tbuckley/cabot-search huggingface dataset:
MNGI-14. PROGNOSTIC FEATURES OF MALIGNANT MENINGIOMA: EVALUATION OF AGGRESSIVE MENINGIOMAS WITHIN A LARGE RURAL HOSPITAL SYSTEM DATABASE AND FIRST REPORT OF A METASTATIC CHORDOID MENINGIOMA TO THE LUNG
Authors: Na Tosha Gatson, Jesse Manikowski, Shane Bross, Bradley Hinger, Tian Mauer, Tiffany Garcia, Michel Lacroix, Anand Mahadevan, Gino Mongelluzzo, Joseph Vadakara, Syed A Jaffar Kazmi
Journal: Neuro-Oncology (2019)

Abstract Meningiomas comprise 37% of primary brain tumors, arise extra-axially from the arachnoid cap cells, and are typically identified by classic imaging and histopathologic features. Blacks, females, and people age 65+ have higher incidence rate - partially correlated with hormonal states, high body mass index, and known genetic predispositions. Prognostication is otherwise based on histopathologic findings and 90% of meningiomas are classified as benign (WHO grade I). Despite use of these prognostic tools, clinicians often observe a more divergent post-operative clinical course. While several pre-clinical studies have identified putative oncogenic influencers, many have failed to show correlation in human trials. Here, we evaluate a single institutional meningioma database stratified by geodemographic and clinical data to identify novel integrated prognostic indicators for aggressive tumor natural history. Our database contains 3,528 image-confirmed meningiomas between 1992–2019. This report focused on 415 pathology-confirmed cases between 2006–2019: WHO grades I, II, III were 73% (n=303), 25% (n=103), and 2% (n=9) respectively, 71% female predominance (n=294), median age at diagnosis 57-years-old, and 97.5% were white race. Thus far, full exome sequencing has been completed on &gt;50% of cases and &gt;80% have available tumor tissue for future testing as part of this rural Pennsylvania database with high incident aggressive and/or multiply recurrent meningiomas. We selected four representative cases to compare post-operative prognostication to observed clinical outcomes and provide molecular/genetic, histopathologic, treatment modality, comorbid, and other clinical features associated with morbidity/mortality. Included in this patient review is the first reported case of a rare (&lt; 1%) chordoid meningioma, multiply recurrent despite 8-years of aggressive treatment modalities, including surgery, radiation, chemotherapy and androgen-blockade, with eventual extracranial metastasis to the lung, a meningiocarcinoma, if you will. Thorough interrogation of the completed database could yield novel predictive indicators of clinically aggressive meningiomas and guide clinical decision-making for optimized surveillance in high-risk patients.
After PCI and 3 mo of DAPT, P2Y12-inhibitor monotherapy was noninferior to DAPT at 12 mo
Authors: Alexander Gallus
Journal: Annals of Internal Medicine (2019)

Source Citation Hahn JY, Song YB, Oh JH, et al; SMART-CHOICE Investigators. Effect of P2Y12 inhibitor monotherapy vs dual antiplatelet therapy on cardiovascular events in patients undergoing percutaneous coronary intervention: the SMART-CHOICE randomized clinical trial. JAMA. 2019;321:2428-37. 31237645
Corticostriatal Flow of Action Selection Bias
Authors: Eun Jung Hwang, Trevor D. Link, Yvonne Yuling Hu, Shan Lu, Eric Hou-Jen Wang, Varoth Lilascharoen, Sage Aronson, Keelin O’Neil, Byung Kook Lim, Takaki Komiyama
Journal: Neuron (2019)
Analysis of CNV in the Genomes of the Marrow Cells of the Patients with AML Revealed That High Numbers of Aberrations Associate with Better Survival and Deletions with the Aberrant Expression of CD19 in the Leukemic Blasts
Authors: Emilia Jaskula, Janusz Lange, Monika Mordak-Domagala, Mariola Sedzimirska, Marta Lemieszewska, Agnieszka Tarnowska, Helena Pakos, Anna Sobczynska-Konefal, Andrzej Lange
Journal: Blood (2019)
Jaundice in Severe Infections
Authors: A. G. Beckett, J. D. Ward
Journal: BMJ (1965)

can the patient be given a sense of continuity. in the process of treatment.By such means it is also possible to avoid the sudden last-minute urgent admission of a dying patient to a totally strange hospital for the final few hours of a prolonged illness; this is not terminal care but terminal mis- management.If patients are to be trans- ferred for terminal care in geriatric units it is desirable that the prognosis should be assessed in weeks or months rather than days.On the other hand, it must also be acknow- ledged that unexpected remissions can occur when it may be desirable for the patient to return home for a time.There are, among 114 women in this hospital to-day, two cases of carcinoma of breast admitted for " terminal care" 21 months and 32 months ago.If, as Dr. Morton states, the teaching hos- pitals fail to set a good example to their students in managing terminal cases of cancer, this particularly thoughtless form of man's mutual inhumanity will bee perpetuated.-I am, etc.
Preliminary Results from CPX-351 Italian Compassionate Use Program Show High Response Rate and Good Tolerability in Poor Prognosis AML Patients
Authors: Fabio Guolo, Paola Minetto, Luana Fianchi, Michela Rondoni, Giulia Daghia, Stefano D'Ardia, Monica Morselli, Crescenza Pasciolla, Francesca Pavesi, Barbara MD Scappini, Francesco Lanza, Marco Gobbi, Livio Pagano, Felicetto Ferrara, Roberto Massimo Lemoli
Journal: Blood (2019)
NIMG-26. EVALUATING THE DAYS GAINED RESPONSE METRIC IN CLINICAL TRIALS USING BEVACIZUMAB PLUS ADDITIONAL AGENTS FOR RECURRENT GLIOBLASTOMA
Authors: Kyle Singleton, Sandra Johnston, Cassandra Rickertsen, S Keith Anderson, Gustavo De Leon, Scott Whitmire, Kamala Clark-Swanson, Bernard Bendok, Maciej Mrugala, Alyx Porter, Evanthia Galanis, Kristin Swanson
Journal: Neuro-Oncology (2019)

Abstract Determining effective therapies for patients with recurrent glioblastoma remains difficult especially in small early phase clinical trials. Currently utilized estimators of treatment response rely on two-dimensional measurements of tumor progression (e.g. RANO, RECIST, MacDonald) that have often fallen short in reliably connecting patients who respond with positive survival outcomes. This has prompted consideration of advanced imaging and volumetric measurements by the RANO working group and others. Our proposed approach, Days Gained (DG), uses volumetric measurements to calculate a personalized response metric based on change in tumor growth characteristics pre/post-treatment. DG has shown promise for connecting imageable treatment response with clinically meaningful (statistically significant) survival benefit when applied in upfront and recurrent therapy settings, even in the context of coincident bevacizumab treatment. In this study, we seek to consider a new cohort of patients receiving bevacizumab in combination with other novel therapies to distinguish any subpopulation of patients with meaningful response. In this work, we identified a subset of 16 patients from bevacizumab clinical trials with data available for DG analysis requiring serial imaging (T1Gd and FLAIR) prior to and after the first cycle of therapy. Each trial evaluated bevacizumab alone versus bevacizumab plus either dasatinib or TRC105 in recurrent disease. Discrimination of time to progression (TTP) was evaluated at DG thresholds identified from our prior analysis of patients treated with bevacizumab. Using previously identified DG thresholds for clinically significant treatment benefit, in our cohort, DG measured by serial FLAIR imaging was significant in predicting longer TTP (120 DG, p=0.014), but T1Gd DG scores did not attain significance (p=0.630). Given the limited insights in connecting response metrics to accurately predicted outcomes, these data further support the use of DG as a burgeoning marker of treatment response (or lack of response) that may be useful for more routine integration into clinical trials.
IMMU-08. THE ANTIGENIC LANDSCAPE OF GLIOBLASTOMA - REFINING THE TARGETS FOR IMMUNOTHERAPY
Authors: Konstantina Kapolou, Lena Katharina Freudenmann, Ekaterina Friebel, Leon Bichmann, Burkhard Becher, Stefan Stevanović, Hans-Georg Rammensee, Michael Weller, Marian Christoph Neidert
Journal: Neuro-Oncology (2019)

Abstract We provide a comprehensive analysis of the antigenic landscape of glioblastoma using a multi-omics approach including ligandome mapping of the Human Leukocyte Antigen (HLA) ligandome, next generation sequencing (NGS) as well as an in-depth characterization of tumor-infiltrating lymphocytes (TIL) using mass cytometry and ultra-deep sequencing of the T-cell receptor (TCR). Tumor-exclusive HLA class I and class II ligands (immune precipitation and LC-MS/MS) of 24 isocitrate dehydrogenase 1 wild type glioblastoma samples and 10 autologous primary glioblastoma cell lines were defined in comparison to an HLA ligandome normal tissue reference database (n &gt; 418). We found 11,496 glioblastoma exclusive HLA class I ligands (2,064 shared with cell lines; 3,754 on ≥ 2 glioblastoma samples). On the source protein level, 239 glioblastoma exclusive proteins were identified; among them 54 were also found in cell lines. For HLA class II ligands the analysis revealed 11,870 glioblastoma exclusive peptides (444 shared with cell lines; 3,420 on ≥ 2 glioblastoma samples) and 278 glioblastoma exclusive proteins; among which 18 were present also in cell lines. Moreover, whole-exome sequencing and whole RNA sequencing of 13 tumor samples was performed with the aim to predict neoantigens. On average 5,662 somatic missense effects were identified per patient (min: 4,258; max: 7,479). Candidate peptides are grouped into (i) in silico predicted neoepitopes, (ii) tumor-exclusivity on HLA, (iii) gene expression (e.g. cancer testis antigens). Top-ranking candidates from each group will be tested with regards to their immunogenicity in an autologous setting (TIL, peripheral blood mononuclear cells, patient derived tumor cells). Finally, the peptide and immunogenicity data is correlated with the immune phenotype of the TIL compartment as well as the TCR repertoire of the sample.
TMOD-09. MODELING TERT PROMOTER MUTATION IN ISOGENIC NEXT GENERATION GBM MODELS
Authors: Shunichiro Miki, Tomoyuki Koga, Alison Parisian, Frank Furnari
Journal: Neuro-Oncology (2019)

Abstract Telomere reverse transcriptase (TERT) promotor mutations increase TERT expression and are known to be the most common single genetic abnormality in Glioblastoma (GBM). Recent studies have revealed this mutation to be an early event in gliomagenesis but it is detected subclonally in a considerable number of cases. Due to the long telomere length and TERT expression in somatic cells of mice, genetically engineered mouse models of GBM do not address the function of this mutation and thus an ideal heterozygous TERT promotor mutation model is yet to be established. Recently, our lab established strategies for generating GBM models using neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (hiPSCs) that have been CRISPR/Cas9 engineered with different combinations of authentic GBM-related genetic drivers which can be used for introduction of mutant TERT promotor (MTP) sequence and examination of its function. We obtained multiple heterozygous MTP hiPS clones in the context of GBM genetic alterations, CDKN2A/B and PTEN deletion, using a two-step targeting approach. Two single-strand guide RNAs (sgRNAs) were used to delete the TERT promotor and a portion of exon 1 followed by repair of the locus with wild type TERT promoter (WTP) and MTP sequence. Following promoter reconstitution, TERT promotor function was tested in iPSCs, NPCs, and astrocytes. This analysis revealed successful TERT expression silencing in WTP astrocytes. Furthermore, orthotopic injection of WTP and MTP NPCs into immunodeficient mice formed pathologically similar GBM-like tumors in same period of time. TERT expression was only detected in cell lines derived from MTP tumors, indicating TERT promotor mutation has little impact in initiation of tumor formation from NPCs, explaining its subclonality in patient tumors. Our model enables further research on MTP function and dependency during gliomagenesis.
Timing of radiotherapy (RT) after radical prostatectomy (RP): First results from the RADICALS RT randomised controlled trial (RCT) [NCT00541047]
Authors: C. Parker, N.W. Clarke, A. Cook, H.G. Kynaston, P. Meidahl Petersen, W. Cross, R. Persad, C. Catton, J. Logue, H. Payne, F. Saad, K. Brasso, H. Lindberg, A. Zarkar, R. Raman, M.A. Roder, C. Heath, W.R. Parulekar, M.K.B. Parmar, M.R. Sydes
Journal: Annals of Oncology (2019)
Toxicity of a Modified Peg-Asparaginase-Based SMILE Regimen Is Comparable to L-Asparaginase-Based SMILE in a Non-Asian Population
Authors: Ryan J Caddell, Hayder Saeed, Rebecca Nelson, Leidy Isenalumhe, Julio Chavez, Celeste Bello, Javier Pinilla Ibarz, Lubomir Sokol, Bijal Shah
Journal: Blood (2019)
P2.26 Budget Impact Analysis of Immunotherapy as Second-line Treatment of NSCLC at MX's National Institute of Cancer
Authors: L.A. Ramírez Tirado, F. Barrón, L. Zatarain Barron, M.P. Peralta Álvarez, A.A. Meneses-García, L.M. Ruíz-Godoy, J. De La Garza Salazar, D.I. Palafox Torres, M.F. Chávez Millan, J.Á. Paladio Hernández, A.F. Cardona, O. Arrieta
Journal: Journal of Thoracic Oncology (2019)
Phase 1 First-in-Human Study of AUTO2, the First Chimeric Antigen Receptor (CAR) T Cell Targeting APRIL for Patients with Relapsed/Refractory Multiple Myeloma (RRMM)
Authors: Rakesh Popat, Sonja Zweegman, Jim Cavet, Kwee Yong, Lydia Lee, Jim Faulkner, Ekaterini Kotsopoulou, Muhammad Al-Hajj, Simon Thomas, Shaun P Cordoba, Martin Pule, Virginie Cerec, Vijay G R Peddareddigari, Nushmia Z Khokhar, Tobias F Menne
Journal: Blood (2019)
Combined Targeting of the Menin-MLL1 Chromatin Complex and FLT3 As a Novel Therapeutic Concept Against NPM1 Mutant or MLL-Rearranged AML with Mutated FLT3
Authors: Margarita M. Dzama, Martha C. Taubert, Kerstin Kunz, Johanna Rausch, Chun-Wei David Chen, Annalisa Mupo, Patricia Hähnel, Matthias Theobald, Thomas Kindler, Richard P. Koche, George S. Vassiliou, Scott A. Armstrong, Michael W.M. Kühn
Journal: Blood (2019)
Results of a Phase II Open-Label Trial of Bortezomib in Patients with Multiple Myeloma Who Have Undergone High-Dose Melphalan Therapy Followed by Autologous Peripheral Blood Stem Cell Transplantation and Failed to Achieve a Complete Response
Authors: Robert M. Rifkin, Gary Spitzer, Andrew Greenspan, John F. Schwerkoske, Romeo A. Mandanas, Joe Stephenson, George T. Kannarkat, Feng Zhan, Lina Asmar, Roy Beveridge
Journal: Blood (2008)
Differential <scp>DNA</scp> Methylation of Networked Signaling, Transcriptional, Innate and Adaptive Immunity, and Osteoclastogenesis Genes and Pathways in Gout
Authors: Zengmiao Wang, Ying Zhao, Amanda Phipps‐Green, Ru Liu‐Bryan, Arnoldas Ceponis, David L. Boyle, Jun Wang, Tony R. Merriman, Wei Wang, Robert Terkeltaub
Journal: Arthritis & Rheumatology (2019)

In gout, autoinflammatory responses to urate crystals promote acute arthritis flares, but the pathogeneses of tophi, chronic synovitis, and erosion are less well understood. Defining the pathways of epigenomic immunity training can reveal novel pathogenetic factors and biomarkers. The present study was undertaken to seminally probe differential DNA methylation patterns utilizing epigenome-wide analyses in patients with gout.
Splenic CD24low Red Pulp Macrophages Provide an Alternate Niche for Chronic Myeloid Leukemia Stem Cells
Authors: Michael A Amrein, Elias D Bührer, Stefan Forster, Stephan Isringhausen, Christian M Schürch, Salil S. Bhate, Mohamad Al Sayed, Cesar Nombela Arrieta, Ramin Radpour, Carsten Riether, Adrian F Ochsenbein
Journal: Blood (2019)
HLA-B27–mediated activation of TNAP phosphatase promotes pathogenic syndesmophyte formation in ankylosing spondylitis
Authors: Chin-Hsiu Liu, Sengupta Raj, Chun-Hsiung Chen, Kuo-Hsuan Hung, Chung-Tei Chou, Ing-Ho Chen, Jui-Teng Chien, I-Ying Lin, Shii-Yi Yang, Takashi Angata, Wen-Chan Tsai, James Cheng-Chung Wei, I-Shiang Tzeng, Shih-Chieh Hung, Kuo-I Lin
Journal: Journal of Clinical Investigation (2019)

Ankylosing spondylitis (AS) is a type of axial inflammation. Over time, some patients develop spinal ankylosis and permanent disability; however, current treatment strategies cannot arrest syndesmophyte formation completely. Here, we used mesenchymal stem cells (MSCs) from AS patients (AS MSCs) within the enthesis involved in spinal ankylosis to delineate that the HLA-B27–mediated spliced X-box–binding protein 1 (sXBP1)/retinoic acid receptor-β (RARB)/tissue-nonspecific alkaline phosphatase (TNAP) axis accelerated the mineralization of AS MSCs, which was independent of Runt-related transcription factor 2 (Runx2). An animal model mimicking AS pathological bony appositions was established by implantation of AS MSCs into the lumbar spine of NOD-SCID mice. We found that TNAP inhibitors, including levamisole and pamidronate, inhibited AS MSC mineralization in vitro and blocked bony appositions in vivo. Furthermore, we demonstrated that the serum bone-specific TNAP (BAP) level was a potential prognostic biomarker to predict AS patients with a high risk for radiographic progression. Our study highlights the importance of the HLA-B27–mediated activation of the sXBP1/RARB/TNAP axis in AS syndesmophyte pathogenesis and provides a new strategy for the diagnosis and prevention of radiographic progression of AS.
Repertoire of Cytomegalovirus-Specific T Cells Is Focused on the Immunodominant Epitopes in Fixed Hierarchy Dependent on HLA Genotype of the Donor
Authors: Alexandra Vladimirovna Maleeva, Vyacheslav Anatolevich Shmarov, Dmitry Olegovych Kiryukhin, Grigory Aleksandrovich Efimov, Valery G. Savchenko
Journal: Blood (2019)
STEM-05. NEURAL G0: A NOVEL QUIESCENT-LIKE STATE IN PROLIFERATING HUMAN NEURAL STEM AND GLIOBLASTOMA TUMOR CELLS
Authors: Heather Feldman, Sonali Arora, Pia Hoellerbauer, Steven Pollard, Anoop Patel, Christopher Plaisier, Patrick Paddison
Journal: Neuro-Oncology (2019)

Abstract Single cell (sc) genomic technologies are rapidly transforming our understanding of cellular states in normal and diseased tissues. Here, we applied scRNA-seq to cultures of proliferating human neural stem cells (NSCs) to better understand the relationship between cell cycle dynamics and developmental gene expression. This analysis revealed both conventional cell cycle states (S, G2, M) and novel G1 and G0-like states. Of note, we identified a Neural G0 phase representing a subpopulation enriched for expression of genes associated with adult quiescent NSCs, including CLU, HOPX, ID3, OLIG2, PTN, SYT11, S100B, SOX9, PTPRZ1, and TTYH1. Remarkably, by applying our hNSC cell cycle phase classifier to human glioblastoma (GBM) tumors, we found that Neural G0 subpopulations as a prominent tumor-specific cellular subclass of GBM tumors, which, similar to NSCs, does not overlap with proliferative cell cycle phases. We further identified modulators of Neural G0 via CRISPR-Cas9 screens, revealing highly significant enrichment for tumor suppressor genes associated with brain tumors. In depth analysis of five of these Neural G0 modulatory genes, including CREBBP, NF2, PTPN14, TAOK1, or TP53, revealed that they promote compartmentalization of G0/G1 phase and expression of genes associated with Neural G0. Our results suggest that Neural G0 is a dynamic cell state in mammalian NSCs, that a subset of GBM cells maintain and is modulated by genes commonly found altered in GBM.
Loss-of-function mutations in MRAP2 are pathogenic in hyperphagic obesity with hyperglycemia and hypertension
Authors: Morgane Baron, Julie Maillet, Marlène Huyvaert, Aurélie Dechaume, Raphaël Boutry, Hélène Loiselle, Emmanuelle Durand, Bénédicte Toussaint, Emmanuel Vaillant, Julien Philippe, Jérémy Thomas, Amjad Ghulam, Sylvia Franc, Guillaume Charpentier, Jean-Michel Borys, Claire Lévy-Marchal, Maïthé Tauber, Raphaël Scharfmann, Jacques Weill, Cécile Aubert, Julie Kerr-Conte, François Pattou, Ronan Roussel, Beverley Balkau, Michel Marre, Mathilde Boissel, Mehdi Derhourhi, Stefan Gaget, Mickaël Canouil, Philippe Froguel, Amélie Bonnefond
Journal: Nature Medicine (2019)
Clinical Outcomes of Cancer-Associated Thrombosis Beyond 6 Months of Anticoagulation
Authors: Shyam K Poudel, Chandana A Reddy, Deborah Y Park, Mailey L Wilks, Vicki Pinkava, Meghan O'Brien, Barbara Tripp, Jung-Min Song, Keith R McCrae, Alok A Khorana, Dana E Angelini
Journal: Blood (2019)
Targeting PRMT5 to Circumvent Acquired Ibrutinib Resistance in Mantle Cell Lymphoma
Authors: Shelby Sloan, Fiona Brown, JI Hyun Chung, Alexander Prouty, Esther Wheeler, Bonnie K Harrington, Eric Brooks, Ayse S Yilmaz, Hatice G Ozer, John C. Byrd, Selina Chen-Kiang, Maurizio Di Liberto, Rosa Lapalombella, Kris Vaddi, Peggy Scherle, Youssef Youssef, Robert A Baiocchi, Lapo Alinari
Journal: Blood (2019)
Early Hyperbilirubinemia Is an Independent Predictor of Outcome after Allogeneic Stem Cell Transplantation and Correlates with Markers of Endothelial Cell Dysfunction
Authors: Thomas Luft, Hao Dai, Aleksandar Radujkovic, David Schult, Joshua Majer-Lauterbach, Olga Blau, Lars Bullinger, Sihe Jiang, Carsten Müller-Tidow, Peter Dreger, Olaf Penack
Journal: Blood (2019)
Dual T-Cell Depletion with a Very Low Dose of ATG and Ptcy Provides an Effective Control of Acute Gvhd in PBSC RIC Allo-HSCT
Authors: Maria Queralt Salas, Arjun Law, Wilson Lam, David Loach, Zeyad Al-Shaibani, Fotios V. Michelis, Dennis Dong Hwan Kim, Jeffrey H. Lipton, Rajat Kumar, Jonas Mattsson, Auro Viswabandya
Journal: Blood (2019)
Subgroup Analyses from L-Mind, a Phase II Study of Tafasitamab (MOR208) Combined with Lenalidomide in Patients with Relapsed or Refractory Diffuse Large B-Cell Lymphoma
Authors: Johannes Duell, Kami J. Maddocks, Eva González-Barca, Wojciech Jurczak, Anna Marina Liberati, Sven de Vos, Zsolt Nagy, Aleš Obr, Gianluca Gaidano, Pau Abrisqueta, Marc André, Martin Dreyling, Tobias F Menne, Maren Dirnberger-Hertweck, Johannes Weirather, Sumeet Ambarkhane, Gilles A. Salles
Journal: Blood (2019)
Selection of Features and Classifiers for EMG-EEG-Based Upper Limb Assistive Devices—A Review
Authors: Salman Mohd Khan, Abid Ali Khan, Omar Farooq
Journal: IEEE Reviews in Biomedical Engineering (2019)

Bio-signals are distinctive factors in the design of human-machine interface, essentially useful for prosthesis, orthosis, and exoskeletons. Despite the progress in the analysis of pattern recognition based devices; the acceptance of these devices is still questionable. One reason is the lack of information to identify the possible combinations of features and classifiers. Besides; there is also a need for optimal selection of various sensors for sensations such as touch, force, texture, along with EMGs/EEGs. This article reviews the two bio-signal techniques, named as electromyography and electroencephalography. The details of the features and the classifiers used in the data processing for upper limb assist devices are summarised here. Various features and their sets are surveyed and different classifiers for feature sets are discussed on the basis of the classification rate. The review was carried out on the basis of the last 10-12 years of published research in this area. This article also outlines the influence of modality of EMGs and EEGs with other sensors on classifications. Also, other bio-signals used in upper limb devices and future aspects are considered.
OrthoFinder: phylogenetic orthology inference for comparative genomics
Authors: David M. Emms, Steven Kelly
Journal: Genome biology (2019)

Abstract Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted gene trees, gene duplication events, the rooted species tree, and comparative genomics statistics. Each output is benchmarked on appropriate real or simulated datasets, and where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .