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Ma J, Wu JY, Zhu L. Detection of orthologous exons and isoforms using EGIO. Bioinformatics 2022; 38:4474-4480. [PMID: 35946527 PMCID: PMC9525004 DOI: 10.1093/bioinformatics/btac548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/15/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Alternative splicing is an important mechanism to generate transcriptomic and phenotypic diversity. Existing methods have limited power to detect orthologous isoforms. RESULTS We develop a new method, EGIO, to detect orthologous exons and orthologous isoforms from two species. EGIO uses unique exonic regions to construct exon groups, in which process dynamic programming strategy is used to do exon alignment. EGIO could cover all the coding exons within orthologous genes. A comparison between EGIO and ExTraMapper shows that EGIO could detect more orthologous isoforms with conserved sequence and exon structures. We apply EGIO to compare human and chimpanzee protein-coding isoforms expressed in the frontal cortex and identify 6912 genes that express human unique isoforms. Unexpectedly, more human unique isoforms are detected than those conserved between humans and chimpanzees. AVAILABILITY AND IMPLEMENTATION Source code and test data of EGIO are available at https://github.com/wu-lab-egio/EGIO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinfa Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jane Y Wu
- To whom correspondence should be addressed. or
| | - Li Zhu
- To whom correspondence should be addressed. or
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2
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A bioinformatics framework for targeted gene expression assay design: Application to in vitro developmental neurotoxicity screening in a rat model. Regul Toxicol Pharmacol 2022; 133:105211. [PMID: 35724854 DOI: 10.1016/j.yrtph.2022.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022]
Abstract
Brain development involves a series of intricately choreographed neuronal differentiation and maturation steps that are acutely vulnerable to interferences from chemical exposures. Many genes involved in neurodevelopmental processes show evolutionarily conserved expression patterns in mammals and may constitute useful indicators/biomarkers for the evaluation of potential developmental neurotoxicity. Based on these premises, this study developed a bioinformatics framework to guide the design of a gene expression-based in vitro developmental neurotoxicity assay targeting evolutionary conserved genes associated with neuronal differentiation and maturation in rat cerebellar granule cells (CGCs). Rat, mouse and human genes involved in neurodevelopment and presenting one-to-one orthology were selected and orthologous exons within these genes were identified. PCR primer sets were designed within these orthologous exons and their specificity was evaluated in silico. The performance and specificity of rat, mouse and human PCR primer sets were then confirmed experimentally. Finally, RT-qPCR analyses in CGCs exposed in vitro to well-known neurotoxicants (Chlorpyrifos and Chlorpyrifos oxon) uncovered perturbations of expression levels for most of the selected genes. This bioinformatics framework for gene and target sequence selection may facilitate the identification of transcriptional biomarkers for developmental neurotoxicity assays and the comparison of gene expression data across experimental models from different mammalian species.
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Schäfer GG, Grebe LJ, Schinkel R, Lieb B. The Evolution of Hemocyanin Genes in Caenogastropoda: Gene Duplications and Intron Accumulation in Highly Diverse Gastropods. J Mol Evol 2021; 89:639-655. [PMID: 34757470 PMCID: PMC8599328 DOI: 10.1007/s00239-021-10036-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022]
Abstract
Hemocyanin is the oxygen transport protein of most molluscs and represents an important physiological factor that has to be well-adapted to their environments because of the strong influences of abiotic factors on its oxygen affinity. Multiple independent gene duplications and intron gains have been reported for hemocyanin genes of Tectipleura (Heterobranchia) and the caenogastropod species Pomacea canaliculata, which contrast with the uniform gene architectures of hemocyanins in Vetigastropoda. The goal of this study was to analyze hemocyanin gene evolution within the diverse group of Caenogastropoda in more detail. Our findings reveal multiple gene duplications and intron gains and imply that these represent general features of Apogastropoda hemocyanins. Whereas hemocyanin exon–intron structures are identical within different Tectipleura lineages, they differ strongly within Caenogastropoda among phylogenetic groups as well as between paralogous hemocyanin genes of the same species. Thus, intron accumulation took place more gradually within Caenogastropoda but finally led to a similar consequence, namely, a multitude of introns. Since both phenomena occurred independently within Heterobranchia and Caenogastropoda, the results support the hypothesis that introns may contribute to adaptive radiation by offering new opportunities for genetic variability (multiple paralogs that may evolve differently) and regulation (multiple introns). Our study indicates that adaptation of hemocyanin genes may be one of several factors that contributed to the evolution of the large diversity of Apogastropoda. While questions remain, this hypothesis is presented as a starting point for the further study of hemocyanin genes and possible correlations between hemocyanin diversity and adaptive radiation.
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Affiliation(s)
- Gabriela Giannina Schäfer
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Lukas Jörg Grebe
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Robin Schinkel
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany
| | - Bernhard Lieb
- Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany.
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Chakraborty A, Ay F, Davuluri RV. ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs. Bioinformatics 2021; 37:3412-3420. [PMID: 34014317 PMCID: PMC8545320 DOI: 10.1093/bioinformatics/btab393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 04/27/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Access to large-scale genomics and transcriptomics data from various tissues and cell lines allowed the discovery of wide-spread alternative splicing events and alternative promoter usage in mammalians. Between human and mouse, gene-level orthology is currently present for nearly 16k protein-coding genes spanning a diverse repertoire of over 200k total transcript isoforms. RESULTS Here, we describe a novel method, ExTraMapper, which leverages sequence conservation between exons of a pair of organisms and identifies a fine-scale orthology mapping at the exon and then transcript level. ExTraMapper identifies more than 350k exon mappings, as well as 30k transcript mappings between human and mouse using only sequence and gene annotation information. We demonstrate that ExTraMapper identifies a larger number of exon and transcript mappings compared to previous methods. Further, it identifies exon fusions, splits, and losses due to splice site mutations, and finds mappings between microexons that are previously missed. By reanalysis of RNA-seq data from 13 matched human and mouse tissues, we show that ExTraMapper improves the correlation of transcript-specific expression levels suggesting a more accurate mapping of human and mouse transcripts. We also applied the method to detect conserved exon and transcript pairs between human and rhesus macaque genomes to highlight the point that ExTraMapper is applicable to any pair of organisms that have orthologous gene pairs. AVAILABILITY The source code and the results are available at https://github.com/ay-lab/ExTraMapper and http://ay-lab-tools.lji.org/extramapper. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA, 92037, USA.,Department of Pediatrics, UC San Diego - School of Medicine, La Jolla, 92093, CA, USA
| | - Ramana V Davuluri
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, 11794, USA
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Characterization of the rat Acetylcholinesterase readthrough (AChE-R) splice variant: Implications for toxicological studies. Biochem Biophys Res Commun 2020; 532:528-534. [PMID: 32896378 DOI: 10.1016/j.bbrc.2020.08.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/23/2022]
Abstract
Exposure to chemicals and other environmental stressors can differentially impact the expression of Acetylcholinesterase (AChE) splice variants. Surprisingly, despite the widespread use of the rat model in toxicological studies and the wealth of literature on this important biomarker of neurotoxicity, AChE coding exons and splice variants are not yet fully annotated in this species. To address this knowledge gap, a short problematic region of the rat AChE genomic DNA present in GenBank was first re-sequenced. This revised genomic sequence was then aligned to rat AChE RefSeq mRNA and compared to orthologous mammalian sequences, in order to map the coding exon and intron boundaries of the rat AChE gene. Based on these bioinformatics analyses, a sequence was predicted for the yet-unannotated rat Acetylcholinesterase readthrough (AChE-R) splice variant. PCR primers designed to specifically amplify rat AChE-R were used to confirm its expression in rat PC12 cells. Compared to the canonical AChE-S splice variant, AChE-R was expressed at much lower levels but presented distinct regulation patterns in PC12 cells and rat primary cerebral granule cells (CGCs) following exposure to Chlorpyrifos (a well-known neurotoxic organophosphate pesticide). Taken together, these observations point to the evolutionary conservation of the AChE-R splicing event between rodents and human and to the distinct regulation of AChE splice variants in response to toxicological challenges.
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A bioinformatics workflow for the evaluation of RT-qPCR primer specificity: Application for the assessment of gene expression data reliability in toxicological studies. Regul Toxicol Pharmacol 2020; 111:104575. [PMID: 31945455 DOI: 10.1016/j.yrtph.2020.104575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
The reliability of Reverse Transcription quantitative real-time PCR (RT-qPCR) gene expression data depends on proper primer design and RNA quality controls. Despite freely available genomic databases and bioinformatics tools, primer design deficiencies can be found across life science publications. In order to assess the prevalence of such deficiencies in the toxicological literature, 504 primer sets extracted from a random selection of 70 recent rat toxicological studies were evaluated. The specificity of each primer set was systematically analysed using a bioinformatics workflow developed from publicly available resources (NCBI Primer BLAST, in silico PCR in UCSC genome browser, Ensembl DNA database). Potential mismatches (9%), cross-matches (13.5%), co-amplification of multiple gene splice variants (9%) and sub-optimal amplicon sizes (25%) were identified for a significant proportion of the primer sets assessed in silico. Quality controls for gDNA contamination of RNA samples were infrequently reported in the surveyed manuscripts. Hence, the impacts of gDNA contamination on RT-qPCR data were further investigated, revealing that lowly expressed genes presented higher susceptibility to contaminating gDNA. In addition to the retrospective identification of potential primer design issues presented in this study, the described bioinformatics workflow can also be used prospectively to select candidate primer sets for experimental validation.
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Gao J, Huang BH, Wan YT, Chang J, Li JQ, Liao PC. Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes. Sci Rep 2017; 7:14830. [PMID: 29093470 PMCID: PMC5666015 DOI: 10.1038/s41598-017-13645-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/29/2017] [Indexed: 12/29/2022] Open
Abstract
The protein encoded by the TERMINAL FLOWER1 (TFL1) gene maintains indeterminacy in inflorescence meristem to repress flowering, and has undergone multiple duplications. However, basal angiosperms have one copy of a TFL1-like gene, which clusters with eudicot TFL1/CEN paralogs. Functional conservation has been reported in the paralogs CENTRORADIALIS (CEN) in eudicots, and ROOTS CURL IN NPA (RCNs) genes in monocots. In this study, long-term functional conservation and selective constraints were found between angiosperms, while the relaxation of selective constraints led to subfunctionalisation between paralogs. Long intron lengths of magnoliid TFL1-like gene contain more conserved motifs that potentially regulate TFL1/CEN/RCNs expression. These might be relevant to the functional flexibility of the non-duplicate TFL1-like gene in the basal angiosperms in comparison with the short, lower frequency intron lengths in eudicot and monocot TFL1/CEN/RCNs paralogs. The functionally conserved duplicates of eudicots and monocots evolved according to the duplication-degeneration-complementation model, avoiding redundancy by relaxation of selective constraints on exon 1 and exon 4. These data suggest that strong purifying selection has maintained the relevant functions of TFL1/CEN/RCNs paralogs on flowering regulation throughout the evolution of angiosperms, and the shorter introns with radical amino acid changes are important for the retention of paralogous duplicates.
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Affiliation(s)
- Jian Gao
- College of Forestry, Beijing Forestry University, No.35, Tsinghua East Rd., Haidian Dist., Beijing, 100083, People's Republic of China
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China
| | - Yu-Ting Wan
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China
| | - JenYu Chang
- Department of Horticulture, Chiayi Agricultural Experiment Branch, Taiwan Agricultural Research Institute No. 1, Nung-Kai-Chang, Lutsao township, Chiayi, 611, Taiwan, Republic of China
| | - Jun-Qing Li
- College of Forestry, Beijing Forestry University, No.35, Tsinghua East Rd., Haidian Dist., Beijing, 100083, People's Republic of China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, No.88, Sec. 4, Tingjhou Rd., Wunshan Dist., Taipei, 116, Taiwan, Republic of China.
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Padhi BK, Rosales M, Pelletier G. Perinatal methylmercury exposure perturbs the expression of Plp1 and Cnp splice variants in cerebellum of rat pups. Neurotoxicology 2015; 48:223-30. [PMID: 25936639 DOI: 10.1016/j.neuro.2015.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/18/2015] [Accepted: 04/22/2015] [Indexed: 01/01/2023]
Abstract
Early life exposure to environmental chemicals can interfere with myelin formation in the developing brain, leading to neurological disorders. The Proteolipid Protein 1 (Plp1), Myelin Basic Protein (Mbp) and 2',3'-Cyclic Nucleotide 3'Phosphodiesterase (Cnp) genes expressed in oligodendrocytes and involved in myelination processes can be useful biomarkers of potential developmental neurotoxicity. In an earlier study, we concluded that the reduction in the expression levels of Mbp splice variants in juvenile rat cerebellum following perinatal methylmercury (MeHg) exposure were compatible with an overall reduction of mature oligodendrocytes population. This observation prompted us to analyze the expression of Plp1 and Cnp in developing rat cerebellum to further confirm and investigate the toxic effects of MeHg on vulnerable oligodendrocytes. Splice variants of Plp1 in human and of Cnp in mouse are curated in NCBI RefSeq database, but not for rat. Lack of annotation of splice variants can pose significant challenge for the reliable quantification of gene expression levels in toxicological studies. Therefore, we applied a "comparative sequence analysis" approach, relying on annotated splice variants in human/mouse and on evolutionary conservation of intron-exon structures, to identify additional splice variants of Plp1 and Cnp in rat. Then, we confirmed their identity by nucleotide sequencing and characterized their temporal expression patterns during brain development by RT-PCR. The measurement of total transcripts and individual splice variants of Plp1 and Cnp in the cerebellum of MeHg-exposed rat pups revealed a relatively similar level of reduction in their expression levels. This study further confirms that perinatal exposure to MeHg can impact oligodendrocytes in pups. Based on these observations, we conclude that monitoring the expression of these oligodendrocyte-enriched genes can be useful to identify toxic chemicals affecting myelination.
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Affiliation(s)
- Bhaja K Padhi
- Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario K1A 0L2, Canada.
| | - Marianela Rosales
- Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario K1A 0L2, Canada
| | - Guillaume Pelletier
- Hazard Identification Division, HECSB, Health Canada, Tunney's Pasture, Ottawa, Ontario K1A 0L2, Canada
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Padhi BK, Zigler JS, Padhi P, Hose S, Sinha D. Expression pattern of an evolutionarily conserved splice variant in the ratTacc2gene. Genesis 2014; 52:378-86. [DOI: 10.1002/dvg.22776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/06/2014] [Accepted: 03/31/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Bhaja K. Padhi
- Ophthalmology; Wilmer Eye Institute, The Johns Hopkins University School of Medicine; Baltimore Maryland
- Hazard Identification Division, Environmental Health Science and Research Bureau; Health Canada; Ottawa Ontario Canada
| | - J. Samuel Zigler
- Ophthalmology; Wilmer Eye Institute, The Johns Hopkins University School of Medicine; Baltimore Maryland
| | - Piyush Padhi
- Ophthalmology; Wilmer Eye Institute, The Johns Hopkins University School of Medicine; Baltimore Maryland
| | - Stacey Hose
- Ophthalmology; Wilmer Eye Institute, The Johns Hopkins University School of Medicine; Baltimore Maryland
| | - Debasish Sinha
- Ophthalmology; Wilmer Eye Institute, The Johns Hopkins University School of Medicine; Baltimore Maryland
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Bradford JR, Farren M, Powell SJ, Runswick S, Weston SL, Brown H, Delpuech O, Wappett M, Smith NR, Carr TH, Dry JR, Gibson NJ, Barry ST. RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib. PLoS One 2013; 8:e66003. [PMID: 23840389 PMCID: PMC3686868 DOI: 10.1371/journal.pone.0066003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/30/2013] [Indexed: 12/30/2022] Open
Abstract
Pre-clinical models of tumour biology often rely on propagating human tumour cells in a mouse. In order to gain insight into the alignment of these models to human disease segments or investigate the effects of different therapeutics, approaches such as PCR or array based expression profiling are often employed despite suffering from biased transcript coverage, and a requirement for specialist experimental protocols to separate tumour and host signals. Here, we describe a computational strategy to profile transcript expression in both the tumour and host compartments of pre-clinical xenograft models from the same RNA sample using RNA-Seq. Key to this strategy is a species-specific mapping approach that removes the need for manipulation of the RNA population, customised sequencing protocols, or prior knowledge of the species component ratio. The method demonstrates comparable performance to species-specific RT-qPCR and a standard microarray platform, and allowed us to quantify gene expression changes in both the tumour and host tissue following treatment with cediranib, a potent vascular endothelial growth factor receptor tyrosine kinase inhibitor, including the reduction of multiple murine transcripts associated with endothelium or vessels, and an increase in genes associated with the inflammatory response in response to cediranib. In the human compartment, we observed a robust induction of hypoxia genes and a reduction in cell cycle associated transcripts. In conclusion, the study establishes that RNA-Seq can be applied to pre-clinical models to gain deeper understanding of model characteristics and compound mechanism of action, and to identify both tumour and host biomarkers.
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Affiliation(s)
- James R. Bradford
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
- * E-mail:
| | - Matthew Farren
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Steve J. Powell
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Sarah Runswick
- Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Susie L. Weston
- Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Helen Brown
- Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Oona Delpuech
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Mark Wappett
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Neil R. Smith
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - T. Hedley Carr
- Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Jonathan R. Dry
- Oncology, AstraZeneca Pharmaceuticals, Gatehouse Park, Massachusetts, United States of America
| | - Neil J. Gibson
- Personalised Healthcare and Biomarkers, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
| | - Simon T. Barry
- Oncology, AstraZeneca Pharmaceuticals, Alderley Park, Cheshire, United Kingdom
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