Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biology
Mustafa Topu, Ugur Sesiz, Harun Bektas, Faruk Toklu, Hakan Ozkan
Summary: In this study, novel SSR markers were identified using next-generation sequencing approach, providing a ready-to-use SSR library for genetic diversity studies and breeding. The effectiveness of the obtained SSR markers in a recombinant inbred line (RIL) population was evaluated.
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemical Research Methods
Timo Lassmann
Summary: SAMStat is an efficient program for extracting quality control metrics from fastq and SAM/BAM files. It displays sequence composition, base quality composition, and mapping error profiles based on mapping quality, allowing users to quickly identify reasons for poor mapping. A major update to SAMStat now supports paired-end and long-read data, with quality control plots drawn using the ploty javascript library.
Review
Medicine, General & Internal
Andrew D. King, Hany Deirawan, Paytra A. Klein, Bahar Dasgeb, Catherine I. Dumur, Darius R. Mehregan
Summary: Over the past decade, Next-Generation Sequencing (NGS) has greatly contributed to the diagnosis and management of various dermatological conditions, including genetic diseases of the skin, cutaneous squamous cell carcinoma, melanoma, and cutaneous T-cell lymphoma.
FRONTIERS IN MEDICINE
(2023)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Review
Genetics & Heredity
Ziga I. Remec, Katarina Trebusak Podkrajsek, Barbka Repic Lampret, Jernej Kovac, Urh Groselj, Tine Tesovnik, Tadej Battelino, Marusa Debeljak
Summary: Newborn screening was introduced in the 1960s, and has expanded over time with the advancement of technology, particularly high-throughput sequencing. Genomic sequencing is now widely used in clinical applications, including newborn screening, but has also raised various concerns and challenges.
FRONTIERS IN GENETICS
(2021)
Review
Biotechnology & Applied Microbiology
Chu Cheng, Zhongjie Fei, Pengfeng Xiao
Summary: Next-generation sequencing (NGS) is widely used in life science research and clinical diagnosis. However, its high error rate poses challenges for detecting SNPs and low-abundance mutations, limiting its clinical applications. Sanger sequencing is still considered the gold standard and is used to verify the results of NGS in practice. Improvements have been made in template preparation, sequencing strategy, and data processing to ensure high-quality NGS data. Challenges and future development of NGS in clinical application are also discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Article
Immunology
Xiao-guang Cao, Shu-sheng Zhou, Chun-yan Wang, Kui Jin, Hua-dong Meng
Summary: This study demonstrates that NGS is accurate and efficient in diagnosing sepsis, and the combination of NGS and ALB for early screening is more effective. NGS and ALB are identified as independent prediction factors for sepsis, with the combined diagnostic approach being more accurate.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Review
Cell Biology
Tamer Butto, Kanak Mungikar, Peter Baumann, Jennifer Winter, Beat Lutz, Susanne Gerber
Summary: In the last decade, there has been a significant increase in nuclei-based studies, especially in combination with next-generation sequencing. These studies aim to understand the molecular states in heterogeneous cell populations using more affordable sequencing approaches and optimized nuclei isolation methods. While these powerful new methods offer unprecedented insights, it is important to consider the associated challenges critically. This article provides a comprehensive overview of the rise of nuclei-based studies and discusses their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improving experimental designs and using various strategies appropriately will lead to biologically accurate and meaningful information.
Review
Biology
Calin Cainap, Ovidiu Balacescu, Simona Sorana Cainap, Laura-Ancuta Pop
Summary: Lung cancer remains one of the most commonly diagnosed and deadly cancers in the world. Early diagnosis is crucial for improving the standard of care. Next generation sequencing has been proven as a helpful tool in early cancer detection, including lung cancer, due to its advantages of low cost, speed, efficacy, low sample usage, and diversity.
Article
Plant Sciences
Beat Boller, Manuel K. Schneider, Cheng Zhao, Jan Bartos, Joanna Majka, David Kopecky
Summary: The occurrence and distribution of Festuca apennina, F. pratensis, and their hybrid were studied in the Swiss Alps. The hybrid showed higher frequency and dominance compared to the parental species, and had a wider elevational distribution. The parental species showed preferences for different environmental conditions, with F. apennina preferring wet and nutrient-rich environments, while F. pratensis colonized dryer and nutrient-poorer environments. The hybrid showed an ability to thrive in both environments, possibly due to its strong expansion by rhizomes.
Article
Plant Sciences
Joanna Majka, Marek Glombik, Alzbeta Dolezalova, Jana Knerova, Marco Tulio Mendes Ferreira, Zbigniew Zwierzykowski, Martin Duchoslav, Bruno Studer, Jaroslav Dolezel, Jan Bartos, David Kopecky
Summary: We analyzed the chromosome composition of interspecific plant hybrids and found that the transmission of parental genomes varied in male and female meiosis. Festuca chromosomes were replaced by Lolium counterparts in female meiosis, while in male meiosis, Festuca chromosomes showed improper attachment and were gradually eliminated. The difference in behavior may be attributed to non-synonymous mutations and the exclusive expression of kinetochore proteins from the Lolium allele.
Article
Multidisciplinary Sciences
Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia Fechete, Deepti Angra, Petr Bednar, Elesandro Bornhofen, Hailin Zhang, Raphael Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Cizkova, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnere, Andrea Koblizkova, Lucie Kobrlova, Petra Krejci, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kaergaard Nielsen, Petr Novak, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Avila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Toronen, Ahmed O. Warsame, Alexander H. J. Wittenberg, Axel Himmelbach, Gregoire Aubert, Pierre-Emmanuel Courty, Jaroslav Dolezel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiri Macas, Martin Mascher, Petr Smykal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Jens Stougaard, Nadim Tayeh, Ana M. Torres, Bjorn Usadel, Ingo Schubert, Donal Martin O'Sullivan, Alan H. Schulman, Stig Uggerhoj Andersen
Summary: Increasing the proportion of locally produced plant protein in diets could reduce greenhouse gas emissions and loss of biodiversity. However, plant protein production is hindered by the lack of a cool-season legume equivalent to soybean. This study presents a high-quality genome assembly of faba bean and demonstrates its potential for sustainable protein production.
Article
Biochemistry & Molecular Biology
Ivona Kubalova, Amanda Souza Camara, Petr Capal, Tomas Beseda, Jean-Marie Rouillard, Gina Marie Krause, Katerina Holusova, Helena Toegelova, Axel Himmelbach, Nils Stein, Andreas Houben, Jaroslav Dolezel, Martin Mascher, Hana Simkova, Veit Schubert
Summary: Hi-C analysis, biopolymer modeling, and structured illumination microscopy were used to reveal the chromonema, a helically-wound chromatin thread forming barley mitotic chromatids. The helical turn size varies along the chromosome length and intermingles chromatin from adjacent turns. The observable dimensions of sister chromatid exchanges further support the helical chromonema model.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yongyu Huang, Roop Kamal, Nandhakumar Shanmugaraj, Twan Rutten, Venkatasubbu Thirulogachandar, Shuangshuang Zhao, Iris Hoffie, Goetz Hensel, Jeyaraman Rajaraman, Yudelsy Antonia Tandron Moya, Mohammad-Reza Hajirezaei, Axel Himmelbach, Naser Poursarebani, Udda Lundqvist, Jochen Kumlehn, Nils Stein, Nicolaus von Wiren, Martin Mascher, Michael Melzer, Thorsten Schnurbusch
Summary: Flowering plants with indeterminate inflorescences often produce more floral structures than necessary. In barley (Hordeum vulgare L.), the initiation and maturation of floral primordia are molecularly decoupled. Initiation is primarily controlled by flowering-time genes, while floral growth is regulated by barley CCT MOTIF FAMILY 4 (HvCMF4) through light signaling, chloroplast, and vascular developmental programs. Mutations in HvCMF4 result in increased primordia death and pollination failure due to reduced rachis greening and limited energy supply to floral tissues. HvCMF4 is proposed to be a light sensory factor that coordinates floral initiation and survival with the vascular-localized circadian clock. Notably, stacking beneficial alleles for primordia number and survival has positive implications for grain production. These findings offer insights into the molecular mechanisms of grain number determination in cereal crops.
Biographical-Item
Biotechnology & Applied Microbiology
Rajeev K. K. Varshney, Nils Stein, Jochen Reif
Summary: Professor Graner has made significant contributions to the field of international crop plant genomics research over the past four decades. His work includes the development of the first integrated RFLP map of barley and advancements in functional genomics. He has also played a key role in plant genetic resources conservation and utilization.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Louis McLeod, Lorenzo Barchi, Giorgio Tumino, Pasquale Tripodi, Jeremy Salinier, Christophe Gros, Hatice Filiz Boyaci, Ramazan Ozalp, Yelena Borovsky, Roland Schafleitner, Derek Barchenger, Richard Finkers, Matthijs Brouwer, Nils Stein, Mark Timothy Rabanus-Wallace, Giovanni Giuliano, Roeland Voorrips, Ilan Paran, Veronique Lefebvre
Summary: Investigating crop diversity through GWAS on core collections helps in deciphering the genetic determinants of complex traits. The G2P-SOL project conducted multi-environment GWAS on a diverse subset of Capsicum annuum accessions and detected environment-specific and multi-environment QTLs for various agronomic traits. This study identified candidate genes potentially implicated in fruit flavor, color, size, shape, plant productivity, vigor, and earliness traits.
Article
Plant Sciences
Lorenzo Barchi, Giuseppe Aprea, M. Timothy Rabanus-Wallace, Laura Toppino, David Alonso, Ezio Portis, Sergio Lanteri, Luciana Gaccione, Emmanuel Omondi, Maarten van Zonneveld, Roland Schafleitner, Paola Ferrante, Andreas Boerner, Nils Stein, Maria Jose Diez, Veronique Lefebvre, Jeremy Salinier, Hatice Filiz Boyaci, Richard Finkers, Matthijs Brouwer, Arnaud G. Bovy, Giuseppe Leonardo Rotino, Jaime Prohens, Giovanni Giuliano
Summary: Eggplant is an important crop widely grown and consumed in Asia, the Mediterranean basin, and Southeast Europe. This study reports the largest collection of georeferenced and genotyped eggplant and its wild relatives to date, providing insights into its domestication centers and migration patterns. The data indicates the existence of at least two main domestication centers in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The study also highlights the preservation of "local" phenotypic characteristics in eggplant populations.
Article
Agronomy
Ronja Wonneberger, Miriam Schreiber, Allison Haaning, Gary J. Muehlbauer, Robbie Waugh, Nils Stein
Summary: Plant breeding and selection have greatly improved agronomic and quality traits of modern crops. In this study, the genetic composition of barley cultivars from the past 190 years was characterized using SNP marker data. A distinct centromeric haplotype on chromosome 5H, introduced in the early to mid-twentieth century, has been under positive selection and non-recombining for the past 70 years. This haplotype carries genes conferring highly beneficial traits and is found in modern European barley germplasm and may have been introduced from North African landraces.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Agronomy
M. Timothy Rabanus-Wallace, Nils Stein
Summary: Accurate and complete taxonomic assignments are crucial for maximizing the benefits of genebank resources. Genebank genomics provides a potential solution by using genetic methods, but since the number of samples is too large, automation is necessary. A recent study on peppers sequenced over 10,000 genebank accessions and presented an opportunity to develop automated taxonomic correction methods.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Shameem Younuskunju, Yasmin A. Mohamoud, Lisa S. Mathew, Klaus F. X. Mayer, Karsten Suhre, Joel A. Malek
Summary: Date palm is an economically and culturally significant crop in the Middle East and North Africa. This study identified genetic loci associated with the color of dry dates using genome sequences and image data.
Article
Plant Sciences
Samira El Hanafi, Yong Jiang, Zakaria Kehel, Albert W. Schulthess, Yusheng Zhao, Martin Mascher, Max Haupt, Axel Himmelbach, Nils Stein, Ahmed Amri, Jochen C. Reif
Summary: Genome-wide prediction is a powerful tool in breeding and shows promise for enhancing the use of genebank material. By predicting the performance of plant genetic resources, the hidden potential and information gap in genebanks can be addressed, supporting prebreeding programs. Across-genebank predictions using different genebanks as training and test sets can significantly improve the predictive characterization of germplasm collections.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Patrick Koenig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Summary: DivBrowse is a web application that allows interactive visualization and exploratory analysis of genomic diversity data stored in VCF files. It combines BLAST as an entry point with features like principal component analysis, providing a unique set of capabilities for studying genomic biodiversity datasets. The application also supports data interoperability and integration with existing web applications.
Correction
Biology
Patrick Konig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Article
Agronomy
Caiyun Liu, Wei Guo, Yang Wang, Bisheng Fu, Jaroslav Dolezel, Ying Liu, Wenling Zhai, Mahmoud Said, Istvan Molnar, Katerina Holusova, Ruiqi Zhang, Jizhong Wu
Summary: This study identified a new wheat-Dasypyrum villosum translocation line that exhibits stable resistance to wheat sharp eyespot. The introgression of this translocation line into wheat cultivars significantly enhanced their resistance. Through sequencing and marker development, the translocated chromosome can be traced and detected. These findings provide novel germplasm and technological tools for wheat breeding.