tbuckley/cabot-search huggingface dataset:
Response to: ‘Semi-quantitative analysis of line blot assay for myositis-specific and myositis-associated antibodies: a better performance?’ by Cavazzana <i>et al</i>
Authors: Johan Rönnelid, Fabricio Espinosa-Ortega, Ingrid E Lundberg
Journal: Annals of the Rheumatic Diseases (2019)

We have with great interest read the response from Cavazzana et al .1 We agree that increasing the cut-off of the line blot test for myositis-specific and myositis-associated autoantibodies could help to avoid false-positive responses. Our experience from more than a decade of using different versions of the Euroline (Euroimmun, Lubeck, Germany) line immunoassays (LIA) is, in agreement with the suggestion from Cavazzana et al that in the absolute majority of sera with multiple autoantibody specificities the autoantibody reactivities are present in the low range. When investigating only moderate and high reactivities from our previous comparison between LIA and an immunoprecipitation-based algorithm,2 we do, however, not generally improve the kappa statistics, in the way described by Cavazzana et al . We obtained an overall agreement between both approaches of 78% (vs previous 76%) and a kappa coefficient 0.48 (vs previous 0.54). Regarding individual specificities, we did not find …
Efficacy of Eculizumab in Patients with Paroxysmal Nocturnal Hemoglobinuria (PNH) and High Disease Activity with or without History of Aplastic Anemia in the International PNH Registry
Authors: Jong-Wook Lee, Regis Peffault De Latour, Robert A. Brodsky, Jun Ho Jang, Anita Hill, Alexander Roeth, Hubert Schrezenmeier, Amanda Wilson, Jing L. Marantz, Jaroslaw P. Maciejewski
Journal: Blood (2017)
Meta-analysis of the accuracy of Liver Imaging Reporting and Data System category 4 or 5 for diagnosing hepatocellular carcinoma
Authors: Dong Hwan Kim, Sang Hyun Choi, Seong Ho Park, Kyung Won Kim, Jae Ho Byun, So Yeon Kim, Seung Soo Lee, Yong Moon Shin, Hyung Jin Won, Pyo-Nyun Kim
Journal: Gut (2019)

We read with great interest the paper by Gerbes et al 1 summarising recent advances in the treatment of hepatocellular carcinoma (HCC), and that by De Toni et al 2 reporting the importance of early diagnosis for survival of HCC. As these papers suggest, early HCC diagnosis needs to be improved, and the use of MRI for diagnosing HCC is increasing.

Contrary to most other cancers, a non-invasive diagnosis based on imaging characteristics without mandatory pathological confirmation is acceptable for HCC.3–5 However, previous major guidelines have lacked exact definitions of the imaging diagnostic criteria for HCC.6 This could be more problematic for MRI, which provides multiparametric information from complex MRI sequences. To standardise the imaging interpretation of lesions in patients at risk of HCC, the Liver Imaging Reporting and Data System (LI-RADS) was introduced in 2011,6 updated in 2018,7 and fully integrated into the American …
Allogeneic stem cell transplantation (AlloSCT) for patients (pts) with lymphoma and chronic lymphocytic leukemia (CLL) following targeted small molecules inhibitors (SMIs).
Authors: Akash Mukherjee, Denai R. Milton, Elias Jabbour, Alison Gulbis, Tapan M. Kadia, Philip A. Thompson, Michael J. Keating, Nitin Jain, Celina Ledesma, Luis Fayad, Loretta J. Nastoupil, Jan Andreas Burger, Alessandra Ferrajoli, Zeev Estrov, Hagop M. Kantarjian, Richard E. Champlin, Issa F. Khouri
Journal: Journal of Clinical Oncology (2019)

7550 Background: SMIs have improved outcomes in lymphoma/CLL. There is paucity of information about the safety and efficacy of alloSCT following SMIs. Methods: Data from 49 pts who received alloSCT between 2013-2018 at MDA and who have been previously treated with SMIs were retrospectively analyzed. Results: Histologies included CLL (n=31, 63%), mantle cell lymphoma (MCL) (n= 13, 27%), and follicular lymphoma (n= 5, 10%). Prior SMIs included ibrutinib [(n=46; 94%); 57% as ≥ 3rd line of therapy], venetoclax [(n=19, 39%); 68% as ≥ 3 rd line of therapy], idelalisib (n=6, 12%). Ibrutinib was discontinued prior alloSCT in 31(67%) pts. due to refractoriness (n=25), or intolerance (n=6). Seven of 19 (37%) pts had venetoclax discontinued to due refractoriness (n=6) or intolerance (n=1). Risk factors for CLL pts at alloSCT included a prior Richter’s (n=14, 45%), unmutated IGHV (15/23, 65%), presence of del17p (n=23; 74%), and complex cytogenetics (n=15; 48%). In addition, 18/20 (90%) CLL pts had abnormal mutations: most frequent were TP53 (n=14; 78%), BTK (n=6; 33%), SF3B1 (n=4; 22%) and 8/18 (44%) pts had &gt; 2 mutations. Risk factors for MCL pts included: Ki67≥ 30 % (n=10/12, 83%), blastoid histology (n=6, 46%). Median age was 51 years, and 9 (18%) pts had a HCT-CI &gt;4. Median prior lines of therapies was 4. Median duration of SMI therapy was 4.6 months. At transplant 40 (82%) pts had sensitive and 9 (18%) had refractory disease. Conditioning was nonmyeloablative (BFR or FCR) in 62%, RIC in 20% and myeloablative in 18%. Most pts (61%) received matched unrelated or matched sibling donors (22%); 8 (16%) had an alternative donor. The median follow-up for survivors was 12.4 months (range, 1-41.6). OS and PFS at 1 year were 77% and 68%, respectively. The CI of acute grade 2-4 and 3-4 GVHD were 33% and 7%, respectively. CI of 1-year chronic GVHD was 19%. Disease refractoriness and acute 3-4 GVHD were predicators for inferior OS and PFS by MV analysis. Similar survival results were observed in pts with or without mutations. Fourteen pts died due to progression (n=9), infection (n=2), acute (n=2) or chronic GVHD (n=1). Conclusions: AlloSCT is an effective therapy in pts with lymphoma/CLL pretreated with SMI. Our results suggest that alloSCT can overcome high-risk mutations associated with exposure to SMIs. Prospective confirmation in a larger # of pts is needed.
Tumor mutational burden (TMB): Assessment of inter- and intra-tumor heterogeneity.
Authors: Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn, Mary Nesline, Blake Burgher, Felicia L. Lenzo, Antonios Papanicolau-Sengos, Mark Gardner, Carl Morrison
Journal: Journal of Clinical Oncology (2019)

27 Background: As an emerging biomarker, a high TMB is associated with response to immune checkpoint inhibitors. The tissue selected for molecular analysis could be critical for accurate TMB assessment and therapeutic selection. We evaluated TMB and the tumor specimen tested to determine the extent tissue selection has on TMB analysis. Methods: TMB profiling was performed on 73 cases representing 8 tumor types. 8 patients with multiple specimens from the same surgical event were evaluated for intra-tumor heterogeneity, and 20 patients with specimens from multiple surgical events spanning up to seven years were tested for inter-tumor heterogeneity. Two to six specimens, including primary, recurrent and metastatic cases, were evaluated per patient. For each patient, TMB values within and between tumors were assessed for concordance using a clinically relevant TMB-high cutoff of ≥ 10 mutations/Mb. Results: TMB values ranged from 0 – 58, with 7 cases scored as TMB-high. One patient with a primary skin melanoma and a lung metastasis biopsied after 34 months was concordant for TMB-high. For 19 patients (76%), all samples were concordant for TMB-low. For intratumor testing, 2 of 8 (25%) patients had discordant specimens (crossed the TMB-cutoff). The first patient had 4 intra-tumor CRC samples with TMB values of 10.6, 10.7, 9.7 and 9.7. The second patient had 5 intra-tumor pancreatic samples with TMB values of 10.7, 4.4, 6.2, 8.8, 7.9. Of the patients with 20 inter-tumor samples, 2 patients (each with melanoma) had discordant TMB-high calls. One had a lymph node metastasis TMB of 12.3 and a liver metastasis collected five months later with a reduced TMB of 0.9. In contrast, the second discordant melanoma patient had a peritoneum metastasis with an elevated TMB of 11.4 collected 14 months after a mesentery metastasis with a TMB of 8.7. Conclusions: TMB variation within tumors and between tumors from different surgical events occurs equally and in 17% of patients. This clinical tumor heterogeneity on the inter- or intra-tumor level may limit the utility and the application of TMB at a cutoff of 10. A careful analysis of tissues to enrich for neoplastic cells may improve assay sensitivity and increase analytical accuracy at this precise cut point.
18F-FDG PET/CT in Lymphomatoid Papulosis Mimicking Primary Cutaneous Anaplastic Large Cell Lymphoma
Authors: Raja Senthil, V. P. Gangadharan, R. Arun Visakh, Pushpa Mahadevan, Thara Pratap, M. G. Jayasree
Journal: Clinical Nuclear Medicine (2019)

Abstract Lymphomatoid papulosis is a benign self-healing condition, presenting as papulonodular skin eruptions and mimicking malignant cutaneous lymphomas histopathologically. 18 F-FDG PET/CT findings in this benign condition have not been described in detail in the literature. We present a case of lymphomatoid papulosis mimicking primary cutaneous anaplastic large cell lymphoma histopathologically and demonstrating intensely FDG-avid cutaneous lesions on 18 F-FDG PET/CT, which disappear spontaneously in the follow-up scan.
Value of Molecular Classification for Prognostic Assessment of Adrenocortical Carcinoma
Authors: Guillaume Assié, Anne Jouinot, Martin Fassnacht, Rossella Libé, Simon Garinet, Louis Jacob, Nadim Hamzaoui, Mario Neou, Julien Sakat, Bruno de La Villéon, Karine Perlemoine, Bruno Ragazzon, Mathilde Sibony, Frédérique Tissier, Sébastien Gaujoux, Bertrand Dousset, Silviu Sbiera, Cristina L. Ronchi, Matthias Kroiss, Esther Korpershoek, Ronald De Krijger, Jens Waldmann, Marcus Quinkler, Magalie Haissaguerre, Antoine Tabarin, Olivier Chabre, Michaela Luconi, Massimo Mannelli, Lionel Groussin, Xavier Bertagna, Eric Baudin, Laurence Amar, Joel Coste, Felix Beuschlein, Jérôme Bertherat
Journal: JAMA Oncology (2019)

The risk stratification of adrenocortical carcinoma (ACC) based on tumor proliferation index and stage is limited. Adjuvant therapy after surgery is recommended for most patients. Pan-genomic studies have identified distinct molecular groups closely associated with outcome.
Pyridoxine impact on patients with myelodysplastic syndromes with ring sideroblasts: Single institution retrospective study.
Authors: Darci Zblewski, Phuong L. Nguyen, Rong He, Patricia T. Greipp, Kebede Begna, Mrinal Mahesh Patnaik, Naseema Gangat, Mithun Vinod Shah, Hassan Alkhateeb, Mark Robert Litzow, Aref Al-Kali
Journal: Journal of Clinical Oncology (2019)

e18549 Background: Many vitamin deficiencies can cause anemia. It is prudent prior to diagnosing a myeloid neoplasm, to check for vitamin deficiencies and correct them. Myelodysplastic syndromes with ring sideroblasts (MDS-RS) are associated with anemia. Pyridoxine (Vit B6) replacement may improve anemia found in sideroblastic anemia. The study was to determine how frequently Vit B6 was assessed, replaced and impact replacement had on outcomes in MDS-RS. Methods: Study subjects were from the Mayo Clinic Myelodysplastic syndrome (MDS) database which contains 1315 patients (pts). Appropriate IRB approval was obtained. Diagnosis of MDS and its sub-classification was done according to World Health Organization 2016 criteria. A response was any improvement in hemoglobin. Overall survival (OS) estimates were calculated using Kaplan-Meier curves and univariate and multivariate analysis was done using JMP software version 13. Results: Among 1315 pts with MDS, 161 pts had a diagnosis of MDS-RS. Median age was 73, and 55 (34%) pts were females. Thirty-nine (36%) pts had very low, 53 (50%) low, 9 (8%) intermediate, 3 (3%) high, and 2 (1%) had very high revised international prognostic score. The median white blood cell count was 5.4 x10 9 , platelet count was 255 x10 9 , and hemoglobin was 9.9 gm/dL. Five pts (3%) had a Vit B6 levels done; out of whom, 4 (80%) were not Vit B6 deficient. Among 42 (26%) pts who had Vit B6 replacement, 21 (50%) had no response, 4 (10%) had a response and 17 (40%) had unknown response. 103 (64%) of the pts were transfusion independent (TI). Overall survival in pts who are transfusion dependent was 68 months compared to 85 in pts who are TI (Wilcoxon P =.03). There was an improvement in OS in the group that had Vit B6 replacement compared to the group with no Vit B6 replacement (92 months vs 68 months, Wilcoxon P =.07). Response to Vit B6 replacement did not show OS benefit. Acute Leukemia transformation in Vit B6 replacement was 2% and 6% in pts. who did not have Vit B6 replacement (P= .4). Conclusions: Vit B6 was not checked often in MDS-RS pts. There was a borderline improvement in OS in Vit B6 replacement group (p= .07). Response did not affect OS. A larger prospective study is needed to study Vit B6 role in MDS-RS.
Correlation of circulating tumor enumeration and immune checkpoint marker expression on CD103+, CD4+ T cells in non-small cell lung cancer tissue.
Authors: Xiaoyang WANG, Pin-I Chen, Maria Jaimes, Humin Gu, Keith Shults, Santosh Putta, Fariba Fazeli, Janine Fernandez, Vishal Sharma, Will Chow, Priya Gogoi, Kalyan Handique, Bruce Kendrick Patterson
Journal: Journal of Clinical Oncology (2019)

109 Background: Non-small cell lung cancer (NSCLC) has a poor prognosis as most patients are at advanced stage when diagnosed. Targeted therapy and immunotherapy in recent years has significantly improved NSCLC patient outcome. In this study, we employed cell-by-cell immune and cancer marker profiling of the primary tumor cells to investigate possible signatures that might predict the presence or absence of circulating tumor cells (CTCs). Methods: We performed a comprehensive study on 10 NSCLC patient tissue samples with paired blood samples. The solid tissue biopsy samples were dissociated into single cells by non-enzymatic tissue homogenization. The single cell suspensions were stained with a total 25 immune, cancer markers and a DNA content dye and analyzed with advanced, high-parameter flow cytometry. CTCs were isolated and analyzed from the paired peripheral blood. Results: Out of the 26 unique cell markers stained, we investigated a total of 72 biomarkers for their correlation with CTC number. Strong correlations were observed between CTC number and the frequency of immune checkpoint marker expressing lymphocytes, especially with the immune checkpoint marker expressing CD103 + CD4 + T lymphocytes. CTC number is also correlated with the frequency of PD-L1 expressing cancer cells and cancer cell DNA content. In contrast, CTC number inversely correlated to the frequency of CD44 + E-cadherin - cancer cells. Unsupervised clustering analysis based on the biomarker analysis separated the CTC negative patients from the CTC positive patients. Conclusions: Profiling multiple immune and cancer markers on cancer samples with multi-parametric flow cytometry allowed us to obtain protein expression information at the single cell level. Clustering analysis of the proteomic data revealed a signature driven by checkpoint marker expression on CD103 + CD4 + T cells that could potentially be predictive of CTCs.
T-Cell Subsets and Macrophages in the Tumor Microenvironment Are Associated with Early Outcome in Follicular Lymphoma
Authors: Angelo Fama, Andrew L Feldman, Matthew J Maurer, Brian K Link, Anne J Novak, Zhi-Zhang Yang, Hyo Jin Kim, Thomas M Habermann, Thomas E Witzig, James R. Cerhan, Stephen M Ansell
Journal: Blood (2017)
Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan
Authors: Jeffrey Umotoy, Bernard S. Bagaya, Collin Joyce, Torben Schiffner, Sergey Menis, Karen L. Saye-Francisco, Trevor Biddle, Sanjay Mohan, Thomas Vollbrecht, Oleksander Kalyuzhniy, Sharon Madzorera, Dale Kitchin, Bronwen Lambson, Molati Nonyane, William Kilembe, Pascal Poignard, William R. Schief, Dennis R. Burton, Ben Murrell, Penny L. Moore, Bryan Briney, Devin Sok, Elise Landais
Journal: Immunity (2019)

The VH1-2 restricted VRC01-class of antibodies targeting the HIV envelope CD4 binding site are a major focus of HIV vaccine strategies. However, a detailed analysis of VRC01-class antibody development has been limited by the rare nature of these responses during natural infection and the lack of longitudinal sampling of such responses. To inform vaccine strategies, we mapped the development of a VRC01-class antibody lineage (PCIN63) in the subtype C infected IAVI Protocol C neutralizer PC063. PCIN63 monoclonal antibodies had the hallmark VRC01-class features and demonstrated neutralization breadth similar to the prototype VRC01 antibody, but were 2- to 3-fold less mutated. Maturation occurred rapidly within ∼24 months of emergence of the lineage and somatic hypermutations accumulated at key contact residues. This longitudinal study of broadly neutralizing VRC01-class antibody lineage reveals early binding to the N276-glycan during affinity maturation, which may have implications for vaccine design.
In Vivo Microbial Targeting of 99mTc-Labeled Human β-Defensin-3 in a Rat Model of Infection
Authors: Giulia Anna Follacchio, Alessandro Pala, Sergio Scaccianoce, Francesco Monteleone, Patrick M. Colletti, Domenico Rubello, Mauro Liberatore
Journal: Clinical Nuclear Medicine (2019)

Differentiation of infection from aseptic inflammation represents a major clinical issue. None of the commercially available compounds (labeled granulocytes, antigranulocyte antibodies, Ga-citrate, labeled immunoglobulin G, F-FDG) is capable of this differentiation, producing a nonnegligible false-positive rate. Recently, our group reported on a reliable labeling procedure of the antimicrobial peptide human β-defensin 3 (HBD-3) with Tc. The aim of this study was to evaluate in vivo Tc-HBD-3 uptake in a rat model of infection.Recombinant HBD-3 was radiolabeled with Tc. Radiolabeling yield and specific activity of the compound were calculated. Chromatographic behavior and biological activity of Tc-HBD-3 were also assessed. An experimental model involving Staphylococcus aureus-induced infection and carrageenan-induced aseptic inflammation was performed in 5 Wistar rats. Serial planar scintigraphic acquisitions were performed from 15 to 180 minutes after Tc-HBD-3 intravenous administration. Radiotracer uptake was evaluated qualitatively and semiquantitatively as a target-to-nontarget ratio.Radiolabeling yield of Tc-HBD-3 was 70% with a specific activity of 6 to 8 MBq/μg. A significant and progressive Tc-HBD-3 uptake was observed in the site of S. aureus-induced infection, with a maximum average target-to-nontarget ratio of 5.7-fold higher in the infection site compared with an inflammation site observed at 140 minutes.In vivo imaging with Tc-HBD-3 in a rat model of S. aureus-induced infection demonstrated favorable uptake in the infection site compared with sterile inflammation and background. These promising results, together with previous ex vivo uptake and toxicity assessment, suggest the potential of Tc-HBD-3 as a novel agent for specific infection imaging.
Abstract 14459: Changes in Gut Microbiota Metabolites and Successful Weight-loss in Response to Weight-Loss Diets: The POUNDS Lost Trial
Authors: Yoriko Heianza, Wenjie Ma, Dianjianyi Sun, Steven R Smith, George A Bray, Frank M Sacks, Lu Qi
Journal: Circulation (2017)

Introduction: Higher levels of gut microbiota-dependent trimethylamine N-oxide (TMAO) and its precursors such as choline and L-carnitine have been associated with increased risks of cardiovascular ...
Vascular Parkinsonism by Infarctions at Different Locations on 18F-FP-CIT PET/CT
Authors: Chanwoo Kim, Deog Yoon Kim, Il Ki Hong
Journal: Clinical Nuclear Medicine (2019)

Abstract Cerebral vascular lesions are integral to the diagnosis of vascular parkinsonism (VP). The VP, also referred to as lower body parkinsonism, is frequently caused by subcortical white matter lesions, but lesions at any levels of the nigro-striato-thalamo-cortical pathway can also cause VP, thus giving rise to various symptoms other than gait disturbance. Previous dopamine transporter imaging studies using SPECT showed heterogeneous patterns suggesting diverse contributing lesions to VP. Here we present 3 cases of VP demonstrated by 18 F-FP-CIT PET/CT, visualizing vascular lesions at different levels between the midbrain and motor cortex. Distinctive clinical manifestations of them recapitulate the pathogenesis of VP.
Combination of Ibrutinib and Short-Course Fludarabine in Previously Untreated Patients with CLL: A Pilot Phase II Study
Authors: Inhye E. Ahn, Susan Soto, Pia Nierman, Xin Tian, Janet Valdez, Jennifer Lotter, Thomas Fleisher, Sergio Rosenzweig, Shakuntala Rampertaap, Irina Maric, Maryalice Stetler-Stevenson, Constance Yuan, Gerald Marti, Adrian Wiestner
Journal: Blood (2017)
Clinical and Echocardiographic Associates of All-Cause Mortality and Cardiovascular Outcomes in Patients With Systemic Sclerosis
Authors: Suzanne E. van Wijngaarden, Maaike Boonstra, Bas Bloem, Daniela Cassani, Felix C. Tanner, Suzana Jordan, Oliver Distler, Victoria Delgado, Jeroen J. Bax, Jeska K. de Vries-Bouwstra, Nina Ajmone Marsan
Journal: JACC. Cardiovascular imaging (2019)
Biomarkers of extracellular matrix turnover in patients with idiopathic pulmonary fibrosis given nintedanib (INMARK study): a randomised, placebo-controlled study
Authors: Toby M Maher, Susanne Stowasser, Yasuhiko Nishioka, Eric S White, Vincent Cottin, Imre Noth, Moisés Selman, Klaus B Rohr, Andreas Michael, Carina Ittrich, Claudia Diefenbach, R Gisli Jenkins, Tamera Corte, Ian Glaspole, Mark Holmes, Lauren Troy, Elizabeth Veitch, Benjamin Bondue, Caroline Dahlqvist, Renaud Louis, Jan Van Meerbeeck, Wim Wuyts, Radka Bittenglova, Vitezslav Kolek, Norbert Pauk, Pavel Reiterer, Martina Sterclova, Maritta Kilpeläinen, Riitta Mäkitaro, Marjukka Myllärniemi, Minna Purokivi, Terhi Rantala, Vincent Cottin, Francis Couturaud, Dominique Israel-Biet, Stéphane Jouneau, Romain Kessler, François Lebargy, Sylvain Marchand-Adam, Tom Bollmann, Andreas Günther, Peter Hammerl, Joachim Kirschner, Anne-Marie Kirsten, Michael Kreuter, Claus Neurohr, Antje Prasse, Nicolas Schönfeld, Rainer Wiewrodt, Somfay Attila, Medgyasszay Balazs, Eszter Csanky, György Losonczy, Hiroki Hayashi, Sakae Homma, Yoshikazu Inoue, Shinyu Izumi, Hideya Kitamura, Yasuhiko Nishioka, Osamu Nishiyama, Takashi Ogura, Masaki Okamoto, Takefumi Saito, Hiroyuki Taniguchi, Yoshiaki Zaizen, Marzena Filipowska, Agnieszka Jarzemska, Wladyslaw Pierzchala, Wojciech Piotrowski, Krzysztof Sladek, Ewa Trawinska, Young Whan Kim, Jong Sun Park, Jin Woo Song, Myriam Aburto, Diego Castillo Villegas, José María Echave-Sustaeta, Christian Garcia Fadul, Susana Herrera, Jorge Moises, María Molina-Molina, Amalia Moreno, Asunción Nieto, María Jesús Rodríguez Nieto, José Antonio Rodriguez-Portal, Belen Safont, Jacobo Sellares, Claudia Valenzuela, Huzaifa Adamali, Nazia Chaudhuri, Michael Gibbons, Rachel Hoyles, Toby Maher, Helen Parfrey, Francis Averill, Steven Chambers, Neil Ettinger, Glenn Giessel, Lisa M Jones, Mitchell G Kaye, David Oelberg, Jan H Westerman, Donald Zoz
Journal: The Lancet Respiratory Medicine (2019)
CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Authors: Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Journal: Genome biology (2019)

We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data. Characterization of a human pluripotent cell differentiation protocol recapitulating deep-layer corticogenesis using CellSIUS reveals unrecognized complexity in human stem cell-derived cellular populations. CellSIUS enables identification of novel rare cell populations and their signature genes providing the means to study those populations in vitro in light of their role in health and disease.