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
Biotechnology & Applied Microbiology
Sadaf Riaz, Meng Xiao, Pengyu Chen, Meijin Li, Yixuan Cui, Maurycy Daroch
Summary: The study highlighted the regulation of genome copy number (ploidy) status in the thermophilic cyanobacterium Thermosynechococcus E542 by growth phase and environmental factors, shedding light on the role of polyploidy. Increased ploidy level is associated with higher metabolic activity and vigor, serving as backup genetic information. Several improved ploidy estimation approaches for cyanobacteria were presented, including a new rapid and accurate spectrofluorometric method.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Oncology
Henry de Traux de Wardin, Josephine K. Dermawan, Marie-Sophie Merlin, Leonard H. Wexler, Daniel Orbach, Fabio Vanoli, Gudrun Schleiermacher, Birgit Geoerger, Stelly Ballet, Delphine Guillemot, Eleonore Frouin, Stacy Cyrille, Olivier Delattre, Gaelle Pierron, Cristina R. Antonescu
Summary: This study explores the genomic spectrum of progression in rhabdomyosarcoma (RMS) and evaluates the best genomic approach using liquid biopsy. The results show that FP-RMS have a stable genome, while FN-RMS acquire more new alterations.
NPJ PRECISION ONCOLOGY
(2023)
Article
Biochemical Research Methods
Fei Qin, Xizhi Luo, Guoshuai Cai, Feifei Xiao
Summary: This study explores the correlation structure of whole-exome sequencing (WES) data and introduces a novel correlation-based CNV detection method, CORRseq, which outperforms existing methods in detecting medium and large CNVs. Modeling genomic correlation structure is advantageous for detecting relatively long CNVs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Cody Ashby, Eileen M. Boyle, Michael A. Bauer, Aneta Mikulasova, Christopher P. Wardell, Louis Williams, Ariel Siegel, Patrick Blaney, Marc Braunstein, David Kaminetsky, Jonathan Keats, Francesco Maura, Ola Landgren, Brian A. Walker, Faith E. Davies, Gareth J. Morgan
Summary: Deciphering genomic architecture helps identify disease drivers and understand myeloma initiation and progression mechanisms. This study demonstrates that structural variants occur nonrandomly in the genome, and their frequencies vary in different genetic contexts. The study also reveals the heterogeneity of transcriptional dysregulation caused by both canonical and novel structural variants, as well as the impact of complex rearrangements on clinical outcomes. Chromothripsis, in particular, has a significant negative effect on clinical outcome.
BLOOD CANCER JOURNAL
(2022)
Review
Biochemical Research Methods
Mian Umair Ahsan, Qian Liu, Jonathan Elliot Perdomo, Li Fang, Kai Wang
Summary: As long-read sequencing technologies become more popular, various methods have been developed for detecting and analyzing structural variants (SVs) from long reads. These methods are needed to adapt to the unique challenges and opportunities presented by long-read sequencing. This review summarizes more than 50 long-read-based methods for SV detection, genotyping, and visualization, and discusses how new telomere-to-telomere genome assemblies and pangenome efforts can enhance accuracy and drive the development of SV callers in the future.
Article
Oncology
Samuel Terkper Ahuno, Anna-Lisa Doebley, Thomas U. Ahearn, Joel Yarney, Nicholas Titiloye, Nancy Hamel, Ernest Adjei, Joe-Nat Clegg-Lamptey, Lawrence Edusei, Baffour Awuah, Xiaoyu Song, Verna Vanderpuye, Mustapha Abubakar, Maire Duggan, Daniel G. Stover, Kofi Nyarko, John M. S. Bartlett, Francis Aitpillah, Daniel Ansong, Kevin L. Gardner, Felix Andy Boateng, Anne M. Bowcock, Carlos Caldas, William D. Foulkes, Seth Wiafe, Beatrice Wiafe-Addai, Montserrat Garcia-Closas, Alexander Kwarteng, Gavin Ha, Jonine D. Figueroa, Paz Polak
Summary: ctDNA sequencing studies conducted on patients in sub-Saharan Africa revealed the detection of ctDNA in a majority of patients, despite not being selected for tumor grade and subtype. Additionally, breast cancer driver copy number alterations were observed in the majority of patients.
NPJ PRECISION ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Shukmei Wong, E. J. Ehrhart, Samuel Stewart, Victoria Zismann, Jacob Cawley, Rebecca Halperin, Natalia Briones, Keith Richter, Karthigayini Sivaprakasam, Nieves Perdigones, Tania Contente-Cuomo, Salvatore Facista, Jeffrey M. Trent, Muhammed Murtaza, Chand Khanna, William P. D. Hendricks
Summary: Cancer genomic heterogeneity is a significant challenge in understanding cancer processes and clinical management. The study of canine splenic hemangiosarcoma revealed both intertumoral and intratumoral genomic heterogeneity. This research provides valuable insights into the origin and clinical impact of cancer heterogeneity.
Article
Genetics & Heredity
Heming Wu, Qingyan Huang, Xia Zhang, Zhikang Yu, Zhixiong Zhong
Summary: This study identified a high rate of chromosomal abnormalities in fetuses with miscarriage during early and middle pregnancy, with a significantly higher numerical chromosomal abnormality rate in pregnant women aged >=35 compared to <35. The early fetal chromosomal abnormality rate was higher than the middle fetal rate, and there were 168 genes enriched in the VOUS + pCNV regions, associated with 41 functions and 12 pathways.
FRONTIERS IN GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Shaolong Cao, Jennifer R. Wang, Shuangxi Ji, Peng Yang, Yaoyi Dai, Shuai Guo, Matthew D. Montierth, John Paul Shen, Xiao Zhao, Jingxiao Chen, Jaewon James Lee, Paola A. Guerrero, Nicholas Spetsieris, Nikolai Engedal, Sinja Taavitsainen, Kaixian Yu, Julie Livingstone, Vinayak Bhandari, Shawna M. Hubert, Najat C. Daw, P. Andrew Futreal, Eleni Efstathiou, Bora Lim, Andrea Viale, Jianjun Zhang, Matti Nykter, Bogdan A. Czerniak, Powel H. Brown, Charles Swanton, Pavlos Msaouel, Anirban Maitra, Scott Kopetz, Peter Campbell, Terence P. Speed, Paul C. Boutros, Hongtu Zhu, Alfonso Urbanucci, Jonas Demeulemeester, Peter Van Loo, Wenyi Wang
Summary: This study presents a method to quantify tumor-specific total mRNA expression from bulk sequencing data and validates it in various cancer types. High total mRNA expression is associated with increased risk of disease progression and death. The expression is influenced by cancer-specific gene alteration, intra-tumor genetic heterogeneity, and pan-cancer trends in metabolic dysregulation.
NATURE BIOTECHNOLOGY
(2022)
Article
Marine & Freshwater Biology
Kyoko Yarimizu, Sirje Sildever, Yoko Hamamoto, Satoshi Tazawa, Hiroshi Oikawa, Haruo Yamaguchi, Leila Basti, Jorge I. Mardones, Javier Paredes-Mella, Satoshi Nagai
Summary: The study successfully quantified the copy numbers of rRNA genes per single cell in 16 phytoplankton species using dPCR technology, utilizing a newly developed universal primer set. Chelex buffer was found suitable for DNA extraction to avoid underestimation of the gene copy numbers.
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
Cell Biology
Miao-Zhen Qiu, Qingjian Chen, Dan-Yang Zheng, Qi Zhao, Qi-Nian Wu, Zhi-Wei Zhou, Li-Qiong Yang, Qiu-Yun Luo, Yu-Ting Sun, Ming-Yu Lai, Sha-Sha Yuan, Feng-Hua Wang, Hui-Yan Luo, Feng Wang, Yu-Hong Li, Hui-Zhong Zhang, Rui-Hua Xu
Summary: Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a heterogeneous tumor composed of adenocarcinoma and neuroendocrine carcinoma. Whole-exome and multi-regional sequencing revealed that MANEC has four significantly mutated genes and shares similarities with chromosomal instability stomach adenocarcinoma. MANEC tumors are of monoclonal origin and the neuroendocrine carcinoma components exhibit more aggressive genomic properties. The phylogenetic trees demonstrate different patterns of tumor divergence, and immunohistochemistry confirms the transition from adenocarcinoma to neuroendocrine carcinoma in MANEC.
Article
Genetics & Heredity
Esther H. Lips, Tapsi Kumar, Anargyros Megalios, Lindy L. Visser, Michael Sheinman, Angelo Fortunato, Vandna Shah, Marlous Hoogstraat, Emi Sei, Diego Mallo, Maria Roman-Escorza, Ahmed A. Ahmed, Mingchu Xu, Alexandra W. Van den Belt-Dusebout, Wim Brugman, Anna K. Casasent, Karen Clements, Helen R. Davies, Liping Fu, Anita Grigoriadis, Timothy M. Hardman, Lorraine M. King, Marielle Krete, Petra Kristel, Michiel de Maaker, Carlo C. Maley, Jeffrey R. Marks, Brian A. Menegaz, Lennart Mulder, Frank Nieboer, Salpie Nowinski, Sarah Pinder, Jelmar Quist, Carolina Salinas-Souza, Michael Schaapveld, Marjanka K. Schmidt, Abeer M. Shaaban, Rana Shami, Mathini Sridharan, John Zhang, Hilary Stobart, Deborah Collyar, Serena Nik-Zainal, Lodewyk F. A. Wessels, E. Shelley Hwang, Nicholas E. Navin, P. Andrew Futreal, Alastair M. Thompson, Jelle Wesseling, Elinor J. Sawyer
Summary: A genomic analysis of ductal carcinoma in situ (DCIS) samples reveals that a significant portion of invasive breast cancer recurrences are unrelated to the initial DCIS and have distinct clonal origins. This finding is crucial for accurately assessing the risk of DCIS, developing effective treatment strategies, and identifying predictive biomarkers.
Article
Biochemical Research Methods
Chunyan Niu, Xia Wang, Yongzhuo Zhang, Lin Lu, Di Wang, Yunhua Gao, Shangjun Wang, Jingyan Luo, Ying Jiang, Nuo Wang, Yong Guo, Lingxiang Zhu, Lianhua Dong
Summary: The COVID-19 pandemic has caused serious harm to global health. RT-dPCR has shown good consistency and comparability in quantifying SARS-CoV-2 RNA, demonstrating its potential for virus detection and testing capabilities in participating laboratories.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Piping Han, Shunsuke Watanabe, Hiroshi Shimada, Atsushi Sakamoto
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Plant Sciences
Florian A. Busch, Jun Tominaga, Masato Muroya, Norihiko Shirakami, Shunichi Takahashi, Wataru Yamori, Takuya Kitaoka, Sara E. Milward, Kohji Nishimura, Erika Matsunami, Yosuke Toda, Chikako Higuchi, Atsuko Muranaka, Tsuneaki Takami, Shunsuke Watanabe, Toshinori Kinoshita, Wataru Sakamoto, Atsushi Sakamoto, Hiroshi Shimada
Article
Biochemistry & Molecular Biology
Kaoru Okamoto Yoshiyama, Naoki Aoshima, Naoki Takahashi, Tomoaki Sakamoto, Kei Hiruma, Yusuke Saijo, Jun Hidema, Masaaki Umeda, Seisuke Kimuraz
PLANT MOLECULAR BIOLOGY
(2020)
Article
Cell Biology
Tomokazu Kurita, Keishi Moroi, Masako Iwai, Kumiko Okazaki, Shinsuke Shimizu, Seiji Nomura, Fumihiko Saito, Shinichiro Maeda, Akihide Takami, Atsushi Sakamoto, Hiroyuki Ohta, Tetsushi Sakuma, Takashi Yamamoto
Review
Plant Sciences
Akie Shimotohno, Shiori S. Aki, Naoki Takahashi, Masaaki Umeda
Summary: This review highlights the importance of plant cell cycle regulation by phytohormones and environmental signals, analyzing their mechanisms of action and focusing on stress-induced G2 arrest. It also discusses the contribution of the transition from the mitotic cycle to the endocycle to plant organ growth.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021
(2021)
Article
Plant Sciences
Xiao Long Zhang, Qi Wu, Ye Tao, Xiao Fang Zhu, Naoki Takahashi, Masaaki Umeda, Ren Fang Shen, Jian Feng Ma
Summary: This study reveals the role of ANAC044-regulated cell wall phosphorus remobilization through ethylene signaling under phosphorus deficiency, leading to an increase in available phosphorus content in plant roots and shoots.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Plant Sciences
Noriko Inada, Naoki Takahashi, Masaaki Umeda
Summary: The study found that specific genes in Arabidopsis thaliana can act as novel regulators of endoreplication, significantly affecting leaf area and ploidy level in cells.
JOURNAL OF PLANT RESEARCH
(2021)
Article
Multidisciplinary Sciences
Naoki Takahashi, Soichi Inagaki, Kohei Nishimura, Hitoshi Sakakibara, Ioanna Antoniadi, Michal Karady, Karin Ljung, Masaaki Umeda
Summary: Plants regulate the balance between stress response and organ growth by spatially coordinating differential DNA damage responses through hormone signaling, which helps maintain genome integrity and minimize cell death for continuous root growth.
Article
Plant Sciences
Xiaojuan Zhang, Mika Nomoto, Marta Garcia-Leon, Naoki Takahashi, Mariko Kato, Kei Yura, Masaaki Umeda, Vicente Rubio, Yasuomi Tada, Tsuyoshi Furumoto, Takashi Aoyama, Tomohiko Tsuge
Summary: This study found that the plant CFI 25 subunit plays an important role in maintaining the diversity of mRNA 3' ends. Multiple forms of CFI exist in plants, and AtCFI 25a is essential for maintaining the proper diversity of 3' end lengths of transcripts coding for CFI subunits and plays important roles in Arabidopsis development.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Tomokazu Kurita, Masako Iwai, Keishi Moroi, Kumiko Okazaki, Seiji Nomura, Fumihiko Saito, Shinichiro Maeda, Akihide Takami, Atsushi Sakamoto, Hiroyuki Ohta, Tetsushi Sakuma, Takashi Yamamoto
Summary: Algal lipids, produced through photosynthesis and carbon dioxide assimilation, are expected to be the basis for sustainable fuels. However, the use of genetically modified organisms (GMOs) in outdoor culture is restricted. Recent research has discovered that plasmids containing yeast centromere and autonomous replication sequence can behave as episomes in Nannochloropsis species. This study aims to develop a genome editing system that allows the removal of expression vectors after introducing mutations, thereby creating mutated Nannochloropsis without any transgenes.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Takeshi Obayashi, Himiko Hibara, Yuki Kagaya, Yuichi Aoki, Kengo Kinoshita
Summary: ATTED-II is a gene coexpression database for nine plant species based on publicly available RNAseq and microarray data. It adopts a coexpression calculation methodology to balance the samples and provides efficient tools for interspecies comparison and analysis of heterogeneous data.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Naoki Takahashi, Masaaki Umeda
Summary: Compared with other organisms, plants possess an extraordinary self-repair capacity. The study reveals that the signaling mediated by plant steroid hormones brassinosteroids is activated during the regeneration of stem cell niche in plants, facilitating efficient tissue regeneration.
PLANT BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Takeshi Obayashi, Shun Kodate, Himiko Hibara, Yuki Kagaya, Kengo Kinoshita
Summary: Gene coexpression refers to the synchronization of gene expression across multiple conditions and is used to infer gene function. COXPRESdb is an animal gene expression database that provides coexpression data and analysis tools. The latest version, COXPRESdb version 8, introduces new features for overview, summary, and examination of coexpression relationships, as well as bridging coexpression and existing knowledge. It also supports interspecies comparisons by integrating different types of coexpression data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yuto Oogo, Miho Takemura, Atsushi Sakamoto, Norihiko Misawa, Hiroshi Shimada
Summary: Orange protein (OR) plays an important regulatory role on phytoene synthase (PSY) in carotenoid biosynthesis. The study reveals the enzymatic characteristics of OR, showing that the N-terminal region of AtOR is important for substrate affinity and catalytic efficiency of protein disulfide reductase (PDR) activity. Moreover, the presence of the N-terminal region and the zinc finger motif in AtOR increases the activity of PSY under reduced circumstances.
PLANT SIGNALING & BEHAVIOR
(2022)
Article
Biochemistry & Molecular Biology
Jun Tominaga, Shunichi Takahashi, Atsushi Sakamoto, Hiroshi Shimada
PLANT SIGNALING & BEHAVIOR
(2020)