Article
Genetics & Heredity
Francesco Musacchia, Marianthi Karali, Annalaura Torella, Steve Laurie, Valeria Policastro, Mariateresa Pizzo, Sergi Beltran, Giorgio Casari, Vincenzo Nigro, Sandro Banfi
Summary: VarGenius-HZD is a sensitive and scalable algorithm for the detection of rare homozygous and hemizygous single-exon deletions. It showed higher sensitivity compared to state-of-the-art algorithms in detecting rare HDs and successfully solved genetic diagnosis cases in patients with Inherited Retinal Dystrophies.
Article
Neurosciences
Cornelis Blauwendraat, Mary B. Makarious, Hampton L. Leonard, Sara Bandres-Ciga, Hirotaka Iwaki, Mike A. Nalls, Alastair J. Noyce, Andrew B. Singleton
Summary: A study on SNCA variations in a large population cohort identified individuals carrying specific mutations, who although without reported Parkinson's disease, may potentially develop the condition in the future. These individuals could be candidates for further investigation to understand how some are able to escape PD.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Biochemistry & Molecular Biology
Thomas F. Eleveld, Chaimaa Bakali, Paul P. Eijk, Phylicia Stathi, Lianne E. Vriend, Pino J. Poddighe, Bauke Ylstra
Summary: Large-scale chromosomal deletions are common in cancer and confer an oncogenic advantage, but the oncogenic drivers behind these deletions are difficult to identify. This study introduced a novel CRISPR-Cas9 technique to engineer large-scale deletions and create isogenic cell line models, successfully inducing deletions in neuroblastoma cell lines. The technique may provide valuable insights into the role of large-scale deletions in tumor development and growth.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Oncology
Bart Vrugt, Michaela B. Kirschner, Mayura Meerang, Kathrin Oehl, Ulrich Wagner, Alex Soltermann, Holger Moch, Isabelle Opitz, Peter J. Wild
Summary: In this study, the suitability of using p16 and MTAP IHC for detecting CDKN2A deletion in pleural mesothelioma was investigated. The results showed that MTAP and p16 IHC had high sensitivity and specificity for detecting any gene loss, and had high concordance with OncoScan CNV arrays.
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Jack M. Fu, F. Kyle Satterstrom, Minshi Peng, Harrison Brand, Ryan L. Collins, Shan Dong, Brie Wamsley, Lambertus Klei, Lily Wang, Stephanie P. Hao, Christine R. Stevens, Caroline Cusick, Mehrtash Babadi, Eric Banks, Brett Collins, Sheila Dodge, Stacey B. Gabriel, Laura Gauthier, Samuel K. Lee, Lindsay Liang, Alicia Ljungdahl, Behrang Mahjani, Laura Sloofman, Andrey N. Smirnov, Mafalda Barbosa, Catalina Betancur, Alfredo Brusco, Brian H. Y. Chung, Edwin H. Cook, Michael L. Cuccaro, Enrico Domenici, Giovanni Battista Ferrero, J. Jay Gargus, Gail E. Herman, Irva Hertz-Picciotto, Patricia Maciel, Dara S. Manoach, Maria Rita Passos-Bueno, Antonio M. Persico, Alessandra Renieri, James S. Sutcliffe, Flora Tassone, Elisabetta Trabetti, Gabriele Campos, Simona Cardaropoli, Diana Carli, Marcus C. Y. Chan, Chiara Fallerini, Elisa Giorgio, Ana Cristina Girardi, Emily Hansen-Kiss, So Lun Lee, Carla Lintas, Yunin Ludena, Rachel Nguyen, Lisa Pavinato, Margaret Pericak-Vance, Isaac N. Pessah, Rebecca J. Schmidt, Moyra Smith, Claudia I. S. Costa, Slavica Trajkova, Jaqueline Y. T. Wang, Mullin H. C. Yu, David J. Cutler, Silvia De Rubeis, Joseph D. Buxbaum, Mark J. Daly, Bernie Devlin, Kathryn Roeder, Stephan J. Sanders, Michael E. Talkowski
Summary: This study investigated genes associated with functional mutations in individuals with autism spectrum disorder (ASD) and found that some of these genes are also associated with developmental delay (DD). The findings suggest that ASD and DD may share common pathological pathways.
Article
Biochemistry & Molecular Biology
Mahdieh Labani, Ali Afrasiabi, Amin Beheshti, Nigel H. Lovell, Hamid Alinejad-Rokny
Summary: Copy Number Variation (CNV) is a type of genetic variation where a segment of chromosome is duplicated or deleted and has been identified to be associated with various diseases and phenotypes. However, conducting a CNV-based genome-wide association study is challenging due to the inconsistency of CNV length and occurrence across different individuals. Researchers have developed a tool called PeakCNV, which uses a new metric called independence ranking score (IR-score) to differentiate false-positive and true positive CNV regions, improving the accuracy of CNV association studies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Agnieszka Piotrowska-Nowak, Krzysztof Safranow, Jakub G. Adamczyk, Ireneusz Soltyszewski, Pawel Cieszczyk, Katarzyna Tonska, Cezary Zekanowski, Beata Borzemska
Summary: Energy efficiency is crucial for athletic performance. This study investigated the relationship between mitochondrial DNA (mtDNA) variants and athletic performance among Polish male athletes. The analysis revealed no correlation between mtDNA variants and athletic performance, but showed a lower mtDNA copy number in both power and endurance athletes compared to controls.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Aditi Hazra, Andrea O'Hara, Kornelia Polyak, Faina Nakhlis, Beth T. Harrison, Antonio Giordano, Beth Overmoyer, Filipa Lynce
Summary: The goal of this study was to identify biomarkers associated with de novo inflammatory breast cancer (IBC). Through examination of breast biopsies, significant copy number variations (CNVs) on chromosome 7p11.2 and 21 were identified. These findings provide insights into the biology of IBC and may lead to the optimization of treatment strategies.
Article
Immunology
Shalini Nair, Xue Li, Standwell C. Nkhoma, Tim Anderson
Summary: This study investigates the fitness costs of parasites carrying pfhrp2 and/or pfhrp3 deletions through gene editing. The results show significant fitness costs for pfhrp2 deletion and pfhrp2/3 double deletion, comparable to those resulting from drug resistance mutations. These findings may explain the increasing frequency of pfhrp deletions in certain locations but not in others.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Genetics & Heredity
Chloe X. Yap, Gail A. Alvares, Anjali K. Henders, Tian Lin, Leanne Wallace, Alaina Farrelly, Tiana McLaren, Jolene Berry, Anna A. E. Vinkhuyzen, Maciej Trzaskowski, Jian Zeng, Yuanhao Yang, Dominique Cleary, Rachel Grove, Claire Hafekost, Alexis Harun, Helen Holdsworth, Rachel Jellett, Feroza Khan, Lauren Lawson, Jodie Leslie, Mira Levis Frenk, Anne Masi, Nisha E. Mathew, Melanie Muniandy, Michaela Nothard, Peter M. Visscher, Paul A. Dawson, Cheryl Dissanayake, Valsamma Eapen, Helen S. Heussler, Andrew J. O. Whitehouse, Naomi R. Wray, Jacob Gratten
Summary: This study based on the data from the Australian Autism Biobank found significant differences in genetic scores for ASD and IQ among different groups, with the IQ genetic score being able to predict the IQ of undiagnosed children and parents. Additionally, the genetic score related to chronotype was associated with sleep disturbances in the ASD group.
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)
Article
Computer Science, Software Engineering
Eric Verner, Helen Petropoulos, Bradley Baker, Henry Jeremy Bockholt, Jill Fries, Anastasia Bohsali, Rajikha Raja, Duc Hoai Trinh, Vince Calhoun
Summary: BrainForge is a cloud-based neuroimaging analysis platform that allows users to archive and process data, as well as share results with colleagues. It addresses various challenges faced by researchers in neuroimaging data analysis, including software, reproducibility, computational resources, and data sharing.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2023)
Article
Neurosciences
Pujie Feng, Rongtao Jiang, Lijiang Wei, Vince D. Calhoun, Bin Jing, Haiyun Li, Jing Sui
Summary: This study investigates the impact of four confounding factors on individual trait prediction using resting-state functional connectivity (RSFC) data. The results suggest that the appropriate time series length and brain parcellation choice can improve prediction performance. Functional connectivity calculated by Pearson, Spearman, and Partial correlation achieves higher accuracy and lower time cost. Moreover, cognitive traits with larger variance among subjects can be better predicted.
Article
Cardiac & Cardiovascular Systems
Rongtao Jiang, Vince D. Calhoun, Stephanie Noble, Jing Sui, Qinghao Liang, Shile Qi, Dustin Scheinost
Summary: This study utilizes machine learning and functional connectivity to investigate the neurobiological correlates of blood pressure at an individual level. The results identify specific brain regions that are associated with blood pressure and provide evidence for meaningful neural representations of blood pressure in connectivity profiles.
CARDIOVASCULAR RESEARCH
(2023)
Article
Neurosciences
Lei Wu, Vince Calhoun
Summary: The study of human brain connectivity provides insights into brain function and its relationship to behavior and cognition. Integrating structural connectivity and functional connectivity into a single framework is challenging. In this study, a new method called joint connectivity matrix independent component analysis (cmICA) is introduced, which allows for the integration of these two types of connectivity measurements using functional magnetic resonance imaging (MRI) and diffusion-weighted MRI data.
HUMAN BRAIN MAPPING
(2023)
Article
Biochemical Research Methods
Yuda Bi, Anees Abrol, Zening Fu, Jiayu Chen, Jingyu Liu, Vince Calhoun
Summary: Deep learning algorithms for predicting neuroimaging data have shown promise and outperform standard machine learning. This study focuses on using structural MRI data from the Adolescent Brain and Cognitive Development (ABCD) dataset to predict gender and identify gender-related changes in brain structure.
JOURNAL OF NEUROSCIENCE METHODS
(2023)
Article
Biochemistry & Molecular Biology
Constantinos Constantinides, Laura K. M. Han, Clara Alloza, Linda Antonella Antonucci, Celso Arango, Rosa Ayesa-Arriola, Nerisa Banaj, Alessandro Bertolino, Stefan Borgwardt, Jason Bruggemann, Juan Bustillo, Oleg Bykhovski, Vince Calhoun, Vaughan Carr, Stanley Catts, Young-Chul Chung, Benedicto Crespo-Facorro, Covadonga M. Diaz-Caneja, Gary Donohoe, Stefan Du Plessis, Jesse Edmond, Stefan Ehrlich, Robin Emsley, Lisa T. Eyler, Paola Fuentes-Claramonte, Foivos Georgiadis, Melissa Green, Amalia Guerrero-Pedraza, Minji Ha, Tim Hahn, Frans A. Henskens, Laurena Holleran, Stephanie Homan, Philipp Homan, Neda Jahanshad, Joost Janssen, Ellen Ji, Stefan Kaiser, Vasily Kaleda, Minah Kim, Woo-Sung Kim, Matthias Kirschner, Peter Kochunov, Yoo Bin Kwak, Jun Soo Kwon, Irina Lebedeva, Jingyu Liu, Patricia Mitchie, Stijn Michielse, David Mothersill, Bryan Mowry, Victor Ortiz-Garcia de la Foz, Christos Pantelis, Giulio Pergola, Fabrizio Piras, Edith Pomarol-Clotet, Adrian Preda, Yann Quide, Paul E. Rasser, Kelly Rootes-Murdy, Raymond Salvador, Marina Sangiuliano, Salvador Sarro, Ulrich Schall, Andre Schmidt, Rodney J. Scott, Pierluigi Selvaggi, Kang Sim, Antonin Skoch, Gianfranco Spalletta, Filip Spaniel, Sophia Thomopoulos, David Tomecek, Alexander S. Tomyshev, Diana Tordesillas-Gutierrez, Therese van Amelsvoort, Javier Vazquez-Bourgon, Daniela Vecchio, Aristotle Voineskos, Cynthia S. Weickert, Thomas Weickert, Paul M. Thompson, Lianne Schmaal, Theo G. M. van Erp, Jessica Turner, James H. Cole, Danai Dima, Esther Walton
Summary: Schizophrenia patients show evidence of advanced brain ageing, which is not associated with clinical characteristics.
MOLECULAR PSYCHIATRY
(2023)
Review
Behavioral Sciences
Oscar Javier Galindo-Caballero, Fraidy-Alonso Alzate-Pamplona, Steven W. Gangestad, Julio Eduardo Cruz
Summary: This article critically analyzes the literature on the effects of ovarian hormones on consumer preferences and financial decisions. The analysis finds evidence for associations between the menstrual cycle and consumer preferences, particularly for appearance-enhancing products. However, no compelling evidence is found for associations between the menstrual cycle and financial decisions or risk-taking. More research with sufficient statistical power is called for in the domain of financial decisions.
HORMONES AND BEHAVIOR
(2023)
Correction
Biochemistry & Molecular Biology
Sean R. McWhinney, Katharina Brosch, Vince D. Calhoun, Benedicto Crespo-Facorro, Nicolas A. Crossley, Udo Dannlowski, Erin Dickie, Lorielle M. F. Dietze, Gary Donohoe, Stefan Du Plessis, Stefan Ehrlich, Robin Emsley, Petra Furstova, David C. Glahn, Alfonso Gonzalez-Valderrama, Dominik Grotegerd, Laurena Holleran, Tilo T. J. Kircher, Pavel Knytl, Marian Kolenic, Rebekka Lencer, Igor Nenadic, Nils Opel, Julia-Katharina Pfarr, Amanda L. Rodrigue, Kelly Rootes-Murdy, Alex J. Ross, Kang Sim, Antonin Skoch, Filip Spaniel, Frederike Stein, Patrik Svancer, Diana Tordesillas-Gutierrez, Juan Undurraga, Javier Vaquez-Bourgon, Aristotle Voineskos, Esther Walton, Thomas W. Weickert, Cynthia Shannon Weickert, Paul M. Thompson, Theo G. M. van Erp, Jessica A. Turner, Tomas Hajek
MOLECULAR PSYCHIATRY
(2023)
Review
Biochemistry & Molecular Biology
Esther Walton, Vilte Baltramonaityte, Vince Calhoun, Bastiaan T. Heijmans, Paul M. Thompson, Charlotte A. M. Cecil
Summary: Epigenetic mechanisms, such as DNA methylation (DNAm), have been studied as potential biomarkers and mechanisms underlying brain-based disorders. However, there is little understanding of the relationship between DNAm and individual differences in the brain, especially during development. This systematic review examines the field of Neuroimaging Epigenetics and finds inconsistent findings regarding DNAm-brain associations and a lack of replication or meta-analysis. The authors propose three recommendations to advance the field, including a focus on development, large prospective studies, and interdisciplinary collaboration.
MOLECULAR PSYCHIATRY
(2023)
Article
Chemistry, Analytical
Hanlu Yang, Trung Vu, Qunfang Long, Vince Calhoun, Tuelay Adali
Summary: This study proposes a framework for subgroup identification of psychiatric patients using functional connectivity profiles obtained from fMRI data. The pipeline incorporates a data-driven method and constraint-based independent component analysis to identify meaningful subgroups with similar activation patterns in certain brain areas. The identified subgroups show significant group differences in multiple meaningful brain areas.
Article
Psychiatry
Zening Fu, Christopher C. Abbott, Jeremy Miller, Zhi-De Deng, Shawn M. McClintock, Mohammad S. E. Sendi, Jing Sui, Vince D. Calhoun
Summary: Electroconvulsive therapy (ECT) is effective for depression treatment, and its mechanism involves changing brain's functional organization through electrical current stimulation. This study investigated the relationship between whole-brain electric field (E-field), cerebro-cerebellar functional network connectivity (FNC), and clinical outcomes of ECT. The results showed that E-field influenced cognitive performance through cerebellum to middle occipital gyrus (MOG)/posterior cingulate cortex (PCC) FNC mediation, and had an effect on antidepressant outcomes through cerebellum to parietal lobule FNC mediation. Furthermore, larger E-field was associated with increased FNC between cerebellum and MOG and decreased FNC between cerebellum and PCC, which were linked with decreased cognitive performance.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Neurosciences
Paul A. Taylor, Richard C. Reynolds, Vince Calhoun, Javier Gonzalez-Castillo, Daniel A. Handwerker, Peter A. Bandettini, Amanda F. Mejia, Gang Chen
Summary: Neuroimaging studies often display only a small fraction of the collected data, which hides important information and leads to issues of selection bias and irreproducibility. Instead, it is suggested to highlight as many results as possible through visualization to improve scientific communication and understanding.
Article
Neuroimaging
Mohammad S. E. Sendi, Elaheh Zendehrouh, Charles A. Ellis, Zening Fu, Jiayu Chen, Robyn L. Miller, Elizabeth C. Mormino, David H. Salat, Vince D. Calhoun
Summary: This study investigated the association between static and dynamic functional network connectivity (FNC) and Alzheimer's disease (AD) genetic risk using a data-driven approach. The results showed that AD genetic risk is related to a weakening of connectivity within the visual sensory network (VSN) and spending more time in a state with reduced VSN connectivity.
NEUROIMAGE-CLINICAL
(2023)
Article
Psychiatry
Lavinia Carmen Uscatescu, Martin Kronbichler, Sarah Said-Yurekli, Lisa Kronbichler, Vince Calhoun, Silvia Corbera, Morris Bell, Kevin Pelphrey, Godfrey Pearlson, Michal Assaf
Summary: Intrinsic neural timescales (INT) determine the duration of information storage in different brain areas. Previous studies have shown a hierarchy of INT from posterior to anterior regions in typically developed individuals (TD), as well as individuals with autism spectrum disorder (ASD) and schizophrenia (SZ), with shorter INT observed in both patient groups. This study aimed to replicate these group differences by comparing INT in TD, ASD, and SZ. The results partially replicated previous findings, showing reduced INT in the left lateral occipital gyrus and the right post-central gyrus in SZ compared to TD. Direct comparison between the patient groups also showed significantly reduced INT in SZ compared to ASD in these two areas. However, the previously reported correlations between INT and symptom severity were not replicated in this study. These findings help identify the brain areas that may play a crucial role in sensory peculiarities observed in ASD and SZ.
Article
Medicine, Research & Experimental
Allen J. Chang, Rebecca Roth, Eleni Bougioukli, Theodor Ruber, Simon S. Keller, Daniel L. Drane, Robert E. Gross, James Welsh, Anees Abrol, Vince Calhoun, Ioannis Karakis, Erik Kaestner, Bernd Weber, Carrie McDonald, Ezequiel Gleichgerrcht, Leonardo Bonilha
Summary: Chang et al. classified individuals with Temporal Lobe Epilepsy (TLE), Alzheimer's disease, and healthy controls using a convolutional neural network algorithm applied to magnetic resonance imaging (MRI) scans. They were able to distinguish people with TLE, including those without easily identifiable TLE-associated MRI features.
COMMUNICATIONS MEDICINE
(2023)