Article
Biochemistry & Molecular Biology
Gelana Khazeeva, Karolis Sablauskas, Bart van der Sanden, Wouter Steyaert, Michael Kwint, Dmitrijs Rots, Max Hinne, Marcel van Gerven, Helger Yntema, Lisenka Vissers, Christian Gilissen
Summary: DeNovoCNN is a new method that utilizes deep convolutional neural network to accurately identify De novo mutations in genetic disorders. Trained on a large dataset, DeNovoCNN excels in recall and precision, outperforming existing methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jing Liu, Qingmiao Shen, Haigang Bao
Summary: This study compared the performance of seven SNP calling pipelines in chicken NGS data. The results showed that, for SNP detection only, the sequencing depth did not need to exceed 20X. When selecting the best SNP calling pipeline, Bcftools-multiple was found to be the most suitable for a single sample or sequencing depth greater than 20X, while 16GT was recommended for lower depths. These findings provide a reference for researchers to obtain SNPs from NGS data of chickens or nonhuman animals.
Article
Biochemical Research Methods
Rasmus Amund Henriksen, Lei Zhao, Thorfinn Sand Korneliussen
Summary: This article presents a multithreaded simulator for next-generation sequencing data, which can simulate reads faster than currently available methods and programs. It can simulate reads with platform-specific characteristics based on nucleotide quality score profiles and includes a post-mortem damage model for simulating ancient DNA. The program is implemented in a multithreading framework and is significantly faster than currently available tools, while also offering additional features and output formats.
Article
Biology
Jesse Farek, Daniel Hughes, William Salerno, Yiming Zhu, Aishwarya Pisupati, Adam Mansfield, Olga Krasheninina, Adam C. English, Ginger Metcalf, Eric Boerwinkle, Donna M. Muzny, Richard Gibbs, Ziad Khan, Fritz J. Sedlazeck
Summary: xAtlas is a fast, lightweight, and accurate method for calling SNVs and small indels, with rapid runtimes, support for various file formats, and retraining capabilities.
Review
Oncology
Y. R. Im, D. W. Y. Tsui, L. A. Diaz, J. C. M. Wan
Summary: This study discusses the opportunities and challenges arising from increasingly complex cancer liquid biopsy data, how to analyze analog signals using machine learning, and the acceptance that these cancer signals do not necessarily come from the tumor itself.
Article
Biochemical Research Methods
Mihai Lefter, Jonathan K. Vis, Martijn Vermaat, Johan T. den Dunnen, Peter E. M. Taschner, Jeroen F. J. Laros
Summary: The Human Genome Variation Society provides guidelines on accurately describing genetic variants, with the Mutalyzer tool suite being able to automatically apply these guidelines for users to check and correct their descriptions. Mutalyzer has successfully processed over 133 million descriptions, with around 50% being reported as correct and able to automatically correct descriptions for approximately 7% of cases.
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Editorial Material
Oncology
Jun Li, Hu Chen, Yumeng Wang, Mei-Ju May Chen, Han Liang
Summary: DrBioRight, a natural language-oriented and artificial intelligence-driven analytics platform, allows the research community to analyze omics data in an intuitive, efficient, transparent, and collaborative manner. The emerging next-generation analytics will maximize the utility of omics data and lead to a new paradigm for biomedical research.
Review
Chemistry, Physical
Bauer L. LeSavage, Riley A. Suhar, Nicolas Broguiere, Matthias P. Lutolf, Sarah C. Heilshorn
Summary: The translation discusses how organotypic models of patient-specific tumors are changing our understanding of cancer heterogeneity and personalized medicine. These models can preserve genetic, proteomic, morphological, and pharmacotypic features of the parent tumor in vitro, and offer genomic and environmental manipulation. However, current cancer organoid culture techniques are uncontrolled and irreproducible, hindering the acceleration of insights into patient care.
Article
Biochemistry & Molecular Biology
Sergey Knyazev, Viachaslau Tsyvina, Anupama Shankar, Andrew Melnyk, Alexander Artyomenko, Tatiana Malygina, Yuri B. Porozov, Ellsworth M. Campbell, William M. Switzer, Pavel Skums, Serghei Mangul, Alex Zelikovsky
Summary: Rapidly evolving RNA viruses continuously produce minority haplotypes that can become dominant if they are drug-resistant or can better evade the immune system. The CliqueSNV technology effectively reduces sequencing noise and enables accurate identification of low-frequency viral haplotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Michael Menzel, Sabine Hurka, Stefan Glasenhardt, Andreas Gogol-Doering
Summary: In this study, a novel approach is presented for reliably identifying transcription factor-binding motifs in ChIP-Seq data without peak detection. By evaluating sequencing reads distributions around k-mers in the genome, binding motifs that are not detected in traditional pipelines can be identified.
Editorial Material
Chemistry, Physical
Steven R. Spurgeon, Colin Ophus, Lewys Jones, Amanda Petford-Long, Sergei V. Kalinin, Matthew J. Olszta, Rafal E. Dunin-Borkowski, Norman Salmon, Khalid Hattar, Wei-Chang D. Yang, Renu Sharma, Yingge Du, Ann Chiaramonti, Haimei Zheng, Edgar C. Buck, Libor Kovarik, R. Lee Penn, Dongsheng Li, Xin Zhang, Mitsuhiro Murayama, Mitra L. Taheri
Summary: Electron microscopy plays a crucial role in various aspects of modern life, including materials development for quantum computing, energy, and medicine. In order to achieve transformative discoveries in the next decade, an open, highly integrated, and data-driven microscopy architecture is essential.
Article
Multidisciplinary Sciences
David L. Hoelscher, Nassim Bouteldja, Mehdi Joodaki, Maria L. Russo, Yu-Chia Lan, Alireza Vafaei Sadr, Mingbo Cheng, Vladimir Tesar, Saskia V. Stillfried, Barbara M. Klinkhammer, Jonathan Barratt, Juergen Floege, Ian S. D. Roberts, Rosanna Coppo, Ivan G. Costa, Roman D. Buelow, Peter Boor
Summary: Pathology diagnostics still rely on tissue morphology assessment by trained experts. Here, the authors perform deep-learning-based segmentation followed by large-scale feature extraction of histological images, i.e., next-generation morphometry, to enable outcome-relevant and disease-specific pathomics analysis of non-tumor kidney pathology.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Akio Miyao, Utako Yamanouchi
Summary: This study developed a new algorithm, TEF, which can detect transposable elements (TEs) with unknown sequences and determine the sequences of both ends and the insertion positions of transposed TEs by directly comparing the NGS data. This method verifies the genotypes of transpositions by counting the junctions of head and tail, and non-insertion sequences in NGS reads. It is easy to use and independent of any TE library, making it useful for detecting insertions from unknown TEs bypassed by common TE annotation pipelines.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Laurel A. Keefer, James R. White, Derrick E. Wood, Kelly M. R. Gerding, Kenneth C. Valkenburg, David Riley, Christopher Gault, Eniko Papp, Christine M. Vollmer, Amy Greer, James Hernandez, Paul M. McGregor, Adriana Zingone, Brid M. Ryan, Kristen Deak, Shannon J. McCall, Michael B. Datto, James L. Prescott, John F. Thompson, Gustavo C. Cerqueira, Sian Jones, John K. Simmons, Abigail McElhinny, Jennifer Dickey, Samuel Angiuoli, Luis A. Diaz, Victor E. Velculescu, Mark Sausen
Summary: This study describes a comprehensive genomic profiling assay with high analytical performance and provides validation of its accuracy and reliability using clinically and biologically relevant samples.
NATURE COMMUNICATIONS
(2022)