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Devanarayan V, Ye Y, Charil A, Andreozzi E, Sachdev P, Llano DA, Tian L, Zhu L, Hampel H, Kramer L, Dhadda S, Irizarry M. Predicting clinical progression trajectories of early Alzheimer's disease patients. Alzheimers Dement 2024; 20:1725-1738. [PMID: 38087949 PMCID: PMC10984448 DOI: 10.1002/alz.13565] [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: 04/26/2023] [Revised: 09/06/2023] [Accepted: 11/07/2023] [Indexed: 03/16/2024]
Abstract
BACKGROUND Models for forecasting individual clinical progression trajectories in early Alzheimer's disease (AD) are needed for optimizing clinical studies and patient monitoring. METHODS Prediction models were constructed using a clinical trial training cohort (TC; n = 934) via a gradient boosting algorithm and then evaluated in two validation cohorts (VC 1, n = 235; VC 2, n = 421). Model inputs included baseline clinical features (cognitive function assessments, APOE ε4 status, and demographics) and brain magnetic resonance imaging (MRI) measures. RESULTS The model using clinical features achieved R2 of 0.21 and 0.31 for predicting 2-year cognitive decline in VC 1 and VC 2, respectively. Adding MRI features improved the R2 to 0.29 in VC 1, which employed the same preprocessing pipeline as the TC. Utilizing these model-based predictions for clinical trial enrichment reduced the required sample size by 20% to 49%. DISCUSSION Our validated prediction models enable baseline prediction of clinical progression trajectories in early AD, benefiting clinical trial enrichment and various applications.
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Affiliation(s)
- Viswanath Devanarayan
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
- Department of MathematicsStatistics and Computer ScienceUniversity of Illinois ChicagoChicagoIllinoisUSA
| | - Yuanqing Ye
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
| | - Arnaud Charil
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
| | | | | | - Daniel A. Llano
- Carle Illinois College of MedicineUrbanaIllinoisUSA
- Department of Molecular and Integrative PhysiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Lu Tian
- Department of Biomedical Data ScienceStanford University School of MedicinePalo AltoCaliforniaUSA
| | - Liang Zhu
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
| | - Harald Hampel
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
| | - Lynn Kramer
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
| | - Shobha Dhadda
- Clinical Evidence GenerationEisai Inc.NutleyNew JerseyUSA
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Tourdot S, Baltrunkonis D, Denies S, Devanarayan V, Grudzinska-Goebel J, Kromminga A, Lotz GP, Malherbe L, Michaut L, Weldingh KN, Pedras-Vasconcelos JA, Salazar-Fontana LI, Spindeldreher S, Sauna Z, Snoeck V, Verthelyi D, Kramer D. Proceedings of the 14th European immunogenicity platform open symposium on immunogenicity of biopharmaceuticals. MAbs 2024; 16:2324801. [PMID: 38441119 PMCID: PMC10936655 DOI: 10.1080/19420862.2024.2324801] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024] Open
Abstract
Biologics have revolutionized disease management in many therapeutic areas by addressing unmet medical needs and overcoming resistance to standard-of-care treatment in numerous patients. However, the development of unwanted immune responses directed against these drugs, humoral and/or cellular, can hinder their efficacy and have safety consequences with various degrees of severity. Health authorities ask that a thorough immunogenicity risk assessment be conducted during drug development to incorporate an appropriate monitoring and mitigation plan in clinical studies. With the rapid diversification and complexification of biologics, which today include modalities such as multi-domain antibodies, cell-based products, AAV delivery vectors, and nucleic acids, developers are faced with the challenge of establishing a risk assessment strategy sometimes in the absence of specific regulatory guidelines. The European Immunogenicity Platform (EIP) Open Symposium on Immunogenicity of Biopharmaceuticals and its one-day training course gives experts and newcomers across academia, industry, and regulatory agencies an opportunity to share experience and knowledge to overcome these challenges. Here, we report the discussions that took place at the EIP's 14th Symposium, held in April 2023. The topics covered included immunogenicity monitoring and clinical relevance, non-clinical immunogenicity risk assessment, regulatory aspects of immunogenicity assessment and reporting, and the challenges associated with new modalities, which were discussed in a dedicated session.
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Affiliation(s)
- Sophie Tourdot
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | - Daniel Baltrunkonis
- Research and Development, Clinical Pharmacology and Bioanalytics, Clinical Bioanalytics, Groton, CT, USA
| | | | | | | | | | - Gregor P. Lotz
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Hoffmann-La Roche Ltd, Penzberg, Germany
| | - Laurent Malherbe
- Lilly Research Laboratories, a Division of Eli Lilly and Company, Indianapolis, IN, USA
| | - Lydia Michaut
- Novartis Biomedical research, PK Sciences, Basel, Switzerland
| | - Karin N. Weldingh
- Department of Clinical Immunogenicity Analysis, Novo Nordisk A/S, Maaloev, Denmark
| | - Joao A. Pedras-Vasconcelos
- Division of Biotech Review and Research III, Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Zuben Sauna
- Division of hemostasis, Office of Plasma Protein Therapeutics; Office of Therapeutic Products, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Veerle Snoeck
- Translational Biomarkers and Bioanalysis, UCB Biopharma SRL, Braine-l’Alleud, Belgium
| | - Daniela Verthelyi
- Division of Biologics Research and Review III; Ofrfice of Biotechnology Products; Center for Drug Evaluation and Research; Office of Pharmaceutical Quality, US Food and Drug Administration, Silver Spring, MD, USA
| | - Daniel Kramer
- Global Scientific Advisor Immunogenicity, Translational Medicine & Early Development, Sanofi Aventis Deutschland GmbH, Frankfurt am Main, Germany
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Li G, Toschi N, Devanarayan V, Batrla R, Boccato T, Cho M, Ferrante M, Frech F, Galvin JE, Henley D, Mattke S, De Santi S, Hampel H. The age-specific comorbidity burden of mild cognitive impairment: a US claims database study. Alzheimers Res Ther 2023; 15:211. [PMID: 38057937 PMCID: PMC10701954 DOI: 10.1186/s13195-023-01358-8] [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: 07/19/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023]
Abstract
BACKGROUND Identifying individuals with mild cognitive impairment (MCI) who are likely to progress to Alzheimer's disease and related dementia disorders (ADRD) would facilitate the development of individualized prevention plans. We investigated the association between MCI and comorbidities of ADRD. We examined the predictive potential of these comorbidities for MCI risk determination using a machine learning algorithm. METHODS Using a retrospective matched case-control design, 5185 MCI and 15,555 non-MCI individuals aged ≥50 years were identified from MarketScan databases. Predictive models included ADRD comorbidities, age, and sex. RESULTS Associations between 25 ADRD comorbidities and MCI were significant but weakened with increasing age groups. The odds ratios (MCI vs non-MCI) in 50-64, 65-79, and ≥ 80 years, respectively, for depression (4.4, 3.1, 2.9) and stroke/transient ischemic attack (6.4, 3.0, 2.1). The predictive potential decreased with older age groups, with ROC-AUCs 0.75, 0.70, and 0.66 respectively. Certain comorbidities were age-specific predictors. CONCLUSIONS The comorbidity burden of MCI relative to non-MCI is age-dependent. A model based on comorbidities alone predicted an MCI diagnosis with reasonable accuracy.
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Affiliation(s)
- Gang Li
- Eisai Inc., 200 Metro Boulevard, Nutley, NJ, 07110, USA.
| | - Nicola Toschi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
- A.A. Martino's Center for Biomedical Imagin, Harvard Medical School, Boston, USA
| | | | | | - Tommaso Boccato
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Min Cho
- Eisai Inc., 200 Metro Boulevard, Nutley, NJ, 07110, USA
| | - Matteo Ferrante
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy
| | - Feride Frech
- Eisai Inc., 200 Metro Boulevard, Nutley, NJ, 07110, USA
| | - James E Galvin
- Miller School of Medicine, University of Miami, 7700 W Camino Real, Suite 200, Boca Raton, FL, 33433, USA
| | - David Henley
- Research and Development, Janssen Pharmaceuticals, Inc., 1125 Bear Tavern Rd, Titusville, NJ, 08560, USA
| | - Soeren Mattke
- The USC Brain Health Observatory, University of Southern California, 635 Downey Way, Los Angeles, CA, 90089, USA
| | | | - Harald Hampel
- Eisai Inc., 200 Metro Boulevard, Nutley, NJ, 07110, USA.
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Hong F, Tian L, Devanarayan V. Improving the Robustness of Variable Selection and Predictive Performance of Regularized Generalized Linear Models and Cox Proportional Hazard Models. Mathematics (Basel) 2023; 11:557. [PMID: 37990696 PMCID: PMC10660556 DOI: 10.3390/math11030557] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
High-dimensional data applications often entail the use of various statistical and machine-learning algorithms to identify an optimal signature based on biomarkers and other patient characteristics that predicts the desired clinical outcome in biomedical research. Both the composition and predictive performance of such biomarker signatures are critical in various biomedical research applications. In the presence of a large number of features, however, a conventional regression analysis approach fails to yield a good prediction model. A widely used remedy is to introduce regularization in fitting the relevant regression model. In particular, a L 1 penalty on the regression coefficients is extremely useful, and very efficient numerical algorithms have been developed for fitting such models with different types of responses. This L 1 -based regularization tends to generate a parsimonious prediction model with promising prediction performance, i.e., feature selection is achieved along with construction of the prediction model. The variable selection, and hence the composition of the signature, as well as the prediction performance of the model depend on the choice of the penalty parameter used in the L 1 regularization. The penalty parameter is often chosen by K-fold cross-validation. However, such an algorithm tends to be unstable and may yield very different choices of the penalty parameter across multiple runs on the same dataset. In addition, the predictive performance estimates from the internal cross-validation procedure in this algorithm tend to be inflated. In this paper, we propose a Monte Carlo approach to improve the robustness of regularization parameter selection, along with an additional cross-validation wrapper for objectively evaluating the predictive performance of the final model. We demonstrate the improvements via simulations and illustrate the application via a real dataset.
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Affiliation(s)
- Feng Hong
- Takeda Pharmaceuticals, Cambridge, MA 02139, USA
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Viswanath Devanarayan
- Eisai Inc., Nutley, NJ 07110, USA
- Department of Mathematics, Statistics, and Computer Science, University of Illinois Chicago, Chicago, IL 60607, USA
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Llano DA, Devanarayan P, Devanarayan V. CSF peptides from VGF and other markers enhance prediction of MCI to AD progression using the ATN framework. Neurobiol Aging 2023; 121:15-27. [PMID: 36368195 DOI: 10.1016/j.neurobiolaging.2022.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 03/13/2022] [Revised: 07/15/2022] [Accepted: 07/23/2022] [Indexed: 12/14/2022]
Abstract
The amyloid beta, tau, neurodegenerative markers framework has been proposed to serve as a system to classify and combine biomarkers for Alzheimer's Disease (AD). Although cerebrospinal (CSF) fluid AT (amyloid beta and tau)-based biomarkers have a well-established track record to distinguish AD from control subjects and to predict conversion from mild cognitive impairment (MCI) to AD, there is not an established non-tau based neurodegenerative ("N") marker from CSF. Here, we examine the ability of several candidate peptides in the CSF to serve as "N" markers to both classify disease state and predict MCI to AD conversion. We observed that although many putative N markers involved in synaptic processing and neuroinflammation were able to, when examined in isolation, distinguish MCI converters from non-converters, a derivative from VGF, when combined with AT markers, most strongly enhanced prediction of MCI to AD conversion. Low CSF VGF levels were also predictive of MCI to dementia conversion in the setting of normal AT markers, suggesting that it may serve as a very early predictor of dementia conversion. Other markers derived from neuronal pentraxin 2, GAP-43 and a 14-3-3 protein were also able to enhance MCI to AD prediction when used as a marker of neurodegeneration, but VGF had the highest predictive capacity. Thus, we propose that low levels of VGF in CSF may serve as "N" in the amyloid beta, tau, neurodegenerative markers framework to enhance the prediction of MCI to AD conversion.
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Affiliation(s)
- Daniel A Llano
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL, USA; Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA; Beckman Institute for Advanced Science and Technology, Urbana, IL, USA; Carle Neuroscience Institute, Urbana, IL, USA.
| | - Priya Devanarayan
- Department of Biology and Schreyer Honors College, Pennsylvania State University, University Park, PA, USA
| | - Viswanath Devanarayan
- Eisai, Inc., Nutley, NJ, USA; Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL, USA
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Charil A, Devanarayan V, Murali L, Qi X, Krause S, Sachdev P, Reyderman L, Koyama A, Dhadda S, Irizarry MC. Baseline regional Tau distribution predicts fast cognitive decline in subjects with mild cognitive impairment. Alzheimers Dement 2022. [DOI: 10.1002/alz.068154] [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: 12/24/2022]
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Devanarayan V, Dhadda S, Koyama A, Swanson CJ, Hampel H, Irizarry MC, Kramer LD. Derivation and evaluation of signatures using plasma β‐amyloid and pTau‐181 for brain amyloid‐β detection. Alzheimers Dement 2022. [DOI: 10.1002/alz.067811] [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: 12/24/2022]
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8
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Saxena S, Devanarayan V, Ye Y, Reyderman L, Koyama A, Sachdev P. Novel peptide‐driven global proteomics platform to identify unique peptide profiles linked to Alzheimer’s disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.066599] [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: 12/24/2022]
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9
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Devanarayan V, Charil A, Nelson T, Qi X, Murali L, Reyderman L, Irizarry MC, Koyama A, Dhadda S. Development and validation of AI‐based tools for brain amyloid‐β detection using MRI. Alzheimers Dement 2022. [DOI: 10.1002/alz.068231] [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: 12/24/2022]
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Huang X, Tian L, Sun Y, Chatterjee S, Devanarayan V. Predictive signature development based on maximizing the area between receiver operating characteristic curves. Stat Med 2022; 41:5242-5257. [PMID: 36053782 PMCID: PMC10681287 DOI: 10.1002/sim.9565] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/02/2021] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Development of marker signatures to predict treatment benefits for a new therapeutic is an important scientific component in advancing the drug discovery and is an important first step toward the goal of precision medicine. In this article, we focus on developing an algorithm to search for optimal linear combination of markers that maximizes the area between two receiver operating characteristic curves of the new therapeutic and the control groups without assuming any parametric model. We further generalize the proposed algorithm for predictive signature development to maximize the difference of Harrel's C-index of the new therapeutic and the control groups when the outcome of interest is time-to-event. The performance of this proposed method is evaluated and compared to existing methods via simulations and real clinical trial data.
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Affiliation(s)
- Xin Huang
- Data and Statistical Sciences, AbbVie Inc, North Chicago, Illinois, USA
| | - Lu Tian
- School of Medicine, Stanford University, Stanford, California, USA
| | - Yan Sun
- Data and Statistical Sciences, AbbVie Inc, North Chicago, Illinois, USA
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Starcevic Manning M, Hassanein M, Partridge MA, Jawa V, Mora J, Ryman J, Barker B, Braithwaite C, Carleton K, Hay L, Hottenstein C, Kubiak RJ, Devanarayan V. Comparison of Titer and Signal to Noise (S/N) for Determination of Anti-drug Antibody Magnitude Using Clinical Data from an Industry Consortium. AAPS J 2022; 24:81. [DOI: 10.1208/s12248-022-00728-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
AbstractDuring biotherapeutic drug development, immunogenicity is evaluated by measuring anti-drug antibodies (ADAs). The presence and magnitude of ADA responses is assessed using a multi-tier workflow where samples are screened, confirmed, and titered. Recent reports suggest that the assay signal to noise ratio (S/N) obtained during the screening tier correlates well with titer. To determine whether S/N could more broadly replace titer, anonymized ADA data from a consortium of sponsors was collected and analyzed. Datasets from clinical programs with therapeutics of varying immunogenicity risk levels (low to high), common ADA assay platforms (ELISA and MSD) and formats (bridging, direct, solid-phase extraction with acid dissociation), and titration approaches (endpoint and interpolated) were included in the analysis. A statistically significant correlation between S/N and titer was observed in all datasets, with a strong correlation (Spearman’s r > 0.8) in 11 out of 15 assays (73%). For assays with available data, conclusions regarding ADA impact on pharmacokinetics and pharmacodynamics were similar using S/N or titer. Subject ADA kinetic profiles were also comparable using the two measurements. Determination of antibody boosting in patients with pre-existing responses could be accomplished using similar approaches for titer and S/N. Investigation of factors that impacted the accuracy of ADA magnitude measurements revealed advantages and disadvantages to both approaches. In general, S/N had superior precision and ability to detect potentially low affinity/avidity responses compared to titer. This analysis indicates that S/N could serve as an equivalent and in some cases preferable alternative to titer for assessing ADA magnitude and evaluation of impact on clinical responses.
Graphical Abstract
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Mathews J, Amaravadi L, Eck S, Stevenson L, Wang YMC, Devanarayan V, Allinson J, Lundsten K, Gunsior M, Ni YG, Pepin MO, Gagnon A, Sheldon C, Trampont PC, Litwin V. Best practices for the development and fit-for-purpose validation of biomarker methods: a conference report. AAPS Open 2022. [DOI: 10.1186/s41120-021-00050-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractThis conference report summarized a full-day workshop, “best practices for the development and fit-for-purpose validation of biomarker methods,” which was held prior to the American Association of Pharmaceutical Scientists (AAPS) PharmSci360 Congress, San Antonio, TX, November 2019. The purpose of the workshop was to bring together thought leaders in biomarker assay development in order to identify which assay parameters and key statistical measures need to be considered when developing a biomarker assay. A diverse group of more than 40 scientists participated in the workshop. The workshop and subsequent working dinner stimulated robust discussion. While a consensus on best practices was not achieved, some common themes and major points to consider for biomarker assay development have been identified and agreed on. The focus of this conference report is to summarize the presentations and discussions which occurred at the workshop. Biomarker assay validation is a complex and an evolving area with discussions ongoing.
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Llano DA, Kwok SS, Devanarayan V. Reported Hearing Loss in Alzheimer's Disease Is Associated With Loss of Brainstem and Cerebellar Volume. Front Hum Neurosci 2021; 15:739754. [PMID: 34630060 PMCID: PMC8498578 DOI: 10.3389/fnhum.2021.739754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple epidemiological studies have revealed an association between presbycusis and Alzheimer’s Disease (AD). Unfortunately, the neurobiological underpinnings of this relationship are not clear. It is possible that the two disorders share a common, as yet unidentified, risk factor, or that hearing loss may independently accelerate AD pathology. Here, we examined the relationship between reported hearing loss and brain volumes in normal, mild cognitive impairment (MCI) and AD subjects using a publicly available database. We found that among subjects with AD, individuals that reported hearing loss had smaller brainstem and cerebellar volumes in both hemispheres than individuals without hearing loss. In addition, we found that these brain volumes diminish in size more rapidly among normal subjects with reported hearing loss and that there was a significant interaction between cognitive diagnosis and the relationship between reported hearing loss and these brain volumes. These data suggest that hearing loss is linked to brainstem and cerebellar pathology, but only in the context of the pathological state of AD. We hypothesize that the presence of AD-related pathology in both the brainstem and cerebellum creates vulnerabilities in these brain regions to auditory deafferentation-related atrophy. These data have implications for our understanding of the potential neural substrates for interactions between hearing loss and AD.
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Affiliation(s)
- Daniel A Llano
- Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Carle Neuroscience Institute, Urbana, IL, United States.,Carle Illinois College of Medicine, Urbana, IL, United States.,Beckman Institute for Advanced Science and Technology, Urbana, IL, United States
| | - Susanna S Kwok
- Carle Illinois College of Medicine, Urbana, IL, United States
| | - Viswanath Devanarayan
- Eisai Inc., Woodcliff Lake, NJ, United States.,Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL, United States
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14
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Llano DA, Devanarayan V. Serum Phosphatidylethanolamine and Lysophosphatidylethanolamine Levels Differentiate Alzheimer's Disease from Controls and Predict Progression from Mild Cognitive Impairment. J Alzheimers Dis 2021; 80:311-319. [PMID: 33523012 DOI: 10.3233/jad-201420] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND There is intense interest in the development of blood-based biomarkers, not only that can differentiate Alzheimer's disease (AD) from controls, but that can also predict conversion from mild cognitive impairment (MCI) to AD. Serum biomarkers carry the potential advantage over imaging or spinal fluid markers both in terms of cost and invasiveness. OBJECTIVE Our objective was to measure the potential for serum lipid markers to differentiate AD from age-matched healthy controls as well as to predict conversion from MCI to AD. METHODS Using a publicly-available dataset, we examined the relationship between baseline serum levels of 349 known lipids from 16 classes of lipids to differentiate disease state as well as to predict the conversion from MCI to AD. RESULTS We observed that several classes of lipids (cholesteroyl ester, phosphatidylethanolamine, lysophosphatidylethanolamine, and acylcarnitine) differentiated AD from normal controls. Among these, only two classes, phosphatidylethanolamine (PE) and lysophosphatidylethanolamine (lyso-PE), predicted time to conversion from MCI to AD. Low levels of PE and high levels of lyso-PE result in two-fold faster median time to progression from MCI to AD, with hazard ratios 0.62 and 1.34, respectively. CONCLUSION These data suggest that serum PE and lyso-PE may be useful biomarkers for predicting MCI to AD conversion. In addition, since PE is converted to lyso-PE by phospholipase A2, an important inflammatory mediator that is dysregulated in AD, these data suggest that the disrupted serum lipid profile here may be related to an abnormal inflammatory response early in the AD pathologic cascade.
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Affiliation(s)
- Daniel A Llano
- Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Carle Neuroscience Institute, Urbana, IL, USA
| | - Viswanath Devanarayan
- GlaxoSmithKline, Collegeville, PA, USA.,Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL, USA
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15
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Llano DA, Issa LK, Devanarayan P, Devanarayan V. Hearing Loss in Alzheimer's Disease Is Associated with Altered Serum Lipidomic Biomarker Profiles. Cells 2020; 9:cells9122556. [PMID: 33260532 PMCID: PMC7760745 DOI: 10.3390/cells9122556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 01/01/2023] Open
Abstract
Recent data have found that aging-related hearing loss (ARHL) is associated with the development of Alzheimer’s Disease (AD). However, the nature of the relationship between these two disorders is not clear. There are multiple potential factors that link ARHL and AD, and previous investigators have speculated that shared metabolic dysregulation may underlie the propensity to develop both disorders. Here, we investigate the distribution of serum lipidomic biomarkers in AD subjects with or without hearing loss in a publicly available dataset. Serum levels of 349 known lipids from 16 lipid classes were measured in 185 AD patients. Using previously defined co-regulated sets of lipids, both age- and sex-adjusted, we found that lipid sets enriched in phosphatidylcholine and phosphatidylethanolamine showed a strong inverse association with hearing loss. Examination of biochemical classes confirmed these relationships and revealed that serum phosphatidylcholine levels were significantly lower in AD subjects with hearing loss. A similar relationship was not found in normal subjects. These data suggest that a synergistic relationship may exist between AD, hearing loss and metabolic biomarkers, such that in the context of a pathological state such as AD, alterations in serum metabolic profiles are associated with hearing loss. These data also point to a potential role for phosphatidylcholine, a molecule with antioxidant properties, in the underlying pathophysiology of ARHL in the context of AD, which has implications for our understanding and potential treatment of both disorders.
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Affiliation(s)
- Daniel A. Llano
- Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Carle Neuroscience Institute, Urbana, IL 61801, USA
- Correspondence:
| | - Lina K. Issa
- Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Priya Devanarayan
- Department of Biology and Schreyer Honors College, Pennsylvania State University, University Park, PA 16802, USA;
| | - Viswanath Devanarayan
- GlaxoSmithKline, Collegeville, PA 19426 USA;
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA
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Bowsher RR, Devanarayan V. Are Lessons Learned in Setting Cut Points for Detection of Anti-Drug Antibodies Also Useful in Serology Assays for Robust Detection of SARS-CoV-2 Reactive Antibodies? AAPS J 2020; 22:127. [PMID: 33025311 PMCID: PMC7538034 DOI: 10.1208/s12248-020-00510-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/08/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ronald R Bowsher
- B2S Life Sciences llc, 97 East Monroe Street, Franklin, Indiana, 46131, USA.
| | - Viswanath Devanarayan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania, 19426, USA
- University of Illinois at Chicago, 1200 W. Harrison Street, Chicago, Illinois, 60607, USA
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17
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Devanarayan P, Devanarayan V, Llano DA. Identification of a Simple and Novel Cut-Point Based Cerebrospinal Fluid and MRI Signature for Predicting Alzheimer's Disease Progression that Reinforces the 2018 NIA-AA Research Framework. J Alzheimers Dis 2020; 68:537-550. [PMID: 30775985 DOI: 10.3233/jad-180905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The 2018 NIA-AA research framework proposes a classification system with Amyloid-β deposition, pathologic Tau, and Neurodegeneration (ATN) for diagnosis and staging of Alzheimer's disease (AD). Data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database can be utilized to identify diagnostic signatures for predicting AD progression, and to determine the utility of this NIA-AA research framework. Profiles of 320 peptides from baseline cerebrospinal fluid (CSF) samples of 287 normal, mild cognitive impairment (MCI), and AD subjects followed over a 3-10-year period were measured via multiple reaction monitoring mass spectrometry. CSF Aβ42, total-Tau (tTau), phosphorylated-Tau (pTau-181), and hippocampal volume were also measured. From these candidate markers, optimal signatures with decision thresholds to separate AD and normal subjects were first identified via unbiased regression and tree-based algorithms. The best performing signature determined via cross-validation was then tested in an independent group of MCI subjects to predict future progression. This multivariate analysis yielded a simple diagnostic signature comprising CSF pTau-181 to Aβ42 ratio, MRI hippocampal volume, and low CSF levels of a novel PTPRN peptide, with a decision threshold on each marker. When applied to a separate MCI group at baseline, subjects meeting these signature criteria experience 4.3-fold faster progression to AD compared to a 2.2-fold faster progression using only conventional markers. This novel 4-marker signature represents an advance over the current diagnostics based on widely used markers, and is easier to use in practice than recently published complex signatures. This signature also reinforces the ATN construct from the 2018 NIA-AA research framework.
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Affiliation(s)
| | - Viswanath Devanarayan
- Charles River Laboratories, Horsham, PA, USA.,Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, IL, USA
| | - Daniel A Llano
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Carle Neuroscience Institute, Urbana, IL, USA
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18
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Civoli F, Kasinath A, Cai XY, Wadhwa M, Exley A, Oldfield P, Alvandkouhi S, Schaffar G, Chappell J, Bowsher R, Devanarayan V, Marini J, Rebarchak S, Anderson M, Koppenburg V, Lester T. Recommendations for the Development and Validation of Immunogenicity Assays in Support of Biosimilar Programs. AAPS J 2019; 22:7. [PMID: 31792633 DOI: 10.1208/s12248-019-0386-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/18/2019] [Indexed: 11/30/2022]
Abstract
For biosimilar drug development programs, it is essential to demonstrate that there are no clinically significant differences between the proposed biosimilar therapeutic (biosimilar) and its reference product (originator). Based on a stepwise comprehensive comparability exercise, the biosimilar must demonstrate similarity to the originator in physicochemical characteristics, biological activity, pharmacokinetics, efficacy, and safety, including immunogenicity. The goal of the immunogenicity assessment is to evaluate potential differences between the proposed biosimilar product and the originator product in the incidence and severity of human immune responses. Establishing that there are no clinically meaningful differences in the immune response between the products is a key element in the demonstration of biosimilarity. An issue of practical, regulatory, and financial importance is to establish whether a two-assay (based on the biosimilar and originator respectively) or a one-assay approach (based on the biosimilar) is optimal for the comparative immunogenicity assessment. This paper recommends the use of a single, biosimilar-based assay for assessing immunogenic similarity in support of biosimilar drug development. The development and validation of an ADA assay used for a biosimilar program should include all the assessments recommended for an innovator program (10-16, 29). In addition, specific parameters also need to be evaluated, to gain confidence that the assay can detect antibodies against both the biosimilar and the originator. Specifically, the biosimilar and the originator should be compared in antigenic equivalence, to assess the ability of the biosimilar and the originator to bind in a similar manner to the positive control(s), as well as in the confirmatory assay and drug tolerance experiments. Practical guidance for the development and validation of anti-drug antibody (ADA) assays to assess immunogenicity of a biosimilar in comparison to the originator, using the one-assay approach, are described herein.
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Affiliation(s)
| | | | - Xiao-Yan Cai
- Accurant Biotech, Inc., Cranbury, New Jersey, USA
| | - Meenu Wadhwa
- Medicines and Healthcare Products Regulatory Agency (MHRA), National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK
| | - Andrew Exley
- Regulatory Division, Medicines and Healthcare Products Regulatory Agency (MHRA), London, UK
| | | | | | | | | | | | | | - Joseph Marini
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Shannon Rebarchak
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | - Todd Lester
- BioAgilytix Labs, Durham, North Carolina, USA
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19
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Srivastava GP, Ravikumar B, Bi Y, Mishra S, Das A, Shah MI, Kamaraj B, Bhattacharyya A, Philip P, Devanarayan V, Bannon AW, Das S, Xi S, Townsend M. P4-670: DISCOVERING ALZHEIMER'S DISEASE NETWORKS IN ACCELERATING MEDICINES PARTNERSHIP - ALZHEIMER'S DISEASE DATASETS. Alzheimers Dement 2019. [DOI: 10.1016/j.jalz.2019.09.036] [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: 10/25/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Sudeshna Das
- Massachusetts General Hospital and Harvard Medical School; Cambridge MA USA
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20
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Myler H, Gorovits B, Phillips K, Devanarayan V, Clements-Egan A, Gunn GR, Kirshner S, DeSilva B, Shah VP. Report on the AAPS Immunogenicity Guidance Forum. AAPS J 2019; 21:55. [DOI: 10.1208/s12248-019-0328-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/03/2019] [Indexed: 01/28/2023]
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21
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Srivastava GP, Devanarayan V. P4‐386: META‐ANALYSIS OF HETEROGENEOUS NETWORKS TO CONSTRUCT
DE‐NOVO
META‐NETWORKS FOR TARGET IDENTIFICATION IN ALZHEIMER'S DISEASE. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.07.210] [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: 11/29/2022]
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22
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Devanarayan P, Devanarayan V, Llano DA. P4‐279: IDENTIFICATION OF A SIMPLE AND NOVEL DIAGNOSTIC FOR PREDICTING ALZHEIMER'S DISEASE PROGRESSION REINFORCES THE 2018 NIA‐AA RESEARCH FRAMEWORK. Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.07.101] [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: 10/28/2022]
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23
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Maudsley S, Devanarayan V, Martin B, Geerts H. Intelligent and effective informatic deconvolution of “Big Data” and its future impact on the quantitative nature of neurodegenerative disease therapy. Alzheimers Dement 2018; 14:961-975. [DOI: 10.1016/j.jalz.2018.01.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 10/03/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Stuart Maudsley
- Department of Biomedical ResearchUniversity of AntwerpAntwerpBelgium
- VIB Center for Molecular NeurologyAntwerpBelgium
| | | | - Bronwen Martin
- Department of Biomedical ResearchUniversity of AntwerpAntwerpBelgium
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24
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Llano DA, Bundela S, Mudar RA, Devanarayan V. A multivariate predictive modeling approach reveals a novel CSF peptide signature for both Alzheimer's Disease state classification and for predicting future disease progression. PLoS One 2017; 12:e0182098. [PMID: 28771542 PMCID: PMC5542644 DOI: 10.1371/journal.pone.0182098] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 11/19/2022] Open
Abstract
To determine if a multi-analyte cerebrospinal fluid (CSF) peptide signature can be used to differentiate Alzheimer’s Disease (AD) and normal aged controls (NL), and to determine if this signature can also predict progression from mild cognitive impairment (MCI) to AD, analysis of CSF samples was done on the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. The profiles of 320 peptides from baseline CSF samples of 287 subjects over a 3–6 year period were analyzed. As expected, the peptide most able to differentiate between AD vs. NL was found to be Apolipoprotein E. Other peptides, some of which are not classically associated with AD, such as heart fatty acid binding protein, and the neuronal pentraxin receptor, also differentiated disease states. A sixteen-analyte signature was identified which differentiated AD vs. NL with an area under the receiver operating characteristic curve of 0.89, which was better than any combination of amyloid beta (1–42), tau, and phospho-181 tau. This same signature, when applied to a new and independent data set, also strongly predicted both probability and rate of future progression of MCI subjects to AD, better than traditional markers. These data suggest that multivariate peptide signatures from CSF predict MCI to AD progression, and point to potentially new roles for certain proteins not typically associated with AD.
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Affiliation(s)
- Daniel A. Llano
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, United States of America
- * E-mail:
| | - Saurabh Bundela
- Exploratory Statistics, AbbVie, Inc., North Chicago, IL, United States of America
| | - Raksha A. Mudar
- Department of Speech and Hearing Science, University of Illinois at Urbana-Champaign, United States of America
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25
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Devanarayan V, Smith WC, Brunelle RL, Seger ME, Krug K, Bowsher RR. Recommendations for Systematic Statistical Computation of Immunogenicity Cut Points. AAPS J 2017; 19:1487-1498. [DOI: 10.1208/s12248-017-0107-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022]
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26
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Huang X, Sun Y, Trow P, Chatterjee S, Chakravartty A, Tian L, Devanarayan V. Patient subgroup identification for clinical drug development. Stat Med 2017; 36:1414-1428. [PMID: 28147447 DOI: 10.1002/sim.7236] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 06/12/2015] [Revised: 11/22/2016] [Accepted: 01/05/2017] [Indexed: 12/26/2022]
Abstract
Causal mechanism of relationship between the clinical outcome (efficacy or safety endpoints) and putative biomarkers, clinical baseline, and related predictors is usually unknown and must be deduced empirically from experimental data. Such relationships enable the development of tailored therapeutics and implementation of a precision medicine strategy in clinical trials to help stratify patients in terms of disease progression, clinical response, treatment differentiation, and so on. These relationships often require complex modeling to develop the prognostic and predictive signatures. For the purpose of easier interpretation and implementation in clinical practice, defining a multivariate biomarker signature in terms of thresholds (cutoffs/cut points) on individual biomarkers is preferable. In this paper, we propose some methods for developing such signatures in the context of continuous, binary and time-to-event endpoints. Results from simulations and case study illustration are also provided. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xin Huang
- AbbVie, Inc., North Chicago, IL, U.S.A
| | - Yan Sun
- AbbVie, Inc., North Chicago, IL, U.S.A
| | - Paul Trow
- AbbVie, Inc., North Chicago, IL, U.S.A
| | | | | | - Lu Tian
- Stanford University School of Medicine, Palo Alto, CA, U.S.A
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27
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Geerts H, Dacks PA, Devanarayan V, Haas M, Khachaturian ZS, Gordon MF, Maudsley S, Romero K, Stephenson D. Big data to smart data in Alzheimer's disease: The brain health modeling initiative to foster actionable knowledge. Alzheimers Dement 2016; 12:1014-1021. [PMID: 27238630 DOI: 10.1016/j.jalz.2016.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 12/23/2015] [Revised: 03/25/2016] [Accepted: 04/26/2016] [Indexed: 02/07/2023]
Abstract
Massive investment and technological advances in the collection of extensive and longitudinal information on thousands of Alzheimer patients results in large amounts of data. These "big-data" databases can potentially advance CNS research and drug development. However, although necessary, they are not sufficient, and we posit that they must be matched with analytical methods that go beyond retrospective data-driven associations with various clinical phenotypes. Although these empirically derived associations can generate novel and useful hypotheses, they need to be organically integrated in a quantitative understanding of the pathology that can be actionable for drug discovery and development. We argue that mechanism-based modeling and simulation approaches, where existing domain knowledge is formally integrated using complexity science and quantitative systems pharmacology can be combined with data-driven analytics to generate predictive actionable knowledge for drug discovery programs, target validation, and optimization of clinical development.
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Affiliation(s)
- Hugo Geerts
- In Silico Biosciences, Inc., Berwyn, PA, USA.
| | - Penny A Dacks
- Alzheimer's Drug Discovery Foundation, New York, NY, USA
| | | | | | | | | | - Stuart Maudsley
- VIB Department of Molecular Genetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
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28
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McKeegan EM, Ansell PJ, Davis G, Chan S, Chandran RK, Gawel SH, Dowell BL, Bhathena A, Chakravartty A, McKee MD, Ricker JL, Carlson DM, Ramalingam SS, Devanarayan V. Plasma biomarker signature associated with improved survival in advanced non-small cell lung cancer patients on linifanib. Lung Cancer 2015; 90:296-301. [DOI: 10.1016/j.lungcan.2015.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 09/01/2015] [Accepted: 09/13/2015] [Indexed: 11/28/2022]
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29
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Jani D, Allinson J, Berisha F, Cowan KJ, Devanarayan V, Gleason C, Jeromin A, Keller S, Khan MU, Nowatzke B, Rhyne P, Stephen L. Recommendations for Use and Fit-for-Purpose Validation of Biomarker Multiplex Ligand Binding Assays in Drug Development. AAPS J 2015; 18:1-14. [PMID: 26377333 DOI: 10.1208/s12248-015-9820-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/12/2015] [Indexed: 11/30/2022]
Abstract
Multiplex ligand binding assays (LBAs) are increasingly being used to support many stages of drug development. The complexity of multiplex assays creates many unique challenges in comparison to single-plexed assays leading to various adjustments for validation and potentially during sample analysis to accommodate all of the analytes being measured. This often requires a compromise in decision making with respect to choosing final assay conditions and acceptance criteria of some key assay parameters, depending on the intended use of the assay. The critical parameters that are impacted due to the added challenges associated with multiplexing include the minimum required dilution (MRD), quality control samples that span the range of all analytes being measured, quantitative ranges which can be compromised for certain targets, achieving parallelism for all analytes of interest, cross-talk across assays, freeze-thaw stability across analytes, among many others. Thus, these challenges also increase the complexity of validating the performance of the assay for its intended use. This paper describes the challenges encountered with multiplex LBAs, discusses the underlying causes, and provides solutions to help overcome these challenges. Finally, we provide recommendations on how to perform a fit-for-purpose-based validation, emphasizing issues that are unique to multiplex kit assays.
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Affiliation(s)
- Darshana Jani
- Pfizer Inc., One Burtt Road, Andover, Massachusetts, 01810, USA.
| | - John Allinson
- LGC Ltd, Newmarket Road, Fordham, Cambridgeshire, CB7 5WW, UK
| | - Flora Berisha
- Kyowa-Kirin Pharmaceuticals, 212 Carnegie Center #101, Princeton, New Jersey, 08540, USA
| | - Kyra J Cowan
- Genentech, 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Carol Gleason
- Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey, 08540, USA
| | - Andreas Jeromin
- Quanterix Corporation, 113 Hartwell Avenue, Lexington, Massachusetts, 02421, USA
| | - Steve Keller
- Abbvie Inc., 1500 Seaport Blvd, Redwood City, California, 94063, USA
| | - Masood U Khan
- KCAS Bioanalytical and Biomarker Services, 12400 Shawnee Mission Parkway, Shawnee, Kansas, 66216, USA
| | - Bill Nowatzke
- Radix Biosolutions, 111 Cooperative Way #120, Georgetown, Texas, 78626, USA
| | - Paul Rhyne
- Quintiles Corporation, 1600 Terrell Mill Road Suite 100, Marietta, Georgia, 30067, USA
| | - Laurie Stephen
- Ampersand Biosciences, LLC, 3 Main St., Saranac Lake, New York, 12983, USA
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30
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Vanderstichele HM, Stephenson D, Shaw LM, Carrillo M, Umek R, Rajapakse H, Luthman J, Soares H, Gordon MF, Devanarayan V, Genius J, Berman R, Hendrix J, Romero K, Kaplow J, Willis B, Hitchcock J, Yu P, Lawson J, Raunig D, Meibach R, Ito K, Beckett L, Engelborghs S, Blennow K, Dean RA. O4‐11‐02: The path to regulatory qualification of cerebrospinal fluid biomarkers as enrichment tools in clinical trials of patients with early Alzheimer's disease: For the coalition against major diseases. Alzheimers Dement 2015. [DOI: 10.1016/j.jalz.2015.07.406] [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: 11/24/2022]
Affiliation(s)
| | - Diane Stephenson
- Coalition Against Major DiseasesCritical Path InstituteTucsonAZUSA
| | | | | | | | - Hemaka Rajapakse
- Coalition Against Major DiseasesCritical Path InstituteTucsonAZUSA
| | | | | | | | | | | | | | | | - Klaus Romero
- Coalition Against Major DiseasesCritical Path InstituteTucsonAZUSA
| | | | | | | | - Peng Yu
- Eli Lilly and CompanyIndianapolisINUSA
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31
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Sharapova T, Devanarayan V, LeRoy B, Liguori MJ, Blomme E, Buck W, Maher J. Evaluation of miR-122 as a Serum Biomarker for Hepatotoxicity in Investigative Rat Toxicology Studies. Vet Pathol 2015; 53:211-21. [DOI: 10.1177/0300985815591076] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
MicroRNAs are short noncoding RNAs involved in regulation of gene expression. Certain microRNAs, including miR-122, seem to have ideal properties as biomarkers due to good stability, high tissue specificity, and ease of detection across multiple species. Recent reports have indicated that miR-122 is a highly liver-specific marker detectable in serum after liver injury. The purpose of the current study was to assess the performance of miR-122 as a serum biomarker for hepatotoxicity in short-term (5–28 days) repeat-dose rat toxicology studies when benchmarked against routine clinical chemistry and histopathology. A total of 23 studies with multiple dose levels of experimental compounds were examined, and they included animals with or without liver injury and with various hepatic histopathologic changes. Serum miR-122 levels were quantified by reverse transcription quantitative polymerase chain reaction. Increases in circulating miR-122 levels highly correlated with serum elevations of liver enzymes, such as alanine aminotransferase (ALT), aspartate aminotransferase (AST) and glutamate dehydrogenase (GLDH). Statistical analysis showed that miR-122 outperformed ALT as a biomarker for histopathologically confirmed liver toxicity and was equivalent in performance to AST and GLDH. Additionally, an increase of 4% in predictive accuracy was obtained using a multiparameter approach incorporating miR-122 with ALT, AST, and GLDH. In conclusion, serum miR-122 levels can be utilized as a biomarker of hepatotoxicity in acute and subacute rat toxicology studies, and its performance can rival or exceed those of standard enzyme biomarkers such as the liver transaminases.
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Affiliation(s)
- T. Sharapova
- Investigative Toxicology and Pathology, Abbvie, North Chicago, IL, USA
| | | | - B. LeRoy
- Investigative Toxicology and Pathology, Abbvie, North Chicago, IL, USA
| | - M. J. Liguori
- Cell, Molecular, and Exploratory Toxicology, Abbvie, North Chicago, IL, USA
| | - E. Blomme
- Investigative Toxicology and Pathology, Abbvie, North Chicago, IL, USA
| | - W. Buck
- Cell, Molecular, and Exploratory Toxicology, Abbvie, North Chicago, IL, USA
| | - J. Maher
- Investigative Toxicology and Pathology, Abbvie, North Chicago, IL, USA
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32
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Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M. Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biol 2015; 16:133. [PMID: 26109056 PMCID: PMC4506430 DOI: 10.1186/s13059-015-0694-1] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/12/2015] [Indexed: 12/22/2022] Open
Abstract
Background Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. Results We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. Conclusions We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0694-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenqian Zhang
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China
| | - Ying Yu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.,University of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Jean Thierry-Mieg
- NIH/NCBI, Bldg 38A/Room 8S808, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Wenwei Zhang
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China
| | | | - Jian Wang
- Eli Lilly and Company Research Informatics, Lilly Corporate Center, Drop Code 0725, Indianapolis, IN, 46285, USA
| | - Cesare Furlanello
- Fondazione Bruno Kessler (FBK), Via Sommarive 18, 38123, Trento Povo, TN, Italy
| | - Viswanath Devanarayan
- AbbVie Inc., Global Pharmaceutical R&D, 32 Knights Crest Court, Souderton, PA, 18964, USA
| | - Jie Cheng
- GlaxoSmithKline, Discovery Analytics, Mailstop UP4335, 1250 South Collegeville Rd, Collegeville, PA, 19426, USA
| | - Youping Deng
- Department of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA
| | - Barbara Hero
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Meiwen Jia
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Li Li
- SAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA
| | - Simon M Lin
- Marshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA
| | - Yuri Nikolsky
- Thomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA
| | - André Oberthuer
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Tao Qing
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Zhenqiang Su
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Ruth Volland
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Charles Wang
- Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - May D Wang
- Department of Biomedical Engineering, GeorgiaTech and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA
| | - Junmei Ai
- Department of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA
| | - Davide Albanese
- Fondazione Edmund Mach, CRI-CBC, San Michele all'Adige, TN, Italy
| | | | - Smadar Avigad
- Department of Pediatric Hematology-Oncology, Molecular Oncology, Felsenstein Medical Research Center, Schneider Children's Medical Center of Israel, Petach Tikva, 49202, Israel
| | - Wenjun Bao
- SAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA
| | - Marina Bessarabova
- Thomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA
| | - Murray H Brilliant
- Marshfield Clinic Research Foundation, Center of Human Genetics, 1000 N Oak Avenue, Marshfield, WI, 54449, USA
| | - Benedikt Brors
- Department of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Marco Chierici
- Fondazione Bruno Kessler (FBK), Via Sommarive 18, 38123, Trento Povo, TN, Italy
| | - Tzu-Ming Chu
- SAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA
| | - Jibin Zhang
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China
| | - Richard G Grundy
- University of Nottingham, Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, D Floor Medical School, Nottingham, NG7 2UH, UK
| | - Min Max He
- Marshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA
| | - Scott Hebbring
- Marshfield Clinic Research Foundation, Center of Human Genetics, 1000 N Oak Avenue, Marshfield, WI, 54449, USA
| | - Howard L Kaufman
- Department of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA
| | - Samir Lababidi
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, WOC1 RM400S, HFM-210, 1401 Rockville Pike, Rockville, MD, 20852, USA
| | - Lee J Lancashire
- Thomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA
| | - Yan Li
- Department of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA
| | - Xin X Lu
- AbbVie Inc., Global Pharmaceutical Research and Development, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Heng Luo
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.,University of Arkansas at Little Rock, UALR/UAMS Joint Bioinformatics Graduate Program, 2801 South University Avenue, Little Rock, AR, 72204, USA
| | - Xiwen Ma
- Eli Lilly and Company, Discovery Statistics, Lilly Corporate Center, Drop Code 2036, Indianapolis, IN, 46285, USA
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Rosa Noguera
- Department of Pathology, University of Valencia, Medical School, Avda. Blasco Ibáñez, 17, 46010, Valencia, Spain
| | - Martin Peifer
- University of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany.,Department of Translational Genomics, University of Cologne, D-50924, Cologne, Germany
| | - John H Phan
- Department of Biomedical Engineering, GeorgiaTech and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA
| | - Frederik Roels
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.,University of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Carolina Rosswog
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Susan Shao
- SAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA
| | - Jie Shen
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Jessica Theissen
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Gian Paolo Tonini
- Neuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy
| | - Jo Vandesompele
- Department of Pediatrics and Genetics, Ghent University, Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Po-Yen Wu
- Georgia Institute of Technology, School of Electrical and Computer Engineering, 777 Atlantic Drive NW, Atlanta, GA, 30332, USA
| | - Wenzhong Xiao
- Harvard Medical School, Massachusetts General Hospital, 51 Blossom Street, Boston, MA, 02114, USA
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weihong Xu
- Stanford University, Stanford Genome Technology Center, 855 South California Avenue, Palo Alto, CA, 94304, USA
| | - Jiekun Xuan
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Yong Yang
- Eli Lilly and Company Research Informatics, Lilly Corporate Center, Drop Code 0725, Indianapolis, IN, 46285, USA
| | - Zhan Ye
- Marshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA
| | - Zirui Dong
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China
| | - Ke K Zhang
- Department of Pathology, University of North Dakota School of Medicine, 501 N. Columbia Road RM 3573, Grand Forks, ND, 58202-9037, USA
| | - Ye Yin
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China
| | - Chen Zhao
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yuanting Zheng
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China
| | | | - Tieliu Shi
- East China Normal University, Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, 500 Dongchuan Road, Shanghai, 200241, China
| | - Linda H Malkas
- Department of Molecular & Cellular Biology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Frank Berthold
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.,University of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany
| | - Jun Wang
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.,King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Leming Shi
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China. .,National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
| | - Zhiyu Peng
- BGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China. .,BGI-Guangzhou, Guangzhou Higher Education Mega Center, No. 280, Waihuan East Rd., Guangzhou, 510006, China.
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany. .,University of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany.
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Kelley M, Stevenson L, Golob M, Devanarayan V, Pedras-Vasconcelos J, Staack RF, Jenkins R, Booth B, Wakshull E, Bowsher R, Rock M, Dudal S, DeSilva B. Workshop Report: AAPS Workshop on Method Development, Validation, and Troubleshooting of Ligand-Binding Assays in the Regulated Environment. AAPS J 2015; 17:1019-24. [PMID: 25921938 DOI: 10.1208/s12248-015-9767-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/25/2015] [Indexed: 12/23/2022]
Abstract
A novel format was introduced at the recent AAPS NBC Workshop on Method Development, Validation and Troubleshooting in San Diego on 18th May 2014. The workshop format was initiated by Binodh De Silva; Marie Rock and Sherri Dudal joined the initiative to develop and chair the workshop. Questions were solicited by a variety of avenues, including a Linked-In Discussion Group. Once collated and clarified, the topics covered assay development, validation, and analysis of PK, Immunogenicity, and Biomarkers with an additional topic on alternative bioanalytical technologies. A panel of experts (workshop report co-authors) was assigned to each topic to bring forward thought-provoking aspects of each topic. The format of the workshop was developed to target the needs of bioanalytical scientists with intermediate to advanced experience in the field ranging to enable robust discussion and to delve deeper into the current bioanalytical hot topics. While the new format allowed for an interactive session with the topical discussion driven by the audience members, it did not foster equal discussion time for all of the proposed topics, especially Biomarkers and alternative LBA technologies.
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Ramalingam SS, Shtivelband M, Soo RA, Barrios CH, Makhson A, Segalla JGM, Pittman KB, Kolman P, Pereira JR, Srkalovic G, Belani CP, Axelrod R, Owonikoko TK, Qin Q, Qian J, McKeegan EM, Devanarayan V, McKee MD, Ricker JL, Carlson DM, Gorbunova VA. Randomized phase II study of carboplatin and paclitaxel with either linifanib or placebo for advanced nonsquamous non-small-cell lung cancer. J Clin Oncol 2015; 33:433-41. [PMID: 25559798 PMCID: PMC5478045 DOI: 10.1200/jco.2014.55.7173] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Linifanib, a potent, selective inhibitor of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) receptors, has single-agent activity in non-small-cell lung cancer (NSCLC). We evaluated linifanib with carboplatin and paclitaxel as first-line therapy of advanced nonsquamous NSCLC. PATIENTS AND METHODS Patients with stage IIIB/IV nonsquamous NSCLC were randomly assigned to 3-week cycles of carboplatin (area under the curve 6) and paclitaxel (200 mg/m(2)) with daily placebo (arm A), linifanib 7.5 mg (arm B), or linifanib 12.5 mg (arm C). The primary end point was progression-free survival (PFS); secondary efficacy end points included overall survival (OS) and objective response rate. RESULTS One hundred thirty-eight patients were randomly assigned (median age, 61 years; 57% men; 84% smokers). Median PFS times were 5.4 months (95% CI, 4.2 to 5.7 months) in arm A (n = 47), 8.3 months (95% CI, 4.2 to 10.8 months) in arm B (n = 44), and 7.3 months (95% CI, 4.6 to 10.8 months) in arm C (n = 47). Hazard ratios (HRs) for PFS were 0.51 for arm B versus A (P = .022) and 0.64 for arm C versus A (P = .118). Median OS times were 11.3, 11.4, and 13.0 months in arms A, B, and C, respectively. HRs for OS were 1.08 for arm B versus A (P = .779) and 0.88 for arm C versus A (P = .650). Both linifanib doses were associated with increased toxicity, including a higher incidence of adverse events known to be associated with VEGF/PDGF inhibition. Baseline plasma carcinoembryonic antigen/cytokeratin 19 fragments biomarker signature was associated with PFS improvement and a trend toward OS improvement with linifanib 12.5 mg. CONCLUSION Addition of linifanib to chemotherapy significantly improved PFS (arm B), with a modest trend for survival benefit (arm C) and increased toxicity reflective of known VEGF/PDGF inhibitory effects.
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Affiliation(s)
- Suresh S Ramalingam
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL.
| | - Mikhail Shtivelband
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Ross A Soo
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Carlos H Barrios
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Anatoly Makhson
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - José G M Segalla
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Kenneth B Pittman
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Petr Kolman
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Jose R Pereira
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Gordan Srkalovic
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Chandra P Belani
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Rita Axelrod
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Taofeek K Owonikoko
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Qin Qin
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Jiang Qian
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Evelyn M McKeegan
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Viswanath Devanarayan
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Mark D McKee
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Justin L Ricker
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Dawn M Carlson
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
| | - Vera A Gorbunova
- Suresh S. Ramalingam and Taofeek K. Owonikoko, Winship Cancer Institute of Emory University, Atlanta, GA; Mikhail Shtivelband, Ironwood Cancer and Research Centers, Chandler, AZ; Ross A. Soo, National University Cancer Institute, National University Health System, Singapore, Singapore; Carlos H. Barrios, Pontifícia Universidade Católica do Rio Grande do Sul School of Medicine, Porto Alegre; José G.M. Segalla, Hospital Amaral Carvalho, Jau; Jose R. Pereira, Instituto Brasileiro de Cancerologia Toracica, Sao Paulo, Brazil; Anatoly Makhson, Moscow City Oncology Hospital No. 62; Vera A. Gorbunova, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, Moscow, Russia; Kenneth B. Pittman, The Queen Elizabeth Hospital, Woodville, South Australia, Australia; Petr Kolman, Hospital Kyjov, Kyjov, Czech Republic; Gordan Srkalovic, Sparrow Regional Cancer Center, Lansing, MI; Chandra P. Belani, Penn State Hershey Cancer Institute, Hershey; Rita Axelrod, Thomas Jefferson University Hospital, Philadelphia, PA; Qin Qin, Jiang Qian, Evelyn M. McKeegan, Viswanath Devanarayan, Mark D. McKee, Justin L. Ricker, and Dawn M. Carlson, AbbVie, North Chicago, IL
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Chen G, Zhong H, Belousov A, Devanarayan V. A PRIM approach to predictive-signature development for patient stratification. Stat Med 2014; 34:317-42. [PMID: 25345685 PMCID: PMC4285951 DOI: 10.1002/sim.6343] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 09/17/2014] [Accepted: 10/07/2014] [Indexed: 11/23/2022]
Abstract
Patients often respond differently to a treatment because of individual heterogeneity. Failures of clinical trials can be substantially reduced if, prior to an investigational treatment, patients are stratified into responders and nonresponders based on biological or demographic characteristics. These characteristics are captured by a predictive signature. In this paper, we propose a procedure to search for predictive signatures based on the approach of patient rule induction method. Specifically, we discuss selection of a proper objective function for the search, present its algorithm, and describe a resampling scheme that can enhance search performance. Through simulations, we characterize conditions under which the procedure works well. To demonstrate practical uses of the procedure, we apply it to two real-world data sets. We also compare the results with those obtained from a recent regression-based approach, Adaptive Index Models, and discuss their respective advantages. In this study, we focus on oncology applications with survival responses.
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Affiliation(s)
- Gong Chen
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center New York, Roche TCRC, Inc., 430 East 29th Street, New York, NY 10016, U.S.A
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Toh HC, Yong WP, Wong Y, tan E, Kollmannsberger CK, Devanarayan V, Zhang K, Luo Y, Chen D, Ashton E, Ricker JL, Carlson D, Chen P. Abstract A105: Phase 2 trials of linifanib (ABT‐869) in advanced hepatocellular, renal cell and non‐small cell lung cancer: Associations of response by CT or DCE‐MRI with patient outcome. Clin Trials 2014. [DOI: 10.1158/1535-7163.targ-09-a105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Skapenko A, Schulze-Koops H, Devanarayan V, Idler K, Hong F, Smolen J, Kavanaugh A, Kupper H, Waring J. OP0034 Identification of Genetic Variants Associated with Response to Methotrexate in Patients with Early Rheumatoid Arthritis: Results from the Optima Study:. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2014-eular.1318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Shankar G, Arkin S, Cocea L, Devanarayan V, Kirshner S, Kromminga A, Quarmby V, Richards S, Schneider CK, Subramanyam M, Swanson S, Verthelyi D, Yim S. Assessment and reporting of the clinical immunogenicity of therapeutic proteins and peptides-harmonized terminology and tactical recommendations. AAPS J 2014; 16:658-73. [PMID: 24764037 DOI: 10.1208/s12248-014-9599-2] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 03/26/2014] [Indexed: 02/08/2023]
Abstract
Immunogenicity is a significant concern for biologic drugs as it can affect both safety and efficacy. To date, the descriptions of product immunogenicity have varied not only due to different degrees of understanding of product immunogenicity at the time of licensing but also due to an evolving lexicon that has generated some confusion in the field. In recent years, there has been growing consensus regarding the data needed to assess product immunogenicity. Harmonization of the strategy for the elucidation of product immunogenicity by drug developers, as well as the use of defined common terminology, can benefit medical practitioners, health regulatory agencies, and ultimately the patients. Clearly, understanding the incidence, kinetics and magnitude of anti-drug antibody (ADA), its neutralizing ability, cross-reactivity with endogenous molecules or other marketed biologic drugs, and related clinical impact may enhance clinical management of patients treated with biologic drugs. To that end, the authors present terms and definitions for describing and analyzing clinical immunogenicity data and suggest approaches to data presentation, emphasizing associations of ADA development with pharmacokinetics, efficacy, and safety that are necessary to assess the clinical relevance of immunogenicity.
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Affiliation(s)
- G Shankar
- Janssen Research & Development, LLC (Johnson & Johnson), 1400 McKean Road, P.O. Box 776, Spring House, Pennsylvania, 19477, USA,
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Mozaffarian N, Smolen JS, Devanarayan V, Hong F, Kavanaugh A. FRI0086 Biomarkers identify radiographic progressors and clinical responders among patients with early rheumatoid arthritis. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2013-eular.1213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Waring JF, Devanarayan V, Idler K, Hong F, Smolen JS, Kavanaugh A, Kupper H, Schulze-Koops H, Skapenko A. FRI0051 Application of a multiplex gene polymorphism assay for variants associated with rheumatoid arthritis susceptibility - results of 168 snps tested in the optima study. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Mc Keegan E, Ansell P, Davis G, Chan S, Chandran R, Gawel S, McKee M, Ricker J, Carlson D, Devanarayan V. Baseline Plasma Biomarker Signature is Associated with Improved Survival in Advanced nsclc Patients on Linifanib. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)33068-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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McKeegan EM, Chakravartty A, Ansell PJ, Davis G, Chen G, Chan S, Chandran R, DeGuzman A, Gawel S, Dowell B, Bhathena A, McKee MD, Ricker JL, Carlson DM, Devanarayan V. Association of baseline plasma biomarker signature with survival in advanced NSCLC patients on linifanib. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.e13583] [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
e13583 Background: Linifanib is a potent and selective VEGF and PDGF receptor inhibitor that has activity in unselected, advanced NSCLC patients (pts) both as monotherapy in the relapsed setting and with carboplatin (C) and paclitaxel (P) in the first-line setting. A baseline plasma biomarker signature identifying NSCLC pts most sensitive to linifanib is needed. Methods: An exploratory retrospective analysis of four randomized clinical trials including linifanib or other treatments in relapsed NSCLC was conducted. Evaluable baseline plasma samples were obtained from 116 pts who received linifanib and 71 pts on other treatments. A signature combining established tumor markers (carcinoembryonic antigen [CEA] and fragments of cytokeratin 19 [CYFRA 21-1]) was derived using a sequential BATTing approach. The signature was then tested across a randomized trial of CP + placebo, linifanib 7.5 mg, or linifanib 12.5 mg in first-line advanced, non-squamous NSCLC. Results: In 2/3L NSCLC, the signature was associated with improvement in survival on linifanib monotherapy (HR=0.51 vs. signature negative; P=0.0017), but no improvement in survival on other treatments (P=0.87). In the first-line setting with CP, the signature was associated with significant PFS improvement with linifanib and a trend towards significant overall survival improvement at high dose (Table). Conclusions: A baseline plasma biomarker signature is associated with improved survival in advanced NSCLC patients on linifanib. Incorporation of this signature should be considered in any further investigation of linifanib in NSCLC. [Table: see text]
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Affiliation(s)
| | | | | | | | - Gong Chen
- Abbott Laboratories, Abbott Park, IL
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Goedken ER, Devanarayan V, Harris CM, Dowding LA, Jakway JP, Voss JW, Wishart N, Jordan DC, Talanian RV. Minimum significant ratio of selectivity ratios (MSRSR) and confidence in ratio of selectivity ratios (CRSR): quantitative measures for selectivity ratios obtained by screening assays. ACTA ACUST UNITED AC 2012; 17:857-67. [PMID: 22584786 DOI: 10.1177/1087057112447108] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Development of inhibitor compounds selective against undesirable targets is critical in drug discovery. Selectivity ratios for candidate compounds are evaluated by dividing potencies from two assays assessing the off-target and target. Because all potency measurements have underlying uncertainty, understanding error propagation is essential to interpreting selectivity data. Assay noise introduces ambiguity in the statistical significance of selectivity ratios, particularly at low replicate numbers when compounds are often prioritized for subsequent testing. The ability to differentiate potency results for any pair of compounds in one assay is evaluated using a metric called minimum significant ratio (MSR). Potency results of one compound tested in a pair of assays can be differentiated by the minimum significant selectivity ratio (MSSR). To differentiate selectivity ratios for any pair of compounds, we extend this concept by proposing two new parameters called the minimum significant ratio of selectivity ratios (MSRSR) and confidence in ratio of selectivity ratios (CRSR). Importantly, these tools can be used after a single selectivity measurement. We describe these methods and illustrate their usefulness using structure-activity relationship data from a Janus kinase inhibitor project, in which these tools informed a cogent retesting strategy and enabled rapid and objective decision making.
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Zhang K, Yang Y, Devanarayan V, Xie L, Deng Y, Donald S. A hidden Markov model-based algorithm for identifying tumour subtype using array CGH data. BMC Genomics 2011; 12 Suppl 5:S10. [PMID: 22369459 PMCID: PMC3287492 DOI: 10.1186/1471-2164-12-s5-s10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background The recent advancement in array CGH (aCGH) research has significantly improved tumor identification using DNA copy number data. A number of unsupervised learning methods have been proposed for clustering aCGH samples. Two of the major challenges for developing aCGH sample clustering are the high spatial correlation between aCGH markers and the low computing efficiency. A mixture hidden Markov model based algorithm was developed to address these two challenges. Results The hidden Markov model (HMM) was used to model the spatial correlation between aCGH markers. A fast clustering algorithm was implemented and real data analysis on glioma aCGH data has shown that it converges to the optimal cluster rapidly and the computation time is proportional to the sample size. Simulation results showed that this HMM based clustering (HMMC) method has a substantially lower error rate than NMF clustering. The HMMC results for glioma data were significantly associated with clinical outcomes. Conclusions We have developed a fast clustering algorithm to identify tumor subtypes based on DNA copy number aberrations. The performance of the proposed HMMC method has been evaluated using both simulated and real aCGH data. The software for HMMC in both R and C++ is available in ND INBRE website http://ndinbre.org/programs/bioinformatics.php.
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Affiliation(s)
- Ke Zhang
- Department of Pathology, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58201, USA.
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Gupta S, Devanarayan V, Finco D, Gunn GR, Kirshner S, Richards S, Rup B, Song A, Subramanyam M. Recommendations for the validation of cell-based assays used for the detection of neutralizing antibody immune responses elicited against biological therapeutics. J Pharm Biomed Anal 2011; 55:878-88. [DOI: 10.1016/j.jpba.2011.03.038] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/23/2011] [Accepted: 03/25/2011] [Indexed: 11/24/2022]
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Devanarayan V, Simon A. P3‐099: Evaluation of the plasma proteomics data from the ADNI database for Alzheimer's disease‐state classification and prediction of 12‐month progression from MCI to AD. Alzheimers Dement 2011. [DOI: 10.1016/j.jalz.2011.05.1539] [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: 10/17/2022]
Affiliation(s)
| | - Adam Simon
- Brain Computer Interface IncDoylestownPennsylvaniaUnited States
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Ohrfelt A, Andreasson U, Simon A, Zetterberg H, Edman A, Potter W, Holder D, Devanarayan V, Seeburger J, Smith AD, Blennow K, Wallin A. Screening for new biomarkers for subcortical vascular dementia and Alzheimer's disease. Dement Geriatr Cogn Dis Extra 2011; 1:31-42. [PMID: 22163231 PMCID: PMC3199889 DOI: 10.1159/000323417] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Novel biomarkers are important for identifying as well as differentiating subcortical vascular dementia (SVD) and Alzheimer's disease (AD) at an early stage in the disease process. Methods In two independent cohorts, a multiplex immunoassay was utilized to analyze 90 proteins in cerebrospinal fluid (CSF) samples from dementia patients and patients at risk of developing dementia (mild cognitive impairment). Results The levels of several CSF proteins were increased in SVD and its incipient state, and in moderate-to-severe AD compared with the control group. In contrast, some CSF proteins were altered in AD, but not in SVD. The levels of heart-type fatty acid binding protein (H-FABP) were consistently increased in all groups with dementia but only in some of their incipient states. Conclusions In summary, these results support the notion that SVD and AD are driven by different pathophysiological mechanisms reflected in the CSF protein profile and that H-FABP in CSF is a general marker of neurodegeneration.
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Affiliation(s)
- Annika Ohrfelt
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Mölndal, Sweden
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Devanarayan V, Scholand MB, Hoidal J, Leppert MF, Crackower MA, O'Neill GP, Gervais FG. Identification of distinct plasma biomarker signatures in patients with rapid and slow declining forms of COPD. COPD 2010; 7:51-8. [PMID: 20214463 DOI: 10.3109/15412550903499530] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a prevalent pulmonary disease characterized by a progressive decline in lung function. The identification of biomarkers capable of predicting the rate of lung function decline or capable of giving an early read on drug efficacy in clinical trials would be very useful. The aim of this study was to identify plasma biomarkers capable of accurately distinguishing patients with COPD from healthy controls. Eighty-nine plasma markers in 40 COPD patients and 20 healthy smoker controls were analyzed. The COPD patients were divided into two subgroups, rapid and slow decliners based on their rate of lung function decline measured over 15 years. Univariate analysis revealed that 25 plasma markers were statistically different between rapid decliners and controls, 4 markers were different between slow decliners and controls, and 10 markers were different between rapid and slow decliners (p < 0.05). Multivariate analysis led to the identification of groups of plasma markers capable of distinguishing rapid decliners from controls (signature 1), slow decliners from controls (signature 2) and rapid from slow decliners (signature 3) with over 90% classification accuracy. Importantly, signature 1 was shown to be longitudinally stable using plasma samples taken a year later from a subset of patients. This study describes a novel set of plasma markers differentiating slow from rapid decline of lung function in COPD. If validated in distinct and larger cohorts, the signatures identified will have important implications in both disease diagnosis, as well as the clinical evaluation of new therapies.
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Llano DA, Laforet GA, Devanarayan V. P2‐195: Enhancement of the ADAS‐Cog using tree‐based multivariate analysis: Prediction of conversion from mild cognitive impairment to Alzheimer's disease using the ADNI dataset. Alzheimers Dement 2010. [DOI: 10.1016/j.jalz.2010.05.1243] [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: 10/19/2022]
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Tahir SK, Wass J, Joseph MK, Devanarayan V, Hessler P, Zhang H, Elmore SW, Kroeger PE, Tse C, Rosenberg SH, Anderson MG. Identification of expression signatures predictive of sensitivity to the Bcl-2 family member inhibitor ABT-263 in small cell lung carcinoma and leukemia/lymphoma cell lines. Mol Cancer Ther 2010; 9:545-57. [PMID: 20179162 DOI: 10.1158/1535-7163.mct-09-0651] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
ABT-263 inhibits the antiapoptotic proteins Bcl-2, Bcl-x(L), and Bcl-w and has single-agent efficacy in numerous small cell lung carcinoma (SCLC) and leukemia/lymphoma cell lines in vitro and in vivo. It is currently in clinical trials for treating patients with SCLC and various leukemia/lymphomas. Identification of predictive markers for response will benefit the clinical development of ABT-263. We identified the expression of Bcl-2 family genes that correlated best with sensitivity to ABT-263 in a panel of 36 SCLC and 31 leukemia/lymphoma cell lines. In cells sensitive to ABT-263, expression of Bcl-2 and Noxa is elevated, whereas expression of Mcl-1 is higher in resistant cells. We also examined global expression differences to identify gene signature sets that correlated with sensitivity to ABT-263 to generate optimal signature sets predictive of sensitivity to ABT-263. Independent cell lines were used to verify the predictive power of the gene sets and to refine the optimal gene signatures. When comparing normal lung tissue and SCLC primary tumors, the expression pattern of these genes in the tumor tissue is most similar to sensitive SCLC lines, whereas normal tissue is most similar to resistant SCLC lines. Most of the genes identified using global expression patterns are related to the apoptotic pathway; however, all but Bcl-rambo are distinct from the Bcl-2 family. This study leverages global expression data to identify key gene expression patterns for sensitivity to ABT-263 in SCLC and leukemia/lymphoma and may provide guidance in the selection of patients in future clinical trials.
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Affiliation(s)
- Stephen K Tahir
- Global Pharmaceutical Product Research Division, Abbott Laboratories, Abbott Park, Illinois 60064-6099, USA
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