Article
Genetics & Heredity
Jill Rafalko, Erica Soster, Samantha Caldwell, Eyad Almasri, Thomas Westover, Vivian Weinblatt, Philip Cacheris
Summary: This study found that genome-wide cfDNA screening can detect chromosomal abnormalities beyond traditional screening, with an overall PPV of >70% for cases with subchromosomal CNVs. Isolated CNVs had a lower PPV of 61.0% compared to complex CNVs at 93.9%. Detected abnormalities included isolated deletions/duplications and unbalanced structural rearrangements.
GENETICS IN MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
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
Kiely N. James, Shimul Chowdhury, Yan Ding, Sergey Batalov, Kelly Watkins, Yong Hyun Kwon, Lucitia Van Der Kraan, Katarzyna Ellsworth, Stephen F. Kingsmore, Lucia Guidugli
Summary: This study used genome sequencing to detect a wide range of copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types. These genetic alterations accounted for 15.8% of reported variants, with deletions being the most common type. The study also found that additional genetic tests were ordered in some cases, but failed to report the variants detected by genome sequencing.
GENETICS IN MEDICINE
(2024)
Article
Genetics & Heredity
Md. Panir Choudhury, Zihao Wang, Min Zhu, Shaohua Teng, Jing Yan, Shuwei Cao, Guoqiang Yi, Yuwen Liu, Yuying Liao, Zhonglin Tang
Summary: This study conducted a comprehensive analysis of copy number variations (CNVs) in different horse breeds, and identified genomic regions associated with miniature features. Functional annotation revealed the biological functions and adaptations related to these CNVs.
Article
Genetics & Heredity
Feyza Yilmaz, Megan Null, David Astling, Hung-Chun Yu, Joanne Cole, Stephanie A. Santorico, Benedikt Hallgrimsson, Mange Manyama, Richard A. Spritz, Audrey E. Hendricks, Tamim H. Shaikh
Summary: This study conducted a genome-wide copy number analysis on over 3400 healthy Bantu Africans from Tanzania, identifying more than 400,000 CNVs. Some of the CNVs detected overlapped with genomic regions associated with congenital anomaly syndromes and developmental disorders.
BMC MEDICAL GENOMICS
(2021)
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
Genetics & Heredity
E. Guang-Xin, Dong-Ke Zhou, Zhu-Qing Zheng, Bai-Gao Yang, Xiang-Long Li, Lan-Hui Li, Rong-Yan Zhou, Wen-Hui Nai, Xun-Ping Jiang, Jia-Hua Zhang, Qiong-Hua Hong, Yue-Hui Ma, Ming-Xing Chu, Hui-Jiang Gao, Yong-Ju Zhao, Xing-Hai Duan, Yong-Meng He, Ri-Su Na, Yan-Guo Han, Yan Zeng, Yu Jiang, Yong-Fu Huang
Summary: The study used whole-genome next-generation sequencing technology to investigate the selective sweep of intersex goats from China, revealing candidate genes related to the intersexuality phenotype. It was confirmed that a duplicated fragment downstream of the PIS region was inserted into the PIS locus in intersex Chinese goats. The study suggested that this novel complex PIS variant genome could serve as a clinical diagnostic marker for XX intersexuality in goats from Europe and China.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Tejashree H. Modak, Robert Literman, Jonathan B. Puritz, Kevin M. Johnson, Erin M. Roberts, Dina Proestou, Ximing Guo, Marta Gomez-Chiarri, Rachel S. Schwartz
Summary: Genomic structural variations are widely observed in the eastern oyster, showing high interindividual variability and potential impacts on gene function; these variations may play a significant role in genetic diversity and evolutionary success.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Psychology, Biological
Jakub Kopal, Kuldeep Kumar, Karin Saltoun, Claudia Modenato, Clara A. Moreau, Sandra Martin-Brevet, Guillaume Huguet, Martineau Jean-Louis, Charles-Olivier Martin, Zohra Saci, Nadine Younis, Petra Tamer, Elise Douard, Anne M. Maillard, Borja Rodriguez-Herreros, Aurelie Pain, Sonia Richetin, Leila Kushan, Ana I. Silva, Marianne B. M. van den Bree, David E. J. Linden, Michael J. Owen, Jeremy Hall, Sarah Lippe, Bogdan Draganski, Ida E. Sonderby, Ole A. Andreassen, David C. Glahn, Paul M. Thompson, Carrie E. Bearden, Sebastien Jacquemont, Danilo Bzdok
Summary: The researchers built computational bridges between rare CNVs in a clinical dataset and their deep phenotypic profiling in a large population. The results showed that CNVs are associated with various organ systems across the body, with implications for major brain disorders.
NATURE HUMAN BEHAVIOUR
(2023)
Article
Oncology
Ruben Van Paemel, Charlotte Vandeputte, Lennart Raman, Jolien Van Thorre, Leen Willems, Jo Van Dorpe, Malaika Van der Linden, Jilke De Wilde, Andries De Koker, Bjorn Menten, Christine Devalck, Ales Vicha, Marek Grega, Gudrun Schleiermacher, Yasmine Iddir, Mathieu Chicard, Lieke van Zogchel, Janine Stutterheim, Nathalie S. M. Lak, G. A. M. Tytgat, Genevieve Laureys, Frank Speleman, Bram De Wilde, Tim Lammens, Katleen De Preter, Nadine Van Roy
Summary: There is a good agreement between DNA copy number alterations (CNAs) in tissue DNA and circulating cell-free DNA (cfDNA) obtained from liquid biopsies. The quality of cfDNA sample can affect the concordance between tissue DNA and cfDNA CNAs. Liquid biopsies can provide complementary analysis to tissue biopsies, as both cfDNA and tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Biochemical Research Methods
Joseph T. Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick M. A. Sleiman, Hakon Hakonarson, Zhi Wei
Summary: Copy number variations (CNVs) are important in disease pathogenesis, but detection and validation remain challenging. DeepCNV, a deep learning-based tool, improves CNV call accuracy and reduces false positives and failures in CNV-disease association results.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Linyong Hu, Liangzhi Zhang, Qi Li, Hongjin Liu, Tianwei Xu, Na Zhao, Xueping Han, Shixiao Xu, Xinquan Zhao, Cunfang Zhang
Summary: This study characterized copy number variations (CNVs) in Tibetan sheep using resequencing data and found a large number of CNVs that are associated with genetic structure, dosage regulation, and expression in the sheep genome. The shared CNV regions (CNVRs) were found to be significantly enriched in various pathways and GO terms related to transporters, sensory perception, and oxygen transport. Several CNVRs were also found to overlap with quantitative trait loci (QTLs) related to growth, body weight, and other traits. Vst analysis revealed significant divergence of certain genes between different ecotypic populations of Tibetan sheep. These findings provide valuable genetic variation resources for further elucidating the genetic basis of distinct phenotypic traits and local adaptation in Tibetan sheep.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Seongmin Hong, Yong Pyo Lim, Suk-Yoon Kwon, Ah-Young Shin, Yong-Min Kim
Summary: In polyploids, whole genome duplication plays a significant role in genome expansion, evolution, and diversification. The flowering-time gene family, one of the largest expanded gene families in plants, has functionally diversified through evolution, providing advantages for plant adaptation and survival.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu, Xiangyu Zhao, Wei Ning, Guangshuai Wang, Jinyu Wang, Jing Chen, Kaixuan Diao, Fuxiang Chen, Xue-Song Liu
Summary: This study developed a mechanism-agnostic method to categorize CNAs based on various fragment properties and revealed novel patterns of CNA. The activities of some CNA signatures consistently predicted cancer patients' prognosis. This study provides important insights into the role of CNA in cancer and its potential implications for cancer prognosis, evolution, and etiology.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Arkadiusz Piotrowski, Magdalena Koczkowska, Andrzej B. Poplawski, Rafal Bartoszewski, Jaroslaw Kroliczewski, Alina Mieczkowska, Alicia Gomes, Michael R. Crowley, David K. Crossman, Yunjia Chen, Ping Lao, Eduard Serra, Meritxell C. Llach, Elisabeth Castellanos, Ludwine M. Messiaen
Summary: Constitutional pathogenic variants in genes LZTR1 or SMARCB1 were identified in a high percentage of familial and sporadic schwannomatosis cases, with additional novel variants and potential predisposing candidate genes revealed through extensive sequencing.
Article
Biochemistry & Molecular Biology
Stylianos Bakoulis, Robert Krautz, Nicolas Alcaraz, Marco Salvatore, Robin Andersson
Summary: Transposable elements are an abundant source of transcription factor binding sites, and they regulate gene expression in specific cell types through their association with open chromatin regions. Different subfamilies of transposable elements contribute differently to pluripotency regulatory programs through their repertoires of transcription factor binding site sequences.
NUCLEIC ACIDS RESEARCH
(2022)
News Item
Biochemical Research Methods
Luiz Carlos Junior Alcantara, Lucas Amenga-Etego, Robin Andersson, Moumita Bhaumik, Young Ki Choi, Helene Decaluwe, Jemma Geoghegan, Bart L. Haagmans, Susana Lopez, Maowia M. Mukhtar, Erni Nelwan, Elias A. Rahal, Kei Sato, Ella H. Sklan, Yvonne Su Chuan Fang
Summary: The article gathers opinions from scientists around the globe regarding the necessary basic research methods, tools, and resources to combat future emerging pathogenic threats.
Article
Multidisciplinary Sciences
Natalia Filipowicz, Kinga Drezek, Monika Horbacz, Agata Wojdak, Jakub Szymanowski, Edyta Rychlicka-Buniowska, Ulana Juhas, Katarzyna Duzowska, Tomasz Nowikiewicz, Wiktoria Stankowska, Katarzyna Chojnowska, Maria Andreou, Urszula Lawrynowicz, Magdalena Wojcik, Hanna Davies, Ewa Srutek, Michal Bienkowski, Katarzyna Milian-Ciesielska, Marek Zdrenka, Aleksandra Ambicka, Marcin Przewoznik, Agnieszka Harazin-Lechowska, Agnieszka Adamczyk, Jacek Kowalski, Dariusz Bala, Dorian Wisniewski, Karol Tkaczynski, Krzysztof Kamecki, Marta Drzewiecka, Pawel Wronski, Jerzy Siekiera, Izabela Ratnicka, Jerzy Jankau, Karol Wierzba, Jaroslaw Skokowski, Karol Polom, Mikolaj Przydacz, Lukasz Belch, Piotr Chlosta, Marcin Matuszewski, Krzysztof Okon, Olga Rostkowska, Andrzej Hellmann, Karol Sasim, Piotr Remiszewski, Marek Sierzega, Stanislaw Hac, Jaroslaw Kobiela, Lukasz Kaska, Michal Jankowski, Diana Hodorowicz-Zaniewska, Janusz Jaszczynski, Wojciech Zegarski, Wojciech Makarewicz, Rafal Peksa, Joanna Szpor, Janusz Rys, Lukasz Szylberg, Arkadiusz Piotrowski, Jan P. Dumanski
Summary: The progress in translational cancer research relies on access to well-characterized samples from a representative number of patients and controls. Our biobanking focuses on exploring pathogenic gene variants that may predispose to cancer in non-tumoral tissue. The collection includes various types of cancer, with breast, colorectal, and prostate carcinoma being the most common diagnoses. Additionally, we have developed program packages to manage patient registration and clinical data, making our biobank a model for dispersed biobanking from multiple hospitals. This resource is important for understanding the genetic mechanisms underlying common cancers and can be utilized by other research groups.
Article
Microbiology
Kjell Rune Jonassen, Ida Ormasen, Clara Duffner, Torgeir R. Hvidsten, Lars R. Bakken, Silas H. W. Vick
Summary: By using a dual enrichment strategy, N2O-respiring bacteria (NRB) with broad catabolic capacity were successfully enriched and isolated from soil and digestates. These NRBs showed promising characteristics as N2O sinks and could effectively reduce N2O emissions from soil.
Review
Biochemistry & Molecular Biology
Judith Barbara Zaugg, Pelin Sahlen, Robin Andersson, Meritxell Alberich-Jorda, Wouter de Laat, Bart Deplancke, Jorge Ferrer, Susanne Mandrup, Gioacchino Natoli, Dariusz Plewczynski, Alvaro Rada-Iglesias, Salvatore Spicuglia
Summary: Enhancers are crucial for the spatiotemporal control of gene expression and are cell-type-specific. They are suggested to contribute to phenotypic variation, evolution, and disease. Dysfunction of enhancers, caused by genetic, structural, or epigenetic mechanisms, has been linked to a broad range of human diseases, known as enhanceropathies. Understanding how enhancer dysfunction affects gene expression remains a challenge.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biology
Hjoerleifur Einarsson, Marco Salvatore, Christian Vaagenso, Nicolas Alcaraz, Jette Bornholdt, Sarah Rennie, Eduardo Eyras, Robin Andersson
Summary: This study investigates the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. The results show that expression variability can be largely explained by a promoter's DNA sequence and its binding sites for specific transcription factors. Additionally, the study reveals a trade-off between stability and plasticity for different types of genes.
Article
Ecology
Thea O. Andersen, Ianina Altshuler, Arturo Vera-Ponce de Leon, Juline M. Walter, Emily McGovern, Kate Keogh, Cecile Martin, Laurence Bernard, Diego P. Morgavi, Tansol Park, Zongjun Li, Yu Jiang, Jeffrey L. Firkins, Zhongtang Yu, Torgeir R. Hvidsten, Sinead M. Waters, Milka Popova, Magnus o. Arntzen, Live H. Hagen, Phillip B. Pope
Summary: Protozoa, including entodiniomorphs and holotrichs, play a major role in the microbial biomass of the rumen microbiome. However, their specific biological and metabolic contributions to rumen function have not been well described. By using metaproteomics, this study reveals the specific metabolic niches occupied by protozoa in relation to their microbial co-habitants in the rumen fluid of cattle and goats fed varying diets.
Article
Biochemistry & Molecular Biology
Lucas van Duin, Robert Krautz, Sarah Rennie, Robin Andersson
Summary: This study investigates the regulatory determinants of gene co-activity in genomic domains using individual variation in gene expression. The researchers identify co-regulatory processes underlying co-activity and quantify their effect sizes. They find that transcription factor expression levels are the main determinant of gene co-activity, with distal trans effects contributing more than local genetic variation.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Chemistry, Analytical
Salvador Daniel Rivas-Carrillo, Evgeny E. E. Akkuratov, Hector Valdez Ruvalcaba, Angel Vargas-Sanchez, Jan Komorowski, Daniel San-Juan, Manfred G. G. Grabherr
Summary: Electroencephalogram (EEG) interpretation is crucial in assessing neurological conditions, especially epilepsy. Manual analysis of EEG recordings is time-consuming and expensive. Automatic detection, like MindReader, offers the potential to shorten diagnosis time and optimize resource allocation. MindReader utilizes an autoencoder network, hidden Markov model (HMM), and generative component to generate labels for pathological and non-pathological phases, reducing the search space for trained personnel. Evaluation on 686 recordings showed MindReader's high sensitivity in detecting epileptic events (99.45%).
Article
Geriatrics & Gerontology
Taoyu Mei, Yuan Li, Anna Orduna Dolado, Zhiquan Li, Robin Andersson, Laura Berliocchi, Lene Juel Rasmussen
Summary: The growing prevalence of Alzheimer's disease (AD) is a global health challenge without effective treatments. Defective mitochondrial function and mitophagy have been suggested as etiological factors in AD. This study integrated transcriptomic data from AD and healthy patients to identify mitophagy-related genes and validate their expression changes in AD-relevant human in vitro models.
FRONTIERS IN AGING NEUROSCIENCE
(2023)
Article
Oncology
Cecilia Arthur, Cecilia Jylha, Teresita Diaz de Stahl, Alia Shamikh, Johanna Sandgren, Richard Rosenquist, Magnus Nordenskjold, Arja Harila, Gisela Barbany, Ulrika Sandvik, Emma Tham
Summary: Researchers have developed a laboratory test based on the genetic makeup of medulloblastomas to detect molecular traces of the disease in liquid biopsies from 12 children. The test found molecular traces of the disease in 75% of the children. This test could open up new technical possibilities for tracking measurable residual disease in children with medulloblastoma, but further studies are needed.
Article
Clinical Neurology
Malin Dorvall, Annie Pedersen, Jan P. Dumanski, Martin Soderholm, Arne G. Lindgren, Tara M. Stanne, Christina Jern
Summary: This study found an association between mosaic loss of chromosome Y (LOY) in male patients and poor outcome after ischemic stroke, which remained significant in patients not receiving recanalization therapy. Further studies on LOY and other somatic genetic alterations in larger stroke cohorts are needed.
Article
Genetics & Heredity
Marco Salvatore, Marc Horlacher, Annalisa Marsico, Ole Winther, Robin Andersson
Summary: Dysfunction of regulatory elements through genetic variants is a central mechanism in disease pathogenesis. Deep learning methods have shown promise in modeling biomolecular data from DNA sequence but require large input data for training. ChromTransfer, a transfer learning method, utilizes a pre-trained model of open chromatin regions to fine-tune on regulatory sequences and demonstrates superior performance in learning cell-type specific chromatin accessibility. It is able to fine-tune on small input data with minimal decrease in accuracy and utilizes sequence features matching binding site sequences of key transcription factors for prediction, making it a promising tool for learning the regulatory code.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Article
Cell Biology
Klev Diamanti, Marco Cavalli, Maria J. Pereira, Gang Pan, Casimiro Castillejo-Lopez, Chanchal Kumar, Filip Mundt, Jan Komorowski, Atul S. Deshmukh, Matthias Mann, Olle Korsgren, Jan W. Eriksson, Claes Wadelius
Summary: Environmental and genetic factors contribute to defects in pancreatic islets and insulin resistance in type 2 diabetes (T2D). Through proteomic analysis of multiple metabolic tissues, we identified tissue-specific metabolic dysregulations in T2D, including inflammatory, immune, and vascular alterations.
CELL REPORTS MEDICINE
(2022)