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Staerk C, Klinkhammer H, Wistuba T, Maj C, Mayr A. Generalizability of polygenic prediction models: how is the R 2 defined on test data? BMC Med Genomics 2024; 17:132. [PMID: 38755654 PMCID: PMC11100126 DOI: 10.1186/s12920-024-01905-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Polygenic risk scores (PRS) quantify an individual's genetic predisposition for different traits and are expected to play an increasingly important role in personalized medicine. A crucial challenge in clinical practice is the generalizability and transferability of PRS models to populations with different ancestries. When assessing the generalizability of PRS models for continuous traits, the R 2 is a commonly used measure to evaluate prediction accuracy. While the R 2 is a well-defined goodness-of-fit measure for statistical linear models, there exist different definitions for its application on test data, which complicates interpretation and comparison of results. METHODS Based on large-scale genotype data from the UK Biobank, we compare three definitions of the R 2 on test data for evaluating the generalizability of PRS models to different populations. Polygenic models for several phenotypes, including height, BMI and lipoprotein A, are derived based on training data with European ancestry using state-of-the-art regression methods and are evaluated on various test populations with different ancestries. RESULTS Our analysis shows that the choice of the R 2 definition can lead to considerably different results on test data, making the comparison of R 2 values from the literature problematic. While the definition as the squared correlation between predicted and observed phenotypes solely addresses the discriminative performance and always yields values between 0 and 1, definitions of the R 2 based on the mean squared prediction error (MSPE) with reference to intercept-only models assess both discrimination and calibration. These MSPE-based definitions can yield negative values indicating miscalibrated predictions for out-of-target populations. We argue that the choice of the most appropriate definition depends on the aim of PRS analysis - whether it primarily serves for risk stratification or also for individual phenotype prediction. Moreover, both correlation-based and MSPE-based definitions of R 2 can provide valuable complementary information. CONCLUSIONS Awareness of the different definitions of the R 2 on test data is necessary to facilitate the reporting and interpretation of results on PRS generalizability. It is recommended to explicitly state which definition was used when reporting R 2 values on test data. Further research is warranted to develop and evaluate well-calibrated polygenic models for diverse populations.
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Affiliation(s)
- Christian Staerk
- Department of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany.
- Institute of Statistics, RWTH Aachen University, Aachen, Germany.
| | - Hannah Klinkhammer
- Department of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Tobias Wistuba
- Department of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Andreas Mayr
- Department of Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
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Sun L, Kienzler JC, Reynoso JG, Lee A, Shiuan E, Li S, Kim J, Ding L, Monteleone AJ, Owens GC, Phillips JJ, Everson RG, Nathanson D, Cloughesy TF, Li G, Liau LM, Hugo W, Kim W, Prins RM. Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors. J Clin Invest 2023; 133:e169314. [PMID: 37655659 PMCID: PMC10471177 DOI: 10.1172/jci169314] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
In comparison with responses in recurrent glioblastoma (rGBM), the intracranial response of brain metastases (BrM) to immune checkpoint blockade (ICB) is less well studied. Here, we present an integrated single-cell RNA-Seq (scRNA-Seq) study of 19 ICB-naive and 9 ICB-treated BrM samples from our own and published data sets. We compared them with our previously published scRNA-Seq data from rGBM and found that ICB led to more prominent T cell infiltration into BrM than rGBM. These BrM-infiltrating T cells exhibited a tumor-specific phenotype and displayed greater activated/exhausted features. We also used multiplex immunofluorescence and spatial transcriptomics to reveal that ICB reduced a distinct CD206+ macrophage population in the perivascular space, which may modulate T cell entry into BrM. Furthermore, we identified a subset of progenitor exhausted T cells that correlated with longer overall survival in BrM patients. Our study provides a comprehensive immune cellular landscape of ICB's effect on metastatic brain tumors and offers insights into potential strategies for improving ICB efficacy for brain tumor patients.
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Affiliation(s)
- Lu Sun
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
| | - Jenny C. Kienzler
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Inflammation Research Group, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Alexander Lee
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
| | | | | | | | - Lizhong Ding
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | | | | | - Joanna J. Phillips
- Helen Diller Family Comprehensive Cancer Center and
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Richard G. Everson
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - David Nathanson
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Timothy F. Cloughesy
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Neurology/Neuro-Oncology, UCLA, Los Angeles, California, USA
| | | | - Linda M. Liau
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Willy Hugo
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Won Kim
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Robert M. Prins
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
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Cloughesy TF, Mochizuki AY, Orpilla JR, Hugo W, Lee AH, Davidson TB, Wang AC, Ellingson BM, Rytlewski JA, Sanders CM, Kawaguchi ES, Du L, Li G, Yong WH, Gaffey SC, Cohen AL, Mellinghoff IK, Lee EQ, Reardon DA, O'Brien BJ, Butowski NA, Nghiemphu PL, Clarke JL, Arrillaga-Romany IC, Colman H, Kaley TJ, de Groot JF, Liau LM, Wen PY, Prins RM. Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma. Nat Med 2019; 25:477-486. [PMID: 30742122 PMCID: PMC6408961 DOI: 10.1038/s41591-018-0337-7] [Citation(s) in RCA: 871] [Impact Index Per Article: 174.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 12/18/2022]
Abstract
Glioblastoma is the most common primary malignant brain tumor in adults and is associated with poor survival. The Ivy Foundation Early Phase Clinical Trials Consortium conducted a randomized, multi-institution clinical trial to evaluate immune responses and survival following neoadjuvant and/or adjuvant therapy with pembrolizumab in 35 patients with recurrent, surgically resectable glioblastoma. Patients who were randomized to receive neoadjuvant pembrolizumab, with continued adjuvant therapy following surgery, had significantly extended overall survival compared to patients that were randomized to receive adjuvant, post-surgical programmed cell death protein 1 (PD-1) blockade alone. Neoadjuvant PD-1 blockade was associated with upregulation of T cell- and interferon-γ-related gene expression, but downregulation of cell-cycle-related gene expression within the tumor, which was not seen in patients that received adjuvant therapy alone. Focal induction of programmed death-ligand 1 in the tumor microenvironment, enhanced clonal expansion of T cells, decreased PD-1 expression on peripheral blood T cells and a decreasing monocytic population was observed more frequently in the neoadjuvant group than in patients treated only in the adjuvant setting. These findings suggest that the neoadjuvant administration of PD-1 blockade enhances both the local and systemic antitumor immune response and may represent a more efficacious approach to the treatment of this uniformly lethal brain tumor.
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Affiliation(s)
- Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Aaron Y Mochizuki
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joey R Orpilla
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Willy Hugo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander H Lee
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tom B Davidson
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Hematology/Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anthony C Wang
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Ellingson
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Radiological Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Eric S Kawaguchi
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lin Du
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gang Li
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - William H Yong
- Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sarah C Gaffey
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam L Cohen
- Department of Neurosurgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eudocia Q Lee
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Barbara J O'Brien
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | | | - Howard Colman
- Department of Neurosurgery, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Thomas J Kaley
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John F de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linda M Liau
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Robert M Prins
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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