Prescott LS, Reid SA, Saif S, Slosky DA, Solorzano CC, Sun T, Vega-Luna K, Wang LL, Aboulafia DM, Carducci TM, Goldsmith KJ, Van Loon S, Topaloglu U, Moore J, Rice RL, Cabalona WD, Cyr S, Barrow McCollough B, Peddi P, Rosen LR, Ravindranathan D, Hafez N, Herbst RS, LoRusso P, Lustberg MB, Masters T, Stratton C. Interplay of Immunosuppression and Immunotherapy Among Patients With Cancer and COVID-19. JAMA Oncol 2023; 9:128-134. [PMID: 36326731 PMCID: PMC9634600 DOI: 10.1001/jamaoncol.2022.5357] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022]
Abstract
Importance Cytokine storm due to COVID-19 can cause high morbidity and mortality and may be more common in patients with cancer treated with immunotherapy (IO) due to immune system activation. Objective To determine the association of baseline immunosuppression and/or IO-based therapies with COVID-19 severity and cytokine storm in patients with cancer. Design, Setting, and Participants This registry-based retrospective cohort study included 12 046 patients reported to the COVID-19 and Cancer Consortium (CCC19) registry from March 2020 to May 2022. The CCC19 registry is a centralized international multi-institutional registry of patients with COVID-19 with a current or past diagnosis of cancer. Records analyzed included patients with active or previous cancer who had a laboratory-confirmed infection with SARS-CoV-2 by polymerase chain reaction and/or serologic findings. Exposures Immunosuppression due to therapy; systemic anticancer therapy (IO or non-IO). Main Outcomes and Measures The primary outcome was a 5-level ordinal scale of COVID-19 severity: no complications; hospitalized without requiring oxygen; hospitalized and required oxygen; intensive care unit admission and/or mechanical ventilation; death. The secondary outcome was the occurrence of cytokine storm. Results The median age of the entire cohort was 65 years (interquartile range [IQR], 54-74) years and 6359 patients were female (52.8%) and 6598 (54.8%) were non-Hispanic White. A total of 599 (5.0%) patients received IO, whereas 4327 (35.9%) received non-IO systemic anticancer therapies, and 7120 (59.1%) did not receive any antineoplastic regimen within 3 months prior to COVID-19 diagnosis. Although no difference in COVID-19 severity and cytokine storm was found in the IO group compared with the untreated group in the total cohort (adjusted odds ratio [aOR], 0.80; 95% CI, 0.56-1.13, and aOR, 0.89; 95% CI, 0.41-1.93, respectively), patients with baseline immunosuppression treated with IO (vs untreated) had worse COVID-19 severity and cytokine storm (aOR, 3.33; 95% CI, 1.38-8.01, and aOR, 4.41; 95% CI, 1.71-11.38, respectively). Patients with immunosuppression receiving non-IO therapies (vs untreated) also had worse COVID-19 severity (aOR, 1.79; 95% CI, 1.36-2.35) and cytokine storm (aOR, 2.32; 95% CI, 1.42-3.79). Conclusions and Relevance This cohort study found that in patients with cancer and COVID-19, administration of systemic anticancer therapies, especially IO, in the context of baseline immunosuppression was associated with severe clinical outcomes and the development of cytokine storm. Trial Registration ClinicalTrials.gov Identifier: NCT04354701.
Collapse
Affiliation(s)
- Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Punita Grover
- Division of Hematology/Oncology, University of Cincinnati Cancer Center, Cincinnati, Ohio
| | - Joy Awosika
- Division of Hematology/Oncology, University of Cincinnati Cancer Center, Cincinnati, Ohio
| | - Shuchi Gulati
- Division of Hematology/Oncology, University of Cincinnati Cancer Center, Cincinnati, Ohio
| | - Chih-Yuan Hsu
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Saif I Alimohamed
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina
| | - Babar Bashir
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Mehmet A Bilen
- Winship Cancer Institute, Emory University, Atlanta, Georgia
| | | | | | - Aakash Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Arielle Elkrief
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Omar E Eton
- Hartford Healthcare Cancer Institute, Hartford, Connecticut
| | | | | | | | | | | | | | | | | | | | | | - Mohamed Hendawi
- Aurora Cancer Center, Advocate Aurora Health, Milwaukee, Wisconsin
| | - Emily Hsu
- Hartford Healthcare Cancer Institute, Hartford, Connecticut
| | - Clara Hwang
- Henry Ford Cancer Institute, Detroit, Michigan
| | - Roman Jandarov
- Division of Hematology/Oncology, University of Cincinnati Cancer Center, Cincinnati, Ohio
| | | | | | - Monika Joshi
- Penn State Cancer Institute, Hershey, Pennsylvania
| | - Hina Khan
- Brown University and Lifespan Cancer Institute, Providence, Rhode Island
| | - Shaheer A Khan
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | - Natalie Knox
- Loyola University Medical Center, Maywood, Illinois
| | - Vadim S Koshkin
- UCSF, Helen Diller Comprehensive Cancer Center, San Francisco
| | | | - Daniel H Kwon
- UCSF, Helen Diller Comprehensive Cancer Center, San Francisco
| | - Sara Matar
- Hollings Cancer Center, MUSC, Charleston
| | - Rana R McKay
- Moores Cancer Center, UCSD, San Diego, California
| | - Sanjay Mishra
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Feras A Moria
- McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Nora L Nock
- Case Comprehensive Cancer Center, Department of Population and Quantitative Health Sciences, Cleveland, Ohio
| | | | - Justin Panasci
- Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | | | | | | | | | - Yuan J Rao
- George Washington University, Washington, DC
| | | | | | - Jacob J Ripp
- University of Kansas Medical Center, Kansas City
| | - Andrea V Rivera
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Andrew L Schmidt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Gary K Schwartz
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York
| | | | - Justin Shaya
- Moores Cancer Center, UCSD, San Diego, California
| | - Suki Subbiah
- Stanley S. Scott Cancer Center, LSU, New Orleans, Louisiana
| | - Lisa M Tachiki
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | | | | | | | | | - Zhuoer Xie
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | | | - Michael A Thompson
- Aurora Cancer Center, Advocate Aurora Health, Milwaukee, Wisconsin.,Tempus Labs, Chicago, Illinois
| | - Dimpy P Shah
- Mays Cancer Center, UT Health, San Antonio, Texas
| | | | - Yu Shyr
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Trisha M Wise-Draper
- Division of Hematology/Oncology, University of Cincinnati Cancer Center, Cincinnati, Ohio
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Omar Butt
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ang Li
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Eric Lau
- for the COVID-19 and Cancer Consortium
| | | | - Kyu Park
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ting Bao
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ji Park
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Erin Cook
- for the COVID-19 and Cancer Consortium
| | | | - Susie Lau
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anup Kasi
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Li C Liu
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | - Chris Su
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tan Ding
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | - Sara Saif
- for the COVID-19 and Cancer Consortium
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Kang AK, Shah AN, Katam N, Davis AA, Gerratana L, Chandra S, Jacob S, Shi M, Srivastava J, D’Amico P, Reduzzi C, Gurley M, Wehbe F, Zhang Q, Behdad A, Cristofanilli M. Abstract P2-14-05: Emerging molecular variants by circulating tumor DNA after immunotherapy in metastatic breast cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-14-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Immune checkpoint inhibition (ICI) in advanced malignancies offers a novel therapeutic approach, often with a more favorable toxicity profile and, in a subset of patients, the allure of a durable response. Unfortunately, the majority of patients with metastatic breast cancer (MBC) treated with a PD-(L)1 inhibitor progress rapidly. Mechanisms of resistance to and emerging genomic alterations after receiving ICI in MBC have not been well described. We aimed to describe the genomic profile of post-ICI therapy for MBC through the lens of circulating tumor DNA (ctDNA). Methods: Under an IRB-approved protocol, we retrospectively collected data from patients (pts) with MBC who had ctDNA analysis by the Guardant 360® assay (Redwood, CA) as part of their routine care between January 2015 and December 2020. We abstracted the demographic, clinical, pathologic, and therapeutic history for these patients. We identified patients who received ICI therapy and a ctDNA analysis within 6 months of completing therapy and, when possible, a paired ctDNA assay no more than 6 months prior to starting ICI. CtDNA variants were annotated by pathogenicity based on the OncoKB classification (Chakravarty et al, JCO PO 2017, date accessed 5/2021). The variant allele frequency (VAF) for a ctDNA sample was determined by the VAF for the dominant alteration in that sample. Results: Of 473 pts with MBC and ctDNA analysis, 49 received ICI therapy. Twenty-four pts had post-immune therapy ctDNA analysis, of whom 17 had paired pre- and post-immune therapy samples. For those with post-ICI ctDNA, the median age was 55 years, and breast cancer subtype was hormone receptor-positive, HER2-negative in 6 pts (25%), HER2-positive in 2 pts (8%), and triple negative in 16 pts (67%). Patients received a median of 2.5 lines of therapy for MBC prior to receiving immune therapy. Eighteen pts (75%) received pembrolizumab and 6 pts (25%) received atezolizumab as standard therapy for 4 pts, a clinical trial for 12 pts, and off label (based on molecular tumor board considerations or physician discretion) for 5 pts. Concurrent therapies were nab-paclitaxel (n=4, 17%), capecitabine (n=10, 42%), carboplatin (n=4, 17%), anti-HER2 (n=2, 8%), liposomal doxorubicin (n=1, 4%), and monotherapy (n=3, 13%). The median time from completing ICI to ctDNA collection was 16 days. In the post-ICI samples, the most common alterations were in TP53 (22%), PIK3CA (7%), KIT (4%), MYC (4%), and PTEN (4%). Across post-ICI samples, 72.46% of alterations were oncogenic or likely oncogenic (n=100). The median VAF in the post-ICI samples was 9.7% (interquartile range [IQR]: 2.2%-23%) compared to 2.8% (IQR: 0.5%-4.8%) in the pre-ICI samples. The median number of detected alterations per ctDNA analysis was 5 (IQR: 3-7) in the post-ICI samples and 2 (IQR: 2-5) in the pre-ICI samples. Among the 17 pts with paired samples, 15 pts had new alterations (44 total alterations gained), of which 68% were oncogenic or likely oncogenic. Twenty-nine alterations detected in the pre-ICI samples were no longer detected in the post-ICI samples. The new alterations were 50% SNV, 48% amplifications, and 2% deletions, and the most common new oncogenic or likely oncogenic alterations were in TP53 in 29%, PTEN in 18%, PIK3CA in 18%, KIT in 18%, and EGFR in 18%. Conclusions: Pathogenic alterations, particularly in the PTEN-PIK3CA-AKT pathway, continue to emerge after ICI treatment. Prospective, standardized evaluation of post-ICI tumor molecular profile in MBC can give insight into rational therapy sequencing approaches and/or novel combinations aimed at delaying resistance to ICI therapy.
Citation Format: Anthony K Kang, Ami N Shah, Neelima Katam, Andrew A Davis, Lorenzo Gerratana, Shruti Chandra, Saya Jacob, Meilynn Shi, Jeeven Srivastava, Paolo D’Amico, Carolina Reduzzi, Michael Gurley, Firas Wehbe, Qiang Zhang, Amir Behdad, Massimo Cristofanilli. Emerging molecular variants by circulating tumor DNA after immunotherapy in metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-14-05.
Collapse
Affiliation(s)
- Anthony K Kang
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Ami N Shah
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Neelima Katam
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | | | - Lorenzo Gerratana
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Shruti Chandra
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Saya Jacob
- University of California San Francisco, San Francisco, CA
| | - Meilynn Shi
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Jeeven Srivastava
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Paolo D’Amico
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Carolina Reduzzi
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Michael Gurley
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Firas Wehbe
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Qiang Zhang
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Amir Behdad
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | | |
Collapse
|
4
|
Shah AN, Gerratana L, Chandra S, Mukhija D, Katam N, Kang AK, Davis AA, Srivastava M, Jacob S, D'Amico P, Zhang Q, Reduzzi C, Gurley M, Wehbe F, Gradishar WJ, Behdad A, Cristofanilli M. Abstract P2-08-04: Progressive metastatic breast cancer with no detectable circulating tumor DNA: Evaluating limitations of this highly sensitive tool. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p2-08-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating tumor DNA (ctDNA) is being evaluated as a tool to monitor disease and guide therapy escalation and de-escalation in advanced breast cancer. The patient, disease, and treatment characteristics that influence whether tumor DNA is isolated and sequenced from the bloodstream are not well understood. We aimed to describe patient and disease characteristics of cases with undetectable ctDNA levels despite progressive metastatic breast cancer (MBC). Methods: We retrospectively identified patients (pts) with MBC who had ctDNA evaluation by the Guardant 360 assay (Redwood City, CA) as part of their routine care from 2015-2020. We correlated the ctDNA assay with the disease status at collection. We identified the patient cohort with no detectable ctDNA despite evaluation at the time of progressive disease but prior to the initiation of a new therapy (ND ctDNA/PD) and compared the clinical, pathologic, and molecular features of this group to those with detected ctDNA. Differences were tested by two proportion z-tests. Results: Of 1151 ctDNA samples collected among 473 pts with MBC, 87 (7.5%) samples had no detectable (ND) ctDNA. 54 of 87 samples with ND ctDNA were collected at a time of stable or responding disease or after a new line of therapy was started, leaving only 33 ctDNA evaluations (2.8%) among 30 pts with ND ctDNA despite collection at the time of PD prior to new therapy. Among this group there were 14 pts (47%) with HR+ HER-, 11 pts (37%) with HER2+, and 5 pts (17%) with TN MBC. This compared to 254 pts (60%) with HR+ HER2-, 82 pts (19%) with HER2+, and 85 pts (20%) with TN MBC and detectable ctDNA. HER2-positive MBC was more common in the ND ctDNA/PD group than detectable ctDNA group (p-0.02). In the ND ctDNA/PD group, the median time from MBC diagnosis to ctDNA evaluation was 7 months and pts had received a median of 0.5 prior lines of therapy for MBC. Four pts (13%) had lobular breast cancer, 24 pts (80%) had recurrent disease, 14 pts (47%) had visceral metastases, and 12 pts (40%) had oligometastatic disease. Sites of metastases at the time of ND ctDNA/PD were bone n=16 (53%), lung n=7 (23%), liver n=6 (20%), lymph node n=11 (37%), skin and soft tissue n=5 (17%), and CNS n=5 (17%). When compared to those with detectable ctDNA these differences in characteristics were not statistically significant, although numerically pts with ND ctDNA had more CNS disease (17% vs 10%) and less liver disease (20% vs 32%). At the time of ND ctDNA, the site of progression was bone n=14 (47%), CNS n=5 (17%), lymph node n=9 (30%), lung n=7 (23%), and liver n=5 (17%). There was a single site of progression in 20 pts (67%). 16 of 30 pts had repeat ctDNA analysis of which 9 pts had subsequent detectable ctDNA with a median VAF of 0.3%, a median of 1 alteration per sample, and oncogenic or likely oncogenic alterations in TP53 in 3 pts and BRCA1, CCNE1, CDH1, and PIK3CA in 1 pt each. Seven had tissue NGS, all of which showed multiple oncogenic alterations. The remaining 22 pts with ND ctDNA but no PD were responding to therapy based on imaging or had already started a new therapy since the last progression. This group also had a high proportion of HER2+ MBC (n=7, 32%) and low proportion with visceral disease (n=6, 27%) Conclusions: Although ctDNA is a highly sensitive tool to detect active MBC (<3% of samples had ND ctDNA), its sensitivity may be less in some clinical scenarios, including HER2+ MBC, when there are limited sites of progression, or when there is isolated CNS progression.
Citation Format: Ami N Shah, Lorenzo Gerratana, Shruti Chandra, Dhruvika Mukhija, Neelima Katam, Anthony K Kang, Andrew A Davis, Millen Srivastava, Saya Jacob, Paolo D'Amico, Qiang Zhang, Carolina Reduzzi, Michael Gurley, Firas Wehbe, William J Gradishar, Amir Behdad, Massimo Cristofanilli. Progressive metastatic breast cancer with no detectable circulating tumor DNA: Evaluating limitations of this highly sensitive tool [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-04.
Collapse
Affiliation(s)
- Ami N Shah
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Lorenzo Gerratana
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Shruti Chandra
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Dhruvika Mukhija
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Neelima Katam
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Anthony K Kang
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | | | - Millen Srivastava
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Saya Jacob
- University of California San Francisco, San Francisco, CA
| | - Paolo D'Amico
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Qiang Zhang
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Carolina Reduzzi
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Michael Gurley
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Firas Wehbe
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - William J Gradishar
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | - Amir Behdad
- Robert H Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
| | | |
Collapse
|
5
|
Danley KT, Tan A, Catalona WJ, Leikin R, Helenowski I, Jovanovic B, Gurley M, Kuzel TM. The association of phosphodiesterase-5 inhibitors with the biochemical recurrence-free and overall survival of patients with prostate cancer following radical prostatectomy. Urol Oncol 2021; 40:57.e1-57.e7. [PMID: 34284930 DOI: 10.1016/j.urolonc.2021.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE To determine whether phosphodiesterase-5 inhibitor documentation is associated with biochemical relapse-free and overall survival of patients with prostate cancer treated with radical prostatectomy. MATERIALS AND METHODS We undertook a retrospective cohort analysis of 3,100 patients with prostate cancer treated with radical prostatectomy between 2003 and 2015. The patients were categorized as a phosphodiesterase- 5- inhibitor user or non-user. The biochemical relapse-free and overall survival at 5-years and 10-years were determined. RESULTS Of the patients, 1,372 reported phosphodiesterase-5 inhibitor documentation, and 1,728 did not. The biochemical recurrence-free survival for non-users at 5- and 10-years follow-up was 87.6% and 85.3%, respectively, and the overall survival at these time intervals was 97.9% and 94.5%. The biochemical recurrence-free survival for phosphodiesterase-5 inhibitor users was 94.3% and 93.2% at 5- and 10-years follow-up, respectively, and overall survival was 99.2% and 95.8% at these intervals. The hazard ratio for biochemical recurrence-free survival was 0.44 (CI 0.34-0.56) and for overall survival was 0.65 (CI 0.45-0.94). On the multivariate analysis, phosphodiesterase-5 inhibitor documentation was associated with a lower risk of biochemical recurrence and death when corrected for the other variables. Age at surgery and Gleason scores >8 was associated with a higher risk of death. Higher pathological stage, higher Gleason score, presence of lymph node metastases, and nonwhite race were associated with a higher risk of recurrence. CONCLUSION This retrospective analysis revealed a significant association of postoperative phosphodiesterase-5 inhibitor documentation with biochemical recurrence-free- and overall survival in patients with localized prostate cancer treated with radical prostatectomy. Larger scale studies are warranted to investigate the clinical significance of this association.
Collapse
Affiliation(s)
- Kelsey T Danley
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL.
| | - Alan Tan
- Division of Hematology/Oncology/Cell Therapy, Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| | | | - Robin Leikin
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Irene Helenowski
- Department of Preventative Medicine, Northwestern University, Chicago, IL
| | - Borko Jovanovic
- Department of Preventative Medicine, Northwestern University, Chicago, IL
| | - Michael Gurley
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Timothy M Kuzel
- Division of Hematology/Oncology/Cell Therapy, Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| |
Collapse
|
6
|
Prabhu N, Kapur N, Catalona W, Leikin R, Helenowski I, Jovanovich B, Gurley M, Okwuosa TM, Kuzel TM. Statin use and risk of prostate cancer biochemical recurrence after radical prostatectomy. Urol Oncol 2020; 39:130.e9-130.e15. [PMID: 33132024 DOI: 10.1016/j.urolonc.2020.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Multiple studies have investigated the role of statins in prostate cancer (CaP), the leading cause of cancer related death in men. Retrospective cohort studies investigating the correlation between statin use and biochemical recurrence free (BCRF) survival in men with CaP have been inconclusive. OBJECTIVES In the largest reported surgical cohort to date, we investigated the effect of statin therapy on BCRF and overall survival in patients with CaP who have undergone radical prostatectomy (RP). PATIENTS AND METHODS We performed a retrospective analysis of men (n = 3,088) participating in the NCI funded Specialized Program of Research Excellence (SPORE) in CaP at Northwestern University (NM) in Chicago, Illinois. Patients were treated with RP between 2002 and 2015. Patients in the statin users group received treatment within 2 years prior to or subsequent to RP. Wilcoxon rank-sum and Fisher's exact tests were used to compare age, race, Gleason score, clinical staging, and pathological stage between statin users and nonstatin users. RESULTS The analysis identified 1,222 statin users and 1,865 nonusers (mean age 71 years, 92% Caucasian). After a median follow-up time of 49.0 months, the 5-year BCRF survival rate was 93.3% (95% confidence interval [CI]: 91.9-94.8%) among statin users and 88.6% (95% CI: 87.1%-90%) among nonusers (log-rank P< 0.001). After 10 years, the progression-free survival (PFS) was 91.7% (95% CI: 90.1%-93.3%) among statin users and 86.5% (95% CI: 84.4%-88.2%) among nonusers (log-rank P< 0.001). CONCLUSIONS Extended follow-up data in this large surgical cohort show statin use improves BCRF but not overall survival in RP patients.
Collapse
Affiliation(s)
- Nicole Prabhu
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| | - Navina Kapur
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL.
| | | | - Robin Leikin
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
| | - Irene Helenowski
- Department of Preventative Medicine, Northwestern University, Chicago, IL
| | - Borko Jovanovich
- Department of Preventative Medicine, Northwestern University, Chicago, IL
| | - Michael Gurley
- Northwestern University Clinical and Translational Sciences Institute, Chicago, IL
| | - Tochi M Okwuosa
- Division of Cardiology, Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| | - Timothy M Kuzel
- Division of Hematology/Oncology/Cell Therapy, Department of Internal Medicine, Rush University Medical Center, Chicago, IL
| |
Collapse
|
7
|
Shah AN, Finkelman B, Gerratana L, Davis AA, Katam N, Lin C, Carroll K, Jacob S, Wehbe F, Gurley M, Lin F, Blanco L, Vagia E, Platanias LC, Gradishar WJ, Behdad A, Cristofanilli M. ERBB2 amplifications and mutations in 109 advanced breast cancer patients by next-generation sequencing. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3565 Background: In advanced breast cancer (ABC) HER2 status is based on ASCO/CAP immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) criteria. Next generation sequencing (NGS) of tissue and blood can detect aberrations in ERBB2 such as copy number gain/amplifications (cng/amp) and mutations. Methods: We retrospectively identified patients (pts) seen at Northwestern University between 2015 and 2019 with ABC and an alteration in ERBB2 identified by tissue and/or circulating tumor DNA (ctDNA) NGS. We included pts with testing by Guardant360, TempusX, and/or FoundationOne platforms. NGS reports were evaluated for non-synonymous mutations and cng/amp. HR and HER2 status were determined based on the most recent pathologic assessment. Mutations were categorized as pathologic if they were consider oncogenic (level 1-2 evidence with direct functional data), likely oncogenic, or predicted oncogenic, based on OncoKB (Chakravarty et al., JCO PO 2017). Results: 109 cases of ABC (6 locally advanced, 103 metastatic) with ERBB2 alterations were identified. Tissue NGS was available from 43%, ctDNA from 72%, and both from 19%. The positive predictive value (PPV) of ERBB2 amp/cng by tissue NGS to predict HER2+ using the gold standard as IHC/FISH was 94% (33/35). The PPV of ERBB2 amp by ctDNA was 93% (40/43). ERBB2 mutations were detected in 52 pts. Of these, 23 pts were considered to harbor pathologic ERBB2 mutations, (19 oncogenic, 2 likely oncogenic, 1 predicted oncogenic) detected by ctDNA and tissue in 4, ctDNA in 16, and tissue in 3 pts. The most frequently detected mutations were V777L and S310. Four pts had co-mutations of ERBB2 V777L and S310F. Disease subtype among those with ERBB2 pathologic mutations was HR+ HER2- in 57%, HER2+ in 26%, and triple negative in 17%. In all patients with serial ctDNA analysis and pathologic ERBB2 mutations, the mutation was detected on the first analysis. Pathologic ERBB2 mutation represented the mutant with the highest mutant allele frequency (MAF) in 30% and top 3 highest MAF in an additional 35%. PIK3CA was co-mutated in 48%. Conclusions: The PPV of ERBB2 amp/cng by tissue and ctDNA NGS was high, and has potential utility for cancers where HER2 IHC/FISH is not standardly assessed or cases where biopsy is challenging. ERBB2 pathologic mutations were found in all breast cancer subtypes. When present, they were identified on the initial ctDNA analysis and often represented a significant clone, supporting its role as a ‘driver mutation’.
Collapse
Affiliation(s)
| | - Brian Finkelman
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Lorenzo Gerratana
- Department of Medicine-Hematology and Oncology, Feinberg School of Medicine, Northwestern University; Department of Medicine (DAME), University of Udine, Chicago, IL
| | - Andrew A. Davis
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | | | - Kristen Carroll
- Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Saya Jacob
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Firas Wehbe
- Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Michael Gurley
- Northwestern University NU Clinical and Translational Sciences Institute, Chicago, IL
| | - Fang Lin
- Northwestern University, Chicago, IL
| | | | | | | | | | - Amir Behdad
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Massimo Cristofanilli
- Robert H. Lurie Cancer Center of Northwestern University, Feinberg School of Medicine, Chicago, IL
| |
Collapse
|
8
|
Belenkaya R, Gurley M, Dymshyts D, Araujo S, Williams A, Chen R, Reich C. Standardized Observational Cancer Research Using the OMOP CDM Oncology Module. Stud Health Technol Inform 2019; 264:1831-1832. [PMID: 31438365 DOI: 10.3233/shti190670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Observational research in cancer requires substantially more detail than most other therapeutic areas. Cancer conditions are defined through histology, affected anatomical structures, staging and grading, and biomarkers, and are treated with complex therapies. Here, we show a new cancer module as part of the OMOP CDM, allowing manual and automated abstraction and standardized analytics. We tested the model in EHR and registry data against a number of typical use cases.
Collapse
Affiliation(s)
- Rimma Belenkaya
- OHDSI Oncology Workgroup, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Michael Gurley
- Clinical and Translational Sciences Institute, Northwestern University, Chicago, IL, USA
| | | | - Sonia Araujo
- Real World Analytics Solution, IQVIA, London, UK
| | - Andrew Williams
- Maine Medical Center Research Institute, Center for Outcomes Research and Evaluation, Portland, ME, USA
| | - RuiJun Chen
- Biomedical Informatics Department, Columbia University Medical Center, New York City, NY, USA
| | | |
Collapse
|
9
|
Roston AB, Helenowski IB, Catalona W, Leikin R, Gurley M, Trapp L, Jovanovic B, Kuzel TM. Impact of use of phosphodiesterase type 5 inhibitors (PDE5-I) after radical prostatectomy (RP) on biochemical recurrence-free (BCRF) and overall survival (OS): A retrospective study from the Northwestern University SPORE in prostate cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.6_suppl.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
27 Background: The correlation between PDE5-I use to improve erectile function post RP and BCRF and OS on prostate cancer (PCa) patients (pts) has yielded conflicting results among prior retrospective cohort studies (Michl, 2015). Recent data suggests that these drugs may have an impact on immunity that may explain possible benefits. This study’s purpose was to determine whether PDE5-I use affects BCRF and OS for pts treated with RP for PCa. Methods: This is an IRB approved retrospective cohort study analyzing a subset of pts consented to the SPORE in PCa at Northwestern University’s Lurie Cancer Center. Inclusion criteria included men diagnosed with PCa and treated with RP with curative intent between 2003-2015. Study population (n = 2,410) showed 834 (34.6%) received a PDE5-I post-RP, while 1,576 (65.4%) did not. Pts were grouped based on PDE5-I use and no PDE5-I use after RP. A PDE5-I user must have filled at least 2 prescriptions or completed at least 2 inpatient administrations of a PDE5-I. Continuous variables were summarized by descriptive statistics and differences between groups were assessed via the Wilcoxon rank sum test. Categorical variables were reported by frequencies and percentages and compared via Fisher’s exact test. OS and BCRF survival were summarized for 10-yr rates using Kaplan-Meier estimates. The difference in BCRF and OS between groups was evaluated via log-rank test. Results: Mean age at RP was 60, and 90.95 % were Caucasian. Except for pairwise comparisons for significance of Gleason 3+3 vs. 3+4 histology with higher prevalence of 3+4 in the PDE5-I group (p = 0.0004) and a higher percent of clinical stage T2b-c than T2a in the no PDE5-I group (p = 0.01), no differences were noted in demographics. The 10-yr BCRF survival among PDE5-I users was 92.53% compared to 79.63% among non-users after RP (p < 0.0001). The 10-yr OS rate among PDE5-I users was 97.22% compared to 92.69% among non-users (p = 0.008). Conclusions: This retrospective analysis suggests that PDE5-I use improves biochemical recurrence free survival and overall survival in pts treated with RP for PCa.
Collapse
Affiliation(s)
- Arden B. Roston
- Northwestern University Robert H. Lurie Comprehensive Cancer Center, Chicago, IL
| | | | | | - Robin Leikin
- Northwestern University Robert H. Lurie Comprehensive Cancer Center, Chicago, IL
| | - Michael Gurley
- Northwestern University NU Clinical and Translational Sciences Institute, Chicago, IL
| | | | - Borko Jovanovic
- Northwestern University Department of Preventive Medicine, Chicago, IL
| | | |
Collapse
|
10
|
Trapp L, Helenowski IB, Gurley M, Leikin R, Catalona W, Jovanovic B, Kuzel T. Use of statins and the risk of prostate cancer biochemical recurrence in men treated with radical prostatectomy. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.5048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Michael Gurley
- Northwestern University NU Clinical and Translational Sciences Institute, Chicago, IL
| | - Robin Leikin
- Northwestern University Robert H. Lurie Comprehensive Cancer Center, Chicago, IL
| | | | - Borko Jovanovic
- Northwestern University Department of Preventive Medicine, Chicago, IL
| | | |
Collapse
|
11
|
Bai C, Maddahi J, Kindem J, Conwell R, Gurley M, Old R. Development and evaluation of a new fully automatic motion detection and correction technique in cardiac SPECT imaging. J Nucl Cardiol 2009; 16:580-9. [PMID: 19488827 PMCID: PMC2708325 DOI: 10.1007/s12350-009-9096-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 03/25/2009] [Accepted: 04/30/2009] [Indexed: 11/03/2022]
Abstract
BACKGROUND In cardiac SPECT perfusion imaging, motion correction of the data is critical to the minimization of motion introduced artifacts in the reconstructed images. Software-based (data-driven) motion correction techniques are the most convenient and economical approaches to fulfill this purpose. However, the accuracy is significantly affected by how the data complexities, such as activity overlap, non-uniform tissue attenuation, and noise are handled. METHODS We developed STASYS, a new, fully automatic technique, for motion detection and correction in cardiac SPECT. We evaluated the performance of STASYS by comparing its effectiveness of motion correcting patient studies with the current industry standard software (Cedars-Sinai MoCo) through blind readings by two readers independently. RESULTS For 204 patient studies from multiple clinical sites, the first reader identified (1) 69 studies with medium to large axial motion, of which STASYS perfectly or significantly corrected 86.9% and MoCo 72.5%; and (2) 20 studies with medium to large lateral motion, of which STASYS perfectly or significantly corrected 80.0% and MoCo 60.0%. The second reader identified (1) 84 studies with medium to large axial motion, of which STASYS perfectly or significantly corrected 82.2% and MoCo 76.2%; and (2) 34 studies with medium to large lateral motion, of which STASYS perfectly or significantly corrected 58.9% and MoCo 50.0%. CONCLUSIONS We developed a fully automatic software-based motion correction technique, STASYS, for cardiac SPECT. Clinical studies showed that STASYS was effective and corrected a larger percent of cardiac SPECT studies than the current industrial standard software.
Collapse
Affiliation(s)
- Chuanyong Bai
- Digirad Corporation, 13950 Stowe Drive, Poway, CA 92064 USA
| | - Jamshid Maddahi
- Department of Molecular and Medical Pharmacology (Nuclear Medicine) and Medicine (Cardiology), UCLA - David Geffen School of Medicine, Los Angeles, CA 90095 USA
| | - Joel Kindem
- Digirad Corporation, 13950 Stowe Drive, Poway, CA 92064 USA
| | | | - Michael Gurley
- Digirad Corporation, 13950 Stowe Drive, Poway, CA 92064 USA
| | - Rex Old
- Digirad Corporation, 13950 Stowe Drive, Poway, CA 92064 USA
| |
Collapse
|
12
|
Weinberg DS, Ault KA, Gurley M, Pinkus GS. The human lymph node germinal center cell: characterization and isolation by using two-color flow cytometry. The Journal of Immunology 1986. [DOI: 10.4049/jimmunol.137.5.1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The germinal center of lymphoid tissues is a critical microenvironmental site of B cell activation and differentiation in response to antigenic stimuli. However, characterization of germinal center cells (GCC) in tissue sections has proved technically difficult. Therefore, we have employed two-color flow cytometric analysis of suspended human tonsillar lymphocytes in order to define more precisely the immunologic features of GCC. These cells were identified in suspension by virtue of their specific surface binding of the lectin peanut agglutinin (PNA), confirmed by tissue immunoperoxidase studies. Phycoerythrin-labeled lectin was used in combination with a variety of fluorescein-labeled antibodies in order to identify subpopulations of tonsillar lymphocytes. The majority of PNA+ cells were B cells, and both PNA+ and PNA- B cells stained for surface immunoglobulin light chains. PNA+ cells lacked surface IgD, but included cells with surface IgG and IgM. Both PNA+ and PNA- cells stained for B1, B2, BA-1, Leu-12, Leu-14, CR-I, and HLA-DR antigens, whereas CALLA was present only on PNA+ cells. There were differences between PNA+ and PNA- cells in the relative expression of B1 and B2 antigens, possibly reflecting differences in B cell activation or maturation. A small proportion of T cells were PNA+, including both helper/inducer and suppressor/cytotoxic phenotypes. PNA+ cells included both small and large lymphoid cells, and almost all DNA synthetic activity was associated with the large PNA+ cells. PNA+ B cells isolated by cell sorting had morphologic features characteristic of GCC. Therefore, PNA+ cells in suspension appeared to represent GCC, and features of these cells that cannot be convincingly shown in tissue section studies were demonstrated by flow cytometry.
Collapse
|
13
|
Weinberg DS, Ault KA, Gurley M, Pinkus GS. The human lymph node germinal center cell: characterization and isolation by using two-color flow cytometry. J Immunol 1986; 137:1486-94. [PMID: 2943795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The germinal center of lymphoid tissues is a critical microenvironmental site of B cell activation and differentiation in response to antigenic stimuli. However, characterization of germinal center cells (GCC) in tissue sections has proved technically difficult. Therefore, we have employed two-color flow cytometric analysis of suspended human tonsillar lymphocytes in order to define more precisely the immunologic features of GCC. These cells were identified in suspension by virtue of their specific surface binding of the lectin peanut agglutinin (PNA), confirmed by tissue immunoperoxidase studies. Phycoerythrin-labeled lectin was used in combination with a variety of fluorescein-labeled antibodies in order to identify subpopulations of tonsillar lymphocytes. The majority of PNA+ cells were B cells, and both PNA+ and PNA- B cells stained for surface immunoglobulin light chains. PNA+ cells lacked surface IgD, but included cells with surface IgG and IgM. Both PNA+ and PNA- cells stained for B1, B2, BA-1, Leu-12, Leu-14, CR-I, and HLA-DR antigens, whereas CALLA was present only on PNA+ cells. There were differences between PNA+ and PNA- cells in the relative expression of B1 and B2 antigens, possibly reflecting differences in B cell activation or maturation. A small proportion of T cells were PNA+, including both helper/inducer and suppressor/cytotoxic phenotypes. PNA+ cells included both small and large lymphoid cells, and almost all DNA synthetic activity was associated with the large PNA+ cells. PNA+ B cells isolated by cell sorting had morphologic features characteristic of GCC. Therefore, PNA+ cells in suspension appeared to represent GCC, and features of these cells that cannot be convincingly shown in tissue section studies were demonstrated by flow cytometry.
Collapse
|
14
|
Abstract
Male mice from three inbred strains (C57B1/10J, BALB/cJ and C3H/2lbg) were assigned to infantile handling or control conditions. In a cross-sectional developmental design, handled and control mice were tested for two-choice selection of 10% (v/v) ethanol vs. tap water at 60, 90 or 120 days of age. The volume of fluid consumed from both tubes was recorded for fifteen days. In 60 day old mice, handling produced a trend toward increased total fluid consumption in the C57 mice and a trend toward increased ethanol selection in the BALBs. In 90 day old mice, there were trends noted toward handling-related decreased fluid consumption in BALBs. Also noted was a trend toward handling related increased ethanol selection in C57 mice. In 120 day old mice, a handling-related increase in alcohol selection was noted in the C3H strain.
Collapse
|
15
|
Jones B, Goldstine R, Gurley M, Reyes E. Appetite for alcohol: influence of genetics and early experience. Neurobehav Toxicol Teratol 1985; 7:125-7. [PMID: 4000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Thirty male mice from three inbred strains (C57BL/10J, BALB/cJ, C3H/2Ibg) were assigned to infantile handling or control conditions. At sixty days of age, all animals were tested in a two-choice situation for selection of 10% ethanol vs. water. Consumption from both drinking tubes was recorded for 15 days and selection ratios for alcohol per total fluid volume were calculated. C57 mice demonstrated increased preference for alcohol as a result of early handling. The BALB strain, known for low preference for alcohol, showed increased preference for alcohol as well. C3H mice evinced a biphasic effect of early handling, showing an initially greater acceptance of alcohol as compared to controls, followed by decreased selection.
Collapse
|