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Journal articles on the topic 'Genomics; DNA sequencing; Bioinformatics'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Shi, Lizhen, and Zhong Wang. "Computational Strategies for Scalable Genomics Analysis." Genes 10, no. 12 (2019): 1017. http://dx.doi.org/10.3390/genes10121017.

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The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness,

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Ow, T. J., K. Upadhyay, T. J. Belbin, M. B. Prystowsky, H. Ostrer, and R. V. Smith. "Bioinformatics in otolaryngology research. Part one: concepts in DNA sequencing and gene expression analysis." Journal of Laryngology & Otology 128, no. 10 (2014): 848–58. http://dx.doi.org/10.1017/s002221511400200x.

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AbstractBackground:Advances in high-throughput molecular biology, genomics and epigenetics, coupled with exponential increases in computing power and data storage, have led to a new era in biological research and information. Bioinformatics, the discipline devoted to storing, analysing and interpreting large volumes of biological data, has become a crucial component of modern biomedical research. Research in otolaryngology has evolved along with these advances.Objectives:This review highlights several modern high-throughput research methods, and focuses on the bioinformatics principles necessa

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Kong, Siyuan, Qing Li, Gaolin Zhang, et al. "Exonuclease combinations reduce noises in 3D genomics technologies." Nucleic Acids Research 48, no. 8 (2020): e44-e44. http://dx.doi.org/10.1093/nar/gkaa106.

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Abstract Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of an

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Yang, Xinmiao, Mark R. Hartman, Kristin T. Harrington, et al. "Using Next-Generation Sequencing to Explore Genetics and Race in the High School Classroom." CBE—Life Sciences Education 16, no. 2 (2017): ar22. http://dx.doi.org/10.1187/cbe.16-09-0281.

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With the development of new sequencing and bioinformatics technologies, concepts relating to personal genomics play an increasingly important role in our society. To promote interest and understanding of sequencing and bioinformatics in the high school classroom, we developed and implemented a laboratory-based teaching module called “The Genetics of Race.” This module uses the topic of race to engage students with sequencing and genetics. In the experimental portion of this module, students isolate their own mitochondrial DNA using standard biotechnology techniques and collect next-generation

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Zheng, Weibo, Jing Chen, Thomas G. Doak, Weibo Song, and Ying Yan. "ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data." Bioinformatics 36, no. 12 (2020): 3632–36. http://dx.doi.org/10.1093/bioinformatics/btaa226.

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Abstract Motivation Programmed DNA elimination (PDE) plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific for the detection of DNA splicing events is scarce. In this paper, we describe Accurate Deletion Finder (ADFinder), an efficient detector of PDEs using high-throughput sequencing data. ADFinder can predict PDEs with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location and calculate the frequency for each

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Utturkar, Sagar M., W. Nathan Cude, Michael S. Robeson, et al. "Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis." Applied and Environmental Microbiology 82, no. 18 (2016): 5698–708. http://dx.doi.org/10.1128/aem.01285-16.

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ABSTRACTBacterial endophytes that colonizePopulustrees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic ba

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Greer, S. U., and H. P. Ji. "Structural variant analysis for linked-read sequencing data with gemtools." Bioinformatics 35, no. 21 (2019): 4397–99. http://dx.doi.org/10.1093/bioinformatics/btz239.

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Abstract Summary Linked-read sequencing generates synthetic long reads which are useful for the detection and analysis of structural variants (SVs). The software associated with 10× Genomics linked-read sequencing, Long Ranger, generates the essential output files (BAM, VCF, SV BEDPE) necessary for downstream analyses. However, to perform downstream analyses requires the user to customize their own tools to handle the unique features of linked-read sequencing data. Here, we describe gemtools, a collection of tools for the downstream and in-depth analysis of SVs from linked-read data. Gemtools

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Voelkerding, Karl V., Shale A. Dames, and Jacob D. Durtschi. "Next-Generation Sequencing: From Basic Research to Diagnostics." Clinical Chemistry 55, no. 4 (2009): 641–58. http://dx.doi.org/10.1373/clinchem.2008.112789.

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Abstract Background: For the past 30 years, the Sanger method has been the dominant approach and gold standard for DNA sequencing. The commercial launch of the first massively parallel pyrosequencing platform in 2005 ushered in the new era of high-throughput genomic analysis now referred to as next-generation sequencing (NGS). Content: This review describes fundamental principles of commercially available NGS platforms. Although the platforms differ in their engineering configurations and sequencing chemistries, they share a technical paradigm in that sequencing of spatially separated, clonall

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Mose, Lisle E., Charles M. Perou, and Joel S. Parker. "Improved indel detection in DNA and RNA via realignment with ABRA2." Bioinformatics 35, no. 17 (2019): 2966–73. http://dx.doi.org/10.1093/bioinformatics/btz033.

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Abstract Motivation Genomic variant detection from next-generation sequencing has become established as an extremely important component of research and clinical diagnoses in both cancer and Mendelian disorders. Insertions and deletions (indels) are a common source of variation and can frequently impact functionality, thus making their detection vitally important. While substantial effort has gone into detecting indels from DNA, there is still opportunity for improvement. Further, detection of indels from RNA-Seq data has largely been an afterthought and offers another critical area for varian

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Bhattacharya, Debashish, Rajat S. Roy, Dana C. Price, and Alexander Schliep. "Single-cell genomics of marine plankton: Studying the single life of eukaryotic microbes." Biochemist 36, no. 1 (2014): 16–22. http://dx.doi.org/10.1042/bio03601016.

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The oceans are full of innumerable numbers of single cells living in microenvironments. Understanding who they are, what they eat and what infects them can inform us about the true diversity of plankton, their biotic interactions and how they may respond to a changing environment. Analysing to significant depth the genomes and ‘gut’ (i.e. the food vacuole and other contents) of individual wild-caught cells would have been thought impossible only a few years ago. However, the rapidly expanding field of single-cell genomics, powered by modern cell-sorting procedures, high-throughput DNA sequenci

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Myers, Matthew A., Simone Zaccaria, and Benjamin J. Raphael. "Identifying tumor clones in sparse single-cell mutation data." Bioinformatics 36, Supplement_1 (2020): i186—i193. http://dx.doi.org/10.1093/bioinformatics/btaa449.

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Abstract Motivation Recent single-cell DNA sequencing technologies enable whole-genome sequencing of hundreds to thousands of individual cells. However, these technologies have ultra-low sequencing coverage (&lt;0.5× per cell) which has limited their use to the analysis of large copy-number aberrations (CNAs) in individual cells. While CNAs are useful markers in cancer studies, single-nucleotide mutations are equally important, both in cancer studies and in other applications. However, ultra-low coverage sequencing yields single-nucleotide mutation data that are too sparse for current sing

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Wu, Peng, Yan Gao, Weilong Guo, and Ping Zhu. "Using local alignment to enhance single-cell bisulfite sequencing data efficiency." Bioinformatics 35, no. 18 (2019): 3273–78. http://dx.doi.org/10.1093/bioinformatics/btz125.

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Abstract Motivation Single-cell bisulfite sequencing (BS-seq) techniques have been developed for DNA methylation heterogeneity detection and studies with limited materials. However, the data deficiency such as low read mapping ratio is still a critical issue. Results We comprehensively characterize single-cell BS-seq data and reveal chimerical molecules to be the major source of alignment failures. These chimerical molecules are produced by recombination of genomic proximal sequences with microhomology regions (MR) after bisulfite conversion. In addition, we find DNA methylation within MR is h

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Trent, Jeffrey, John Carpten, Michael Reich, et al. "The Multiple Myeloma Research Consortium Genomics Initiative." Blood 110, no. 11 (2007): 2498. http://dx.doi.org/10.1182/blood.v110.11.2498.2498.

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Abstract The Multiple Myeloma Research Consortium (MMRC) Genomics Initiative is a three-year program to analyze tumor tissue from hundreds of multiple myeloma (MM) patients via gene expression profiling (GEP), comparative genomic hybridization (aCGH), and exon re-sequencing. In addition, RNAi knockdown of selected genes in MM tumor cell lines is being evaluated to identify potential new targets. All genomic data generated is scheduled for placement in an open-access Multiple Myeloma Genomics Portal pre-publication and in near real-time (www.broad.mit.edu/mmgp). Additionally, samples are also d

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Turudić, Ante, Zlatko Liber, Martina Grdiša, Jernej Jakše, Filip Varga, and Zlatko Šatović. "Towards the Well-Tempered Chloroplast DNA Sequences." Plants 10, no. 7 (2021): 1360. http://dx.doi.org/10.3390/plants10071360.

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With the development of next-generation sequencing technology and bioinformatics tools, the process of assembling DNA sequences has become cheaper and easier, especially in the case of much shorter organelle genomes. The number of available DNA sequences of complete chloroplast genomes in public genetic databases is constantly increasing and the data are widely used in plant phylogenetic and biotechnological research. In this work, we investigated possible inconsistencies in the stored form of publicly available chloroplast genome sequence data. The impact of these inconsistencies on the resul

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Parmen, Adibah, MOHD NOOR MAT ISA, FARAH FADWA BENBELGACEM, Hamzah Mohd Salleh, and Ibrahim Ali Noorbatcha. "COMPARATIVE METAGENOMICS ANALYSIS OF PALM OIL MILL EFFLUENT (POME) USING THREE DIFFERENT BIOINFORMATICS PIPELINES." IIUM Engineering Journal 20, no. 1 (2019): 1–11. http://dx.doi.org/10.31436/iiumej.v20i1.909.

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ABSTRACT: The substantial cost reduction and massive production of next-generation sequencing (NGS) data have contributed to the progress in the rapid growth of metagenomics. However, production of the massive amount of data by NGS has revealed the challenges in handling the existing bioinformatics tools related to metagenomics. Therefore, in this research we have investigated an equal set of DNA metagenomics data from palm oil mill effluent (POME) sample using three different freeware bioinformatics pipelines’ websites of metagenomics RAST server (MG-RAST), Integrated Microbial Genomes with M

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Hardy, Alexis, Mélody Matelot, Amandine Touzeau, et al. "DNAModAnnot: a R toolbox for DNA modification filtering and annotation." Bioinformatics 37, no. 17 (2021): 2738–40. http://dx.doi.org/10.1093/bioinformatics/btab032.

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Abstract Motivation Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or Oxford Nanopore Technologies (ONT) data. Here, we present DNA Modification Annotation (DNAModAnnot), a R package designed for the global analysis of DNA modification patterns using adapted filtering and visualization tools. Results We tested

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Garner, Chad, Sandip Reddy, John Z. Sanborn, Stephen Charles Benz, Patrick Soon-Shiong, and Shahrooz Rabizadeh. "Tumor-normal sequencing to reveal frequency of false positive error rates with tumor-only sequencing in GI cancers and with RNA sequencing as a new standard of precision molecular profiling." Journal of Clinical Oncology 36, no. 4_suppl (2018): 224. http://dx.doi.org/10.1200/jco.2018.36.4_suppl.224.

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224 Background: Tumor-only sequencing to identify somatic tumor genomic variants increases the risk of mistakenly identifying germline mutations as somatically derived driver mutations. Simultaneous bioinformatics analysis of both normal germline and the tumor genome with RNA analysis is necessary for precise identification of molecular targets for cancer therapy. The objective of this study was to compare the accuracy and precision of tumor somatic SNV calling with a 45-gene GI cancer molecular actionability panel, analyzing tumor tissue alone versus analyzing tumor DNA with normal germline D

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Wu, Jiaqi, and Mohammed El-Kebir. "ClonArch: visualizing the spatial clonal architecture of tumors." Bioinformatics 36, Supplement_1 (2020): i161—i168. http://dx.doi.org/10.1093/bioinformatics/btaa471.

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Abstract Motivation Cancer is caused by the accumulation of somatic mutations that lead to the formation of distinct populations of cells, called clones. The resulting clonal architecture is the main cause of relapse and resistance to treatment. With decreasing costs in DNA sequencing technology, rich cancer genomics datasets with many spatial sequencing samples are becoming increasingly available, enabling the inference of high-resolution tumor clones and prevalences across different spatial coordinates. While temporal and phylogenetic aspects of tumor evolution, such as clonal evolution over

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Nakazato, Takeru. "A Challenge to Integrate Bioinformatics and Biodiversity Informatics Data as Museomics." Biodiversity Information Science and Standards 2 (May 22, 2018): e26102. http://dx.doi.org/10.3897/biss.2.26102.

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Museum-preserved samples are attracting attention as a rich resource for DNA studies. Museomics aims to link DNA sequence data back to the museum collection. Molecular biologists are interested in morphological information including body size, pattern, and colors, and sequence data have also become essential for biodiversity research as evidence for species identification and phylogenetic analysis. For more than 30 years, molecular data, such as DNA and protein sequences, have been captured by the DNA Data Bank of Japan (DDBJ), the European Bioinformatics Institute (EBI, UK), and the National

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Gartland, Kevan M. A., Munis Dundar, Tommaso Beccari, Mariapia Viola Magni, and Jill S. Gartland. "Advances in biotechnology: Genomics and genome editing." EuroBiotech Journal 1, no. 1 (2017): 2–9. http://dx.doi.org/10.24190/issn2564-615x/2017/01.02.

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Abstract Genomics, the study of genes, their functions and related techniques has become a crucial science for developing understanding of life processes and how they evolve. Since the advent of the human genome project, huge strides have been made in developing understanding of DNA and RNA sequence information and how it can be put to good use in the biotechnology sector. Newly derived sequencing and bioinformatics tools have added to the torrent of new insights gained, so that ‘sequence once and query often’ type DNA apps are now becoming reality. Genome editing, using tools such as CRISPR/C

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Deakin, Janine E., Sally Potter, Rachel O’Neill, et al. "Chromosomics: Bridging the Gap between Genomes and Chromosomes." Genes 10, no. 8 (2019): 627. http://dx.doi.org/10.3390/genes10080627.

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The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate

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Müller, Sören, Ara Cho, Siyuan J. Liu, Daniel A. Lim, and Aaron Diaz. "CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones." Bioinformatics 34, no. 18 (2018): 3217–19. http://dx.doi.org/10.1093/bioinformatics/bty316.

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Abstract Motivation Single-cell RNA-sequencing (scRNA-seq) has enabled studies of tissue composition at unprecedented resolution. However, the application of scRNA-seq to clinical cancer samples has been limited, partly due to a lack of scRNA-seq algorithms that integrate genomic mutation data. Results To address this, we present CONICS COpy-Number analysis In single-Cell RNA-Sequencing. CONICS is a software tool for mapping gene expression from scRNA-seq to tumor clones and phylogenies, with routines enabling: the quantitation of copy-number alterations in scRNA-seq, robust separation of neop

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Timp, Winston, and Gregory Timp. "Beyond mass spectrometry, the next step in proteomics." Science Advances 6, no. 2 (2020): eaax8978. http://dx.doi.org/10.1126/sciadv.aax8978.

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Proteins can be the root cause of a disease, and they can be used to cure it. The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. With the advent of scalable, single-molecule DNA sequencing, genomics and transcriptomics have since propelled medicine through improved sensitivity and lower costs, but proteomics has lagged behind. Currently, proteomics relies mainly on mass spectrometry (MS), but instead of truly sequencing, it classifies a protein and typically requires about a billion copies of a protein to do

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Vu, Trung Nghia, Ha-Nam Nguyen, Stefano Calza, Krishna R. Kalari, Liewei Wang, and Yudi Pawitan. "Cell-level somatic mutation detection from single-cell RNA sequencing." Bioinformatics 35, no. 22 (2019): 4679–87. http://dx.doi.org/10.1093/bioinformatics/btz288.

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Abstract Motivation Both single-cell RNA sequencing (scRNA-seq) and DNA sequencing (scDNA-seq) have been applied for cell-level genomic profiling. For mutation profiling, the latter seems more natural. However, the task is highly challenging due to the limited input materials from only two copies of DNA molecules, while whole-genome amplification generates biases and other technical noises. ScRNA-seq starts with a higher input amount, so generally has better data quality. There exists various methods for mutation detection from DNA sequencing, it is not clear whether these methods work for scR

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Назипова, Н. Н., and N. N. Nazipova. "Big Data in Bioinformatics." Mathematical Biology and Bioinformatics 12, no. 1 (2017): 102–19. http://dx.doi.org/10.17537/2017.12.102.

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Sequencing of the human genome began in 1994. It took 10 years of collaborative work of many research groups from different countries in order to provide a draft of the human DNA. Modern technologies allow sequencing of a whole genome in a few days. We discuss here the advances in modern bioinformatics related to the emergence of high-performance sequencing platforms, which not only contributed to the expansion of capabilities of biology and related sciences, but also gave rise to the phenomenon of Big Data in biology. The necessity for development of new technologies and methods for organizat

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Petrosino, Joseph F., Sarah Highlander, Ruth Ann Luna, Richard A. Gibbs, and James Versalovic. "Metagenomic Pyrosequencing and Microbial Identification." Clinical Chemistry 55, no. 5 (2009): 856–66. http://dx.doi.org/10.1373/clinchem.2008.107565.

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Abstract Background: The Human Microbiome Project has ushered in a new era for human metagenomics and high-throughput next-generation sequencing strategies. Content: This review describes evolving strategies in metagenomics, with a special emphasis on the core technology of DNA pyrosequencing. The challenges of microbial identification in the context of microbial populations are discussed. The development of next-generation pyrosequencing strategies and the technical hurdles confronting these methodologies are addressed. Bioinformatics-related topics include taxonomic systems, sequence databas

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Feng, RuiJuan, Xin Wang, Min Tao, Guanchao Du, and Qishuo Wang. "Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa." PeerJ 5 (October 31, 2017): e3982. http://dx.doi.org/10.7717/peerj.3982.

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Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR

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Jung, Hyungtaek, Tomer Ventura, J. Sook Chung, et al. "Twelve quick steps for genome assembly and annotation in the classroom." PLOS Computational Biology 16, no. 11 (2020): e1008325. http://dx.doi.org/10.1371/journal.pcbi.1008325.

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Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the

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Soualmia, L. F., and T. Lecroq. "From Genome Sequencing to Bedside." Yearbook of Medical Informatics 22, no. 01 (2013): 175–77. http://dx.doi.org/10.1055/s-0038-1638852.

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Summary Objectives: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine. Method: We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review. Results: The selec

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Rossi, Ernest, Kathryn Rossi, Garret Yount, Mauro Cozzolino, and Salvador Iannotti. "The Bioinformatics of Integrative Medical Insights: Proposals for an International Psycho-Social and Cultural Bioinformatics Project." Integrative Medicine Insights 1 (January 2006): 117863370600100. http://dx.doi.org/10.1177/117863370600100002.

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We propose the formation of an International Psycho-Social and Cultural Bioinformatics Project (IPCBP) to explore the research foundations of Integrative Medical Insights (IMI) on all levels from the molecular-genomic to the psychological, cultural, social, and spiritual. Just as The Human Genome Project identified the molecular foundations of modern medicine with the new technology of sequencing DNA during the past decade, the IPCBP would extend and integrate this neuroscience knowledge base with the technology of gene expression via DNA/proteomic microarray research and brain imaging in deve

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Teixeira, Luis, Françoise Rothé, and Christos Sotiriou. "Genomic Drivers in Breast Cancers." European Oncology & Haematology 12, no. 01 (2016): 28. http://dx.doi.org/10.17925/eoh.2016.12.01.28.

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Significant advances in next-generation sequencing technologies have allowed the identification of genomic alterations in breast cancer. These alterations offer the opportunity to conduct studies with targeted drugs. However, there are still several scientific challenges to be addressed before precision medicine is widely used in the clinic. Nonetheless, different solutions are developed to overcome these obstacles such as the improvement of bioinformatics tools and the use of “liquid biopsy” to assess circulating tumour DNA.

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Hynst, Jakub, Veronika Navrkalova, Karol Pal, and Sarka Pospisilova. "Bioinformatic strategies for the analysis of genomic aberrations detected by targeted NGS panels with clinical application." PeerJ 9 (March 31, 2021): e10897. http://dx.doi.org/10.7717/peerj.10897.

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Molecular profiling of tumor samples has acquired importance in cancer research, but currently also plays an important role in the clinical management of cancer patients. Rapid identification of genomic aberrations improves diagnosis, prognosis and effective therapy selection. This can be attributed mainly to the development of next-generation sequencing (NGS) methods, especially targeted DNA panels. Such panels enable a relatively inexpensive and rapid analysis of various aberrations with clinical impact specific to particular diagnoses. In this review, we discuss the experimental approaches

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Loh, Jui Wan, Caitlin Guccione, Frances Di Clemente, Gregory Riedlinger, Shridar Ganesan, and Hossein Khiabanian. "All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data." Bioinformatics 36, no. 7 (2019): 2173–80. http://dx.doi.org/10.1093/bioinformatics/btz865.

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Abstract Summary Clinical sequencing aims to identify somatic mutations in cancer cells for accurate diagnosis and treatment. However, most widely used clinical assays lack patient-matched control DNA and additional analysis is needed to distinguish somatic and unfiltered germline variants. Such computational analyses require accurate assessment of tumor cell content in individual specimens. Histological estimates often do not corroborate with results from computational methods that are primarily designed for normal–tumor matched data and can be confounded by genomic heterogeneity and presence

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Lee, Dohoon, Sangseon Lee, and Sun Kim. "PRISM: methylation pattern-based, reference-free inference of subclonal makeup." Bioinformatics 35, no. 14 (2019): i520—i529. http://dx.doi.org/10.1093/bioinformatics/btz327.

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Abstract Motivation Characterizing cancer subclones is crucial for the ultimate conquest of cancer. Thus, a number of bioinformatic tools have been developed to infer heterogeneous tumor populations based on genomic signatures such as mutations and copy number variations. Despite accumulating evidence for the significance of global DNA methylation reprogramming in certain cancer types including myeloid malignancies, none of the bioinformatic tools are designed to exploit subclonally reprogrammed methylation patterns to reveal constituent populations of a tumor. In accordance with the notion of

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Macas, Jiří, Pavel Neumann, Petr Novák, and Jiming Jiang. "Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data." Bioinformatics 26, no. 17 (2010): 2101–8. http://dx.doi.org/10.1093/bioinformatics/btq343.

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Abstract Motivation: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. R

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Lee, Guinevere Q. "Chemistry and Bioinformatics Considerations in Using Next-Generation Sequencing Technologies to Inferring HIV Proviral DNA Genome-Intactness." Viruses 13, no. 9 (2021): 1874. http://dx.doi.org/10.3390/v13091874.

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HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences a

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Magi, Alberto, Davide Bolognini, Niccoló Bartalucci, et al. "Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data." Bioinformatics 35, no. 21 (2019): 4213–21. http://dx.doi.org/10.1093/bioinformatics/btz241.

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Abstract Motivation The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially. Results In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6–12 h allow to obtain a resolution comparable to currently available array-ba

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Jaschke, Paul R., Gabrielle A. Dotson, Kay S. Hung, Diane Liu, and Drew Endy. "Definitive demonstration by synthesis of genome annotation completeness." Proceedings of the National Academy of Sciences 116, no. 48 (2019): 24206–13. http://dx.doi.org/10.1073/pnas.1905990116.

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We develop a method for completing the genetics of natural living systems by which the absence of expected future discoveries can be established. We demonstrate the method using bacteriophage øX174, the first DNA genome to be sequenced. Like many well-studied natural organisms, closely related genome sequences are available—23 Bullavirinae genomes related to øX174. Using bioinformatic tools, we first identified 315 potential open reading frames (ORFs) within the genome, including the 11 established essential genes and 82 highly conserved ORFs that have no known gene products or assigned functi

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Chorbadjiev, Lubomir, Jude Kendall, Joan Alexander, et al. "Integrated Computational Pipeline for Single-Cell Genomic Profiling." JCO Clinical Cancer Informatics, no. 4 (September 2020): 464–71. http://dx.doi.org/10.1200/cci.19.00171.

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PURPOSE Copy-number profiling of multiple individual cells from sparse sequencing may be used to reveal a detailed picture of genomic heterogeneity and clonal organization in a tissue biopsy specimen. We sought to provide a comprehensive computational pipeline for single-cell genomics, to facilitate adoption of this molecular technology for basic and translational research. MATERIALS AND METHODS The pipeline comprises software tools programmed in Python and in R and depends on Bowtie, HISAT2, Matplotlib, and Qt. It is installed and used with Anaconda. RESULTS Here we describe a complete pipeli

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Brown, Angela, Mansour Zamanpoor, Donald R. Love, and Debra O. Prosser. "Determination of Pathogenicity of Breast Cancer 1 Gene Variants using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines." Sultan Qaboos University Medical Journal [SQUMJ] 19, no. 4 (2019): 324. http://dx.doi.org/10.18295/squmj.2019.19.04.008.

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Objectives: Molecular diagnostic laboratories screen for mutations in disease-causing genes in order to confirm a clinical diagnosis. The classification of DNA variants as ‘pathogenic’ or ‘likely pathogenic’ mutations creates a workflow bottleneck, which becomes increasingly challenging as greater number of genes are screened. The classification challenge is also acute if there are conflicting reports regarding pathogenicity and differing classification criteria between laboratories. This study aimed to compare two procedures for the classification of variants in the breast cancer (BRCA)1 gene

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Nowrousian, Minou. "Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems." Eukaryotic Cell 9, no. 9 (2010): 1300–1310. http://dx.doi.org/10.1128/ec.00123-10.

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ABSTRACT Over the past 5 years, large-scale sequencing has been revolutionized by the development of several so-called next-generation sequencing (NGS) technologies. These have drastically increased the number of bases obtained per sequencing run while at the same time decreasing the costs per base. Compared to Sanger sequencing, NGS technologies yield shorter read lengths; however, despite this drawback, they have greatly facilitated genome sequencing, first for prokaryotic genomes and within the last year also for eukaryotic ones. This advance was possible due to a concomitant development of

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YOSHINO, TIMOTHY P., NATHALIE DINGUIRARD, and MARINA DE MORAES MOURÃO. "In vitro manipulation of gene expression in larval Schistosoma: a model for postgenomic approaches in Trematoda." Parasitology 137, no. 3 (2009): 463–83. http://dx.doi.org/10.1017/s0031182009991302.

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SUMMARYWith rapid developments in DNA and protein sequencing technologies, combined with powerful bioinformatics tools, a continued acceleration of gene identification in parasitic helminths is predicted, potentially leading to discovery of new drug and vaccine targets, enhanced diagnostics and insights into the complex biology underlying host-parasite interactions. For the schistosome blood flukes, with the recent completion of genome sequencing and comprehensive transcriptomic datasets, there has accumulated massive amounts of gene sequence data, for which, in the vast majority of cases, lit

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Chatterjee, Aniruddha, Euan J. Rodger, Peter A. Stockwell, Robert J. Weeks, and Ian M. Morison. "Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries." Journal of Biomedicine and Biotechnology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/741542.

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Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform hav

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Friedman, Sam, Laura Gauthier, Yossi Farjoun, and Eric Banks. "Lean and deep models for more accurate filtering of SNP and INDEL variant calls." Bioinformatics 36, no. 7 (2019): 2060–67. http://dx.doi.org/10.1093/bioinformatics/btz901.

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Abstract Summary We investigate convolutional neural networks (CNNs) for filtering small genomic variants in short-read DNA sequence data. Errors created during sequencing and library preparation make variant calling a difficult task. Encoding the reference genome and aligned reads covering sites of genetic variation as numeric tensors allows us to leverage CNNs for variant filtration. Convolutions over these tensors learn to detect motifs useful for classifying variants. Variant filtering models are trained to classify variants as artifacts or real variation. Visualizing the learned weights o

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Biswas, Anushua, and Leelavati Narlikar. "Resolving diverse protein–DNA footprints from exonuclease-based ChIP experiments." Bioinformatics 37, Supplement_1 (2021): i367—i375. http://dx.doi.org/10.1093/bioinformatics/btab274.

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Abstract Motivation High-throughput chromatin immunoprecipitation (ChIP) sequencing-based assays capture genomic regions associated with the profiled transcription factor (TF). ChIP-exo is a modified protocol, which uses lambda exonuclease to digest DNA close to the TF-DNA complex, in order to improve on the positional resolution of the TF-DNA contact. Because the digestion occurs in the 5′–3′ orientation, the protocol produces directional footprints close to the complex, on both sides of the double stranded DNA. Like all ChIP-based methods, ChIP-exo reports a mixture of different regions asso

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Lomsadze, Alexandre, Tengguo Li, Mangalathu S. Rajeevan, Elizabeth R. Unger, and Mark Borodovsky. "Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine." Viruses 12, no. 7 (2020): 710. http://dx.doi.org/10.3390/v12070710.

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We recently developed a test based on the Agilent SureSelect target enrichment system capturing genomic fragments from 191 human papillomaviruses (HPV) types for Illumina sequencing. This enriched whole genome sequencing (eWGS) assay provides an approach to identify all HPV types in a sample. Here we present a machine learning algorithm that calls HPV types based on the eWGS output. The algorithm based on the support vector machine (SVM) technique was trained on eWGS data from 122 control samples with known HPV types. The new algorithm demonstrated good performance in HPV type detection for de

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Tian, Shaozhou Ken, J. Keith Killian, Natasha Rekhtman, et al. "Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience." Archives of Pathology & Laboratory Medicine 140, no. 11 (2016): 1200–1205. http://dx.doi.org/10.5858/arpa.2016-0108-ra.

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The value and suitability of cytology specimens for molecular diagnosis has been demonstrated by numerous studies. In practice, however, the success rates vary widely across institutions depending on the disease setting, institutional practices of acquisition, handling/processing, and testing methodologies. As the number of clinically relevant biomarkers continues to increase, more laboratories are turning to next-generation sequencing platforms for testing. Although amplicon-based next-generation sequencing assays, interrogating a limited genomic territory, can be performed with minimal input

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Gu, Wei, Steve Miller, and Charles Y. Chiu. "Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection." Annual Review of Pathology: Mechanisms of Disease 14, no. 1 (2019): 319–38. http://dx.doi.org/10.1146/annurev-pathmechdis-012418-012751.

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Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional d

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Mansukhani, Sonia, Louise J. Barber, Dimitrios Kleftogiannis, et al. "Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing." Clinical Chemistry 64, no. 11 (2018): 1626–35. http://dx.doi.org/10.1373/clinchem.2018.289629.

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Abstract BACKGROUND Circulating free DNA sequencing (cfDNA-Seq) can portray cancer genome landscapes, but highly sensitive and specific technologies are necessary to accurately detect mutations with often low variant frequencies. METHODS We developed a customizable hybrid-capture cfDNA-Seq technology using off-the-shelf molecular barcodes and a novel duplex DNA molecule identification tool for enhanced error correction. RESULTS Modeling based on cfDNA yields from 58 patients showed that this technology, requiring 25 ng of cfDNA, could be applied to &gt;95% of patients with metastatic color

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Hesse, U., P. Maynard, S. Macmil, et al. "The genome and genes of Epichloe festucae." NZGA: Research and Practice Series 13 (January 1, 2007): 461–65. http://dx.doi.org/10.33584/rps.13.2006.3123.

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The ascomycete EpichloÃ« festucae is a model endophyte that 1) switches between mutualistic and antagonistic states, 2) is seed transmissible, 3) has a sexual state amenable to genetic analysis, and 4) is rich in bioprotective alkaloids. This fungus grows systemically and intercellularly throughout the life of its host plant. On each reproductive tiller the fungus either infects benignly and transmits clonally in seeds, or produces its sexual state (stroma) and chokes inflorescence development. The E. festucae genome was estimated at 29 Mb in six chromosomes. The genome sequence was assembled

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