Article
Oncology
Joseph Driver, Samantha E. Hoffman, Sherwin Tavakol, Eleanor Woodward, Eduardo A. Maury, Varun Bhave, Noah F. Greenwald, Farshad Nassiri, Kenneth Aldape, Gelareh Zadeh, Abrar Choudhury, Harish N. Vasudevan, Stephen T. Magill, David R. Raleigh, Malak Abedalthagafi, Ayal A. Aizer, Brian M. Alexander, Keith L. Ligon, David A. Reardon, Patrick Y. Wen, Ossama Al-Mefty, Azra H. Ligon, Adrian M. Dubuc, Rameen Beroukhim, Elizabeth B. Claus, Ian F. Dunn, Sandro Santagata, Wenya Linda Bi
Summary: A molecularly integrated grading scheme for meningiomas was proposed, which significantly improved upon the current WHO grading system in predicting progression-free survival. This framework can be broadly adopted by clinicians using widely available genomic technologies and presents an advance in the care of meningioma patients.
Article
Neurosciences
Jennifer K. Forsyth, Eva Mennigen, Amy Lin, Daqiang Sun, Ariana Vajdi, Leila Kushan-Wells, Christopher R. K. Ching, Julio E. Villalon-Reina, Paul M. Thompson, Carrie E. Bearden
Summary: 22q11.2 deletion syndrome is associated with alterations in brain morphology, including reduced total surface area and increased cortical thickness in certain regions. Genes such as DGCR8, AIFM3, and P2RX6 play key roles in these cortical changes. The findings highlight the importance of integrating neuroanatomical and transcriptomic data to understand the molecular mechanisms underlying complex genetic disorders.
Article
Oncology
Aline Neves Araujo, Cleber Pinto Camacho, Thais Biude Mendes, Susan Chow Lindsey, Lais Moraes, Marta Miyazawa, Rosana Delcelo, Renata Pellegrino, Diego Robles Mazzotti, Rui Monteiro de Barros Maciel, Janete Maria Cerutti
Summary: Medullary thyroid cancer (MTC) is a rare disease with poor prognosis in advanced cases, often requiring palliative treatment. This study identified recurrent copy number alterations (CNA) possibly related to the pathogenesis and progression of MTC. The findings suggest common CNA landscape in both sporadic and hereditary MTC, providing new insights into MTC biology.
Article
Multidisciplinary Sciences
Jiwei Bai, Jianxin Shi, Chuzhong Li, Shuai Wang, Tongwu Zhang, Xing Hua, Bin Zhu, Hela Koka, Ho-Hsiang Wu, Lei Song, Difei Wang, Mingyi Wang, Weiyin Zhou, Bari J. Ballew, Belynda Hicks, Lisa Mirabello, Dilys M. Parry, Yixuan Zhai, Mingxuan Li, Jiang Du, Junmei Wang, Shuheng Zhang, Qian Liu, Peng Zhao, Songbai Gui, Alisa M. Goldstein, Yazhuo Zhang, Xiaohong R. Yang
Summary: Whole genome sequencing of 80 skull-base chordomas revealed PBRM1 mutations and homozygous deletions of the CDKN2A/2B locus as common events, associated with poor survival and high recurrence rates. Somatic copy number alterations play a vital role in chordoma initiation, showing highly concordant profiles between primary and recurrence/metastasis samples.
NATURE COMMUNICATIONS
(2021)
Article
Obstetrics & Gynecology
Xinyue Meng, Lili Jiang
Summary: This study aimed to evaluate the risk of chromosomal aberrations and copy number variations (CNVs) in different types of congenital gastrointestinal obstruction (CGIO) and explore the genetic etiology of CGIO using CNV-seq. It was found that the risk of pathogenic chromosomal abnormalities and CNVs increased in the complicated CGIO group, especially in cases of duodenal obstruction (DO) and anorectal malformation. CNV-seq was recommended for detecting submicroscopic chromosomal aberrations when the karyotype was normal.
BMC PREGNANCY AND CHILDBIRTH
(2022)
Article
Multidisciplinary Sciences
Yuxuan Wang, Christopher Douville, Joshua D. Cohen, Austin Mattox, Sam Curtis, Natalie Silliman, Maria Popoli, Janine Ptak, Lisa Dobbyn, Nadine Nehme, Jonathan C. Dudley, Mahmoud Summers, Ming Zhang, Lan T. Ho-Pham, Bich N. H. Tran, Thach S. Tran, Tuan Nguyen, Chetan Bettegowda, Nickolas Papadopoulos, Kenneth W. Kinzlera, Bert Vogelsteina
Summary: The analysis of cell-free DNA (cfDNA) from plasma has great potential for early cancer detection. A new method called MethylSaferSeqS allows the evaluation of DNA molecules for changes in sequence, methylation, or copy number, increasing the sensitivity of cancer detection assays. The method involves copying both strands of each DNA-barcoded molecule and separating the original strands from the copied strands to obtain epigenetic and genetic alterations. By applying this method to plasma samples from individuals with different types of cancer, the study successfully detected expected patterns of mutations, copy number alterations, and methylation. MethylSaferSeqS has the potential to address various genetics and epigenetics-related questions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Oncology
Elaine S. Tan, Todd C. Knepper, Xuefeng Wang, Jennifer B. Permuth, Liang Wang, Jason B. Fleming, Hao Xie
Summary: Somatic mutations and copy number alterations (CNAs) play important roles in colorectal cancer, serving as prognostic and predictive biomarkers. CNAs occur when changes in DNA structure result in gain/amplification or loss/deletion of DNA sections, leading to changes in protein expression. Various techniques, including comparative genomic hybridization, low pass whole genome sequencing, and digital droplet PCR, have been developed to detect CNAs. This review summarizes key findings on the role of CNAs in the pathogenesis of colorectal cancer and discusses their roles as prognostic and predictive biomarkers.
Article
Oncology
Ming-Hung Shen, Chi-Jung Huang, Thien-Fiew Ho, Chih-Yi Liu, Ying-Yih Shih, Ching-Shui Huang, Chi-Cheng Huang
Summary: This study aims to enhance the prognostication of colorectal cancer by integrating SNP and GE microarrays and identifying genes with concurrent gains and losses to develop a prognostic signature. The results show that the colorectal cancer concurrent gene signature has the potential to predict recurrence, metastasis, or mortality among 1746 patients.
Article
Oncology
Mohannad Rajab, Saruchi Bandargal, Marc Philippe Pusztaszeri, Veronique-Isabelle Forest, Sama Alohali, Sabrina Daniela da Silva, Michael Tamilia, Richard J. Payne
Summary: Copy number alterations (CNAs) are commonly found in thyroid tumors, but their clinicopathological implications are not well understood. In this study, we reviewed 67 thyroid nodules with positive CNAs that underwent surgery and found that most of them were malignant or non-invasive follicular thyroid neoplasm with papillary-like nuclear features. The presence of coexisting molecular alterations increased the risk of malignancy in these nodules.
Article
Biotechnology & Applied Microbiology
Lin Chen, Li Wang, Daishu Yin, Feng Tang, Yang Zeng, Hongmei Zhu, Jing Wang
Summary: The study investigated the genetic origin and pregnancy outcomes of copy number loss (CNL) involving autosomal dominant (AD) genes in fetuses without structural abnormalities. Amniotic fluid samples from 24,844 fetuses were tested and 134 fetuses (0.5%) were found to have small CNL containing AD genes. The majority of the pregnancies had good outcomes, while a small proportion had adverse outcomes. Only a few cases had phenotypes consistent with diseases caused by the AD genes involved in the CNL.
Article
Oncology
Can Li, Erik B. Wendlandt, Benjamin Darbro, Hongwei Xu, Gregory S. Thomas, Guido Tricot, Fangping Chen, John D. Shaughnessy, Fenghuang Zhan
Summary: This study utilized gene expression profiling and genomic arrays to investigate molecular alterations in multiple myeloma (MM) and identified eight CNV events as possible MM drivers. By integrating gene expression and copy number variations data, eight unique MM subgroups were defined, each exhibiting common and unique protein network signatures that can be utilized for new therapeutic interventions. The study highlights the central role of 1q gains and the upregulated expression of certain genes as potential drivers of MM aggressiveness, presenting a novel approach to identify potential driver CNV events and areas for therapeutic intervention in MM.
Article
Genetics & Heredity
Zheng Zhao, Zheng Wang, Zhao-Shi Bao, Wei-Zhen Gao, Yuan-Da Zhang, Ci-Jie Ruan, Tao Lv, Yong Wang, Li-Hua Sun
Summary: This study utilized whole-exome sequencing to identify a low frequency of missense mutations in the KIF23 coding region in 319 gliomas, with a stronger association found between amplification of KIF23 and its high expression. Gene ontology analysis revealed that the increased copy number of KIF23 was associated with specific pathways, leading to the upregulation of KIF23 expression.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Rosario Aschero, Jasmine H. Francis, Daiana Ganiewich, Soledad Gomez-Gonzalez, Claudia Sampor, Santiago Zugbi, Daniela Ottaviani, Lauriane Lemelle, Marcela Mena, Ursula Winter, Genoveva Correa Llano, Gabriela Lamas, Fabiana Lubieniecki, Irene Szijan, Jaume Mora, Osvaldo Podhajcer, Francois Doz, Francois Radvanyi, David H. Abramson, Andrea S. Llera, Paula S. Schaiquevich, Cinzia Lavarino, Guillermo L. Chantada
Summary: Relapse of retinoblastoma outside the eye is a rare event in developed countries but remains the main cause of death in patients worldwide. A study of 23 cases from different countries revealed a characteristic pattern of chromosomal copy number alterations in these patients, providing valuable guidance for future clinical management. Previously underrecognized CNAs such as 11q deletions, 17q gains, 19q loss, and BCOR alterations were found to be more common in extraocular retinoblastoma, potentially indicating a more aggressive tumor phenotype that requires careful consideration in patient management.
Article
Psychiatry
Kazusa Miyahara, Mizuki Hino, Risa Shishido, Atsuko Nagaoka, Ryuta Izumi, Hideki Hayashi, Akiyoshi Kakita, Hirooki Yabe, Hiroaki Tomita, Yasuto Kunii
Summary: In this study, the postmortem brains of 26 patients with schizophrenia and 51 controls were used to identify gene sets associated with schizophrenia symptoms. The research also investigated the correlation between these gene sets and genetic background. Pathway and upstream analysis revealed the functions and regulators of these gene sets. This study provides insights into the pathophysiology of schizophrenia and identifies potential therapeutic targets.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Oncology
Karen Gambaro, Maud Marques, Suzan McNamara, Mathilde Couetoux du Tertre, Zuanel Diaz, Cyrla Hoffert, Archana Srivastava, Steven Hebert, Benoit Samson, Bernard Lesperance, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Ronald Burkes, Mohammed Harb, Errol Camlioglu, Adrian Gologan, Vincent Pelsser, Andre Constantin, Celia M. T. Greenwood, Sabine Tejpar, Petr Kavan, Claudia L. Kleinman, Gerald Batist
Summary: A study on genomic plasticity in liver metastatic samples of colorectal cancer revealed an increased frequency of specific CN in metastatic lesions after first-line treatment. Comparison of CNA profiles in lesions with different treatment responses showed focal genomic divergences in post-treatment resistant lesions but not in responder lesions. Examining metastatic lesions is crucial as 15 out of 18 independently validated CNA regions associated with progression-free survival were only identified in metastatic lesions, not in primary tumors.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Letter
Rheumatology
Pedro M. Machado, Martin Schaefer, Anja Strangfeld, Laure Gossec, Milena Gianfrancesco, Saskia Lawson-Tovey, Elsa F. Mateus, Loreto Carmona, Kimme L. Hyrich, Philip C. Robinson, Jinoos Yazdany
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Letter
Rheumatology
Martin Schaefer, Anja Strangfeld, Kimme L. Hyrich, Loreto Carmona, Milena Gianfrancesco, Saskia Lawson-Tovey, Elsa F. Mateus, Laure Gossec, Philip C. Robinson, Jinoos Yazdany, Pedro M. Machado
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Letter
Rheumatology
Kimme L. Hyrich, Martin Schaefer, Anja Strangfeld, Loreto Carmona, Laure Gossec, Elsa F. Mateus, Saskia Lawson-Tovey, Milena Gianfrancesco, Philip C. Robinson, Jinoos Yazdany, Pedro M. Machado
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Article
Rheumatology
Imke Redeker, Katinka Albrecht, Joern Kekow, Gerd Ruediger Burmester, Juergen Braun, Martin Schaefer, Angela Zink, Anja Strangfeld
Summary: The study compared the occurrence of herpes zoster in patients with rheumatoid arthritis undergoing different treatments, showing a higher risk associated with targeted synthetic and biologic DMARDs.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Rheumatology
Manuel Francisco Ugarte-Gil, Graciela S. Alarcon, Zara Izadi, Ali Duarte-Garcia, Cristina Reategui-Sokolova, Ann Elaine Clarke, Leanna Wise, Guillermo J. Pons-Estel, Maria Jose Santos, Sasha Bernatsky, Sandra Lucia Euzebio Ribeiro, Samar Al Emadi, Jeffrey A. Sparks, Tiffany Y-T Hsu, Naomi J. Patel, Emily L. Gilbert, Maria O. Valenzuela-Almada, Andreas Jonsen, Gianpiero Landolfi, Micaela Fredi, Tiphaine Goulenok, Mathilde Devaux, Xavier Mariette, Viviane Queyrel, Vasco C. Romao, Graca Sequeira, Rebecca Hasseli, Bimba Hoyer, Reinhard E. Voll, Christof Specker, Roberto Baez, Vanessa Castro-Coello, Hernan Maldonado Ficco, Edgard Torres Reis Neto, Gilda Aparecida Aparecida Ferreira, Odirlei Andre Andre Monticielo, Emily Sirotich, Jean Liew, Jonathan Hausmann, Paul Sufka, Rebecca Grainger, Suleman Bhana, Wendy Costello, Zachary S. Wallace, Lindsay Jacobsohn, Tiffany Taylor, Clairissa Ja, Anja Strangfeld, Elsa F. Mateus, Kimme L. Hyrich, Loreto Carmona, Saskia Lawson-Tovey, Lianne Kearsley-Fleet, Martin Schaefer, Pedro M. Machado, Philip C. Robinson, Milena Gianfrancesco, Jinoos Yazdany
Summary: The severity of COVID-19 outcomes in individuals with SLE is associated with factors such as gender, age, steroid dosage, comorbidities, and the activity of SLE.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Rheumatology
Manuel F. Ugarte-Gil, Graciela S. Alarcon, Andrea M. Seet, Zara Izadi, Anna D. Montgomery, Ali Duarte-Garcia, Emily L. Gilbert, Maria O. Valenzuela-Almada, Leanna Wise, Jeffrey A. Sparks, Tiffany Y. -T. Hsu, Kristin M. D'Silva, Naomi J. Patel, Emily Sirotich, Jean W. Liew, Jonathan S. Hausmann, Paul Sufka, Rebecca Grainger, Suleman Bhana, Zachary Wallace, Lindsay Jacobsohn, Anja Strangfeld, Elsa F. Mateus, Kimme L. Hyrich, Laure Gossec, Loreto Carmona, Saskia Lawson-Tovey, Lianne Kearsley-Fleet, Martin Schaefer, Pedro M. Machado, Philip C. Robinson, Milena Gianfrancesco, Jinoos Yazdany
Summary: A study on individuals with SLE in the US found that Black and Hispanic patients had higher odds of experiencing more severe COVID-19 outcomes compared to White patients, which may be attributed to socioeconomic and health disparities.
ARTHRITIS CARE & RESEARCH
(2023)
Article
Biochemical Research Methods
Jonas Kupschus, Stefan Janssen, Andreas Hoek, Jan Kuska, Jonathan Rathjens, Carsten Sonntag, Katja Ickstadt, Lisa Budzinski, Hyun-Dong Chang, Andrea Rossi, Charlotte Esser, Katrin Hochrath
Summary: Short-read 16S rRNA gene sequencing is the main technology for profiling microbial communities in different habitats. Flow cytometry can quickly profile the microbiota of various sources. FlowSoFine is an open-source analyzing tool that enables the comparison of cytometric fingerprints of microbial communities from different sources.
Review
Health Care Sciences & Services
Sarah Friedrich, Andreas Groll, Katja Ickstadt, Thomas Kneib, Markus Pauly, Joerg Rahnenfuhrer, Tim Friede
Summary: This article reviews regularization approaches in data science for overcoming overfitting and improving prediction, and discusses their limited application in medical research. The authors suggest increased use of regularization approaches in medicine, despite the added complexity they bring to analyses. Proper investments in computing facilities and educational resources can help overcome these challenges.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2023)
Article
Mathematical & Computational Biology
Julian Riehl, Arno Fritsch, Katja Ickstadt
Summary: This study discussed the increasing importance of subgroup analyses in pharmaceutical research, and compared the traditional methods with shrinkage methods for treatment effect estimation. The results showed that shrinkage methods outperformed traditional methods in applicability extension and solving computational problems.
STATISTICS IN BIOPHARMACEUTICAL RESEARCH
(2022)
Article
Environmental Sciences
S. M. Seyedpour, C. Henning, P. Kirmizakis, S. Herbrandt, K. Ickstadt, R. Doherty, T. Ricken
Summary: In order to improve the usefulness of groundwater flow models, it is necessary to reduce uncertainty associated with major parameters like permeability. A coupled Random Field and extended Theory of Porous Media (eTPM) simulation is used to develop a robust model that reduces uncertainty and is validated with a physical sandbox experiment. The results show that random field realizations of permeability can strongly affect contaminant arrival time compared to a homogenous parameter model.
Article
Rheumatology
Pedro M. Machado, Martin Schaefer, Satveer K. Mahil, Jean Liew, Laure Gossec, Nick Dand, Alexander Pfeil, Anja Strangfeld, Anne Constanze Regierer, Bruno Fautrel, Carla Gimena Alonso, Carla G. S. Saad, Christopher E. M. Griffiths, Claudia Lomater, Corinne Miceli-Richard, Daniel Wendling, Deshire Alpizar Rodriguez, Dieter Wiek, Elsa F. Mateus, Emily Sirotich, Enrique R. Soriano, Francinne Machado Ribeiro, Felipe Omura, Frederico Rajao Martins, Helena Santos, Jonathan Dau, Jonathan N. Barker, Jonathan Hausmann, Kimme L. Hyrich, Lianne Gensler, Ligia Silva, Lindsay Jacobsohn, Loreto Carmona, Marcelo M. Pinheiro, Marcos David Zelaya, Maria de los Angeles Severina, Mark Yates, Maureen Dubreuil, Monique Gore-Massy, Nicoletta Romeo, Nigil Haroon, Paul Sufka, Rebecca Grainger, Rebecca Hasseli, Saskia Lawson-Tovey, Suleman Bhana, Thao Pham, Tor Olofsson, Wilson Bautista-Molano, Zachary S. Wallace, Zenas Z. N. Yiu, Jinoos Yazdany, Philip C. Robinson, Catherine H. Smith
Summary: This study investigated factors associated with severe COVID-19 in patients with psoriasis, psoriatic arthritis, and axial spondyloarthritis. The study found that age, sex, comorbidities, disease activity, and glucocorticoid use were associated with the severity of COVID-19. Additionally, later pandemic time periods, psoriasis, and the use of TNFi, IL17i, and IL-23i/IL-12+23i were associated with a reduced risk of severe COVID-19.
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Article
Computer Science, Interdisciplinary Applications
Frank Weber, Katja Ickstadt, Aenne Glass
Summary: This article introduces the R package shinybrms, which provides a graphical user interface for fitting Bayesian regression models. The authors hope that this package can increase the popularity of Bayesian regression models in applied research, data analysis, and teaching.
Article
Chemistry, Multidisciplinary
Silvia Chines, Christiane Ehrt, Marco Potowski, Felix Biesenkamp, Lars Gruetzbach, Susanne Brunner, Frederik van den Broek, Shilpa Bali, Katja Ickstadt, Andreas Brunschweiger
Summary: To support compound synthesis design, we developed Reaction Navigator, a tool that can process and cluster a large amount of reaction data, helping users select suitable reactions for synthesis according to their needs. It has been successfully applied to DEL synthesis and mapping of reaction space under different reaction conditions.
Article
Rheumatology
Kanon Jatuworapruk, Anna Montgomery, Milena Gianfrancesco, Richard Conway, Laura Durcan, Elizabeth R. Graef, Aruni Jayatilleke, Helen Keen, Adam Kilian, Kristen Young, Loreto Carmona, Adriana Karina Cogo, Ali Duarte-Garcia, Laure Gossec, Rebecca Hasseli, Kimme L. Hyrich, Vincent Langlois, Saskia Lawson-Tovey, Armando Malcata, Elsa F. Mateus, Martin Schafer, Carlo Alberto Scire, Valgerdur Sigurdardottir, Jeffrey A. Sparks, Anja Strangfeld, Ricardo M. Xavier, Suleman Bhana, Monique Gore-Massy, Jonathan Hausmann, Jean W. Liew, Emily Sirotich, Paul Sufka, Zach Wallace, Pedro M. Machado, Jinoos Yazdany, Rebecca Grainger, Philip C. Robinson
Summary: This study describes the characteristics and outcomes of people with gout who were diagnosed with COVID-19 and hospitalized. The results suggest that hospitalized gout patients with COVID-19 have high rates of ventilatory support and death. This may be related to known risk factors such as age and comorbidity.
ACR OPEN RHEUMATOLOGY
(2022)
Article
Rheumatology
Zara Izadi, Milena A. Gianfrancesco, Alfredo Aguirre, Anja Strangfeld, Elsa F. Mateus, Kimme L. Hyrich, Laure Gossec, Loreto Carmona, Saskia Lawson-Tovey, Lianne Kearsley-Fleet, Martin Schaefer, Andrea M. Seet, Gabriela Schmajuk, Lindsay Jacobsohn, Patricia Katz, Stephanie Rush, Samar Al-Emadi, Jeffrey A. Sparks, Tiffany Y-T Hsu, Naomi J. Patel, Leanna Wise, Emily Gilbert, Ali Duarte-Garcia, Maria O. Valenzuela-Almada, Manuel F. Ugarte-Gil, Sandra Lucia Euzebio Ribeiro, Adriana de Oliveira Marinho, Lilian David de Azevedo Valadares, Daniela Di Giuseppe, Rebecca Hasseli, Jutta G. Richter, Alexander Pfeil, Tim Schmeiser, Carolina A. Isnardi, Alvaro A. Reyes Torres, Gelsomina Alle, Veronica Saurit, Anna Zanetti, Greta Carrara, Julien Labreuche, Thomas Barnetche, Muriel Herasse, Samira Plassart, Maria Jose Santos, Ana Maria Rodrigues, Philip C. Robinson, Pedro M. Machado, Emily Sirotich, Jean W. Liew, Jonathan S. Hausmann, Paul Sufka, Rebecca Grainger, Suleman Bhana, Wendy Costello, Zachary S. Wallace, Jinoos Yazdany
Summary: A prediction model and risk score calculator for COVID-19 acute respiratory distress syndrome (ARDS) were developed in patients with rheumatic diseases. The model showed good sensitivity in predicting ARDS using readily available information at COVID-19 diagnosis. The proposed risk score calculator has the potential to guide risk stratification for treatments and reduce disease progression.
ACR OPEN RHEUMATOLOGY
(2022)