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CopywriteR: DNA copy number detection from off-target sequence data

Thomas Kuilman, Arno Velds, Kristel Kemper, Marco Ranzani, Lorenzo Bombardelli, Marlous Hoogstraat, Ekaterina Nevedomskaya, Guotai Xu, Julian de Ruiter, Martijn P Lolkema, Bauke Ylstra, Jos Jonkers (+5 others)
2015 Genome Biology  
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons.  ...  CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin  ...  Acknowledgements We would like to acknowledge the Center of Personalized Cancer Treatment (CPCT) for providing samples, Daniel Vis and Sander Canisius for data acquisition and the High Performance Computing  ... 
doi:10.1186/s13059-015-0617-1 pmid:25887352 pmcid:PMC4396974 fatcat:al5tih2njzhxffida5brigtyhm

CRISPR GUARD protects off-target sites from Cas9 nuclease activity using short guide RNAs

Matthew A. Coelho, Etienne De Braekeleer, Mike Firth, Michal Bista, Sebastian Lukasiak, Maria Emanuela Cuomo, Benjamin J. M. Taylor
2020 Nature Communications  
Finally, we create an online tool for CRISPR GUARD design.  ...  Precise genome editing using CRISPR-Cas9 is a promising therapeutic avenue for genetic diseases, although off-target editing remains a significant safety concern.  ...  Code and analyses used to analyse sequencing data are available from:  ... 
doi:10.1038/s41467-020-17952-5 pmid:32807781 fatcat:j2hyln4zpjaihhbup3vtbfuwti

Determining the quality and complexity of next-generation sequencing data without a reference genome

Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, Michiel van Galen, Irina Pulyakhina, Yavuz Ariyurek, Ken Kraaijeveld, Johan T den Dunnen, Peter de Knijff, Peter AC 't Hoen, Jeroen FJ Laros
2014 Genome Biology  
Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely  ...  such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a  ...  This work was partially supported by the European Community's Seventh Framework Program (FP7/2007-2013) GEUVADIS (grant 261123), the Center for Medical Systems Biology and the Center for Genome Diagnostics  ... 
doi:10.1186/s13059-014-0555-3 pmid:25514851 pmcid:PMC4298064 fatcat:ygfuz6dflnfsrfc73stmhv6uqa

Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice [article]

Yuechao Wu, Qiurong Ren, Zhaohui Zhong, Guanqing Liu, Yu Bao, Li Liu Liu, Shuyue Xiang, Shuo Liu, Xu Tang, Jianping Zhou, Xuelian Zheng, Simon Sretenovic (+3 others)
2022 bioRxiv   pre-print
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants.  ...  Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice.  ...  Taken together, these analyses indicate that ABE8e has a strong preference of the TA motif for both off-target and ontarget editing.  ... 
doi:10.1101/2022.02.09.479813 fatcat:63nv4j6skzhshawmgvjohq5yhi

B1MG D3.1 - Quality metrics for sequencing

Ivo Gut, Lucia Estelles, Edwin Cuppen, Valtteri Wirta, Eivind Hovig, Pim Volkert, Gert Matthijs
2021 Zenodo  
Hence, there is a need to establish guidelines that cover the minimum quality requirements for the generation of whole genome sequencing (WGS) and whole exome sequencing (WES) data.  ...  Next Generation Sequencing (NGS) is becoming increasingly used in clinical settings for the genomic analysis of germline and cancer samples.  ...  cross-border access to genomics and personalised medicine data Methods Next-generation sequencing (NGS) is starting to be used in clinical diagnostics.  ... 
doi:10.5281/zenodo.5018495 fatcat:qwhvj5ykk5eo5gyevfjtxuhjyq

A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data [article]

Shifu Chen, Changshou He, Yingqiang Li, Zhicheng Li, Charles E Melancon
2020 bioRxiv   pre-print
In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data.  ...  Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, MERS, and other coronaviruses  ...  Acknowledgement The authors would like to thank the community users for testing these tools and reporting bugs. CONFLICT OF INTEREST The authors declare no conflicts of interest.  ... 
doi:10.1101/2020.05.12.092163 fatcat:vncgisbd55e3zfgw4tf3wipoti

Analyzing the cancer methylome through targeted bisulfite sequencing

Eun-Joon Lee, Junfeng Luo, James M. Wilson, Huidong Shi
2013 Cancer Letters  
Bisulfite conversion of genomic DNA combined with next-generation sequencing (NGS) has become a very effective approach for mapping the whole-genome and sub-genome wide DNA methylation landscapes.  ...  In addition, the bioinformatic tools that can be used for sequence capture probe design as well as downstream sequence analyses are also addressed.  ...  Justin Choi for helpful discussion throughout this work. Huidong Shi is a Georgia Cancer Coalition Distinguished Cancer Scientist.  ... 
doi:10.1016/j.canlet.2012.10.040 pmid:23200671 pmcid:PMC3616138 fatcat:ccvyzl4rtjg5pkfliopapl6ncm

Global analysis of ZNF217 chromatin occupancy in the breast cancer cell genome reveals an association with ERalpha

Seth Frietze, Henriette O'Geen, Laurie E Littlepage, Catalina Simion, Colleen A Sweeney, Peggy J Farnham, Sheryl R Krig
2014 BMC Genomics  
Frietze was supported by 1U54HG004558 as a component of the ENCODE Project from the National Cancer Institute to P. Farnham; L.  ...  H3K27ac and H3K4me1 ChIP-seq data generated in asynchronously grown MCF7 cells was obtained from [57] .  ...  (A) A scatterplot of expression data from RNA-seq experiments.  ... 
doi:10.1186/1471-2164-15-520 pmid:24962896 pmcid:PMC4082627 fatcat:l6pinrgd2jggpl6lccvii37zdq

Computational approaches for effective CRISPR guide RNA design and evaluation

Guanqing Liu, Yong Zhang, Tao Zhang
2019 Computational and Structural Biotechnology Journal  
The review provides a comprehensive and up-to-date overview of computational approaches for guide RNA design that could help users to select the optimal tools for their research.  ...  Furthermore, we summarise these tools and give some suggestions for their usage. We also recommend three versatile web-based tools with user-friendly interfaces and preferable functions.  ...  First, tools like Bowtie and BWA cannot identify small PAMs, since these alignment tools were developed for next- generation sequencing (NGS) read alignment.  ... 
doi:10.1016/j.csbj.2019.11.006 pmid:31890142 pmcid:PMC6921152 fatcat:3wm675m6qzdsdnkql74zxmgxbe

Phage Peptides Mediate Precision Base Editing with Focused Targeting Window [article]

Kun Jia, Yan-ru Cui, Shisheng Huang, Peihong Yu, Zhengxing Lian, Peixiang Ma, Jia Liu
2020 bioRxiv   pre-print
Cytidine base editors (CBE) are novel genome engineering tools that can generate C-to-T nucleotide substitutions without introducing double-stranded breaks (DSBs).  ...  In this study, we investigated the feasibility of using a bacteriophage-derived peptide, referred to as G8PPD, as the off-switch of CBEs.  ...  Next-generation sequencing (NGS) analyses of sorted HEK293T cells revealed efficient base editing by A3A CBE at the four selected genomic sites ( Supplementary Fig. 3a) .  ... 
doi:10.1101/2020.11.02.364430 fatcat:y5ad73yftveozepkjh7ujmqh7u

CONTRA: copy number analysis for targeted resequencing

Jason Li, Richard Lupat, Kaushalya C. Amarasinghe, Ella R. Thompson, Maria A. Doyle, Georgina L. Ryland, Richard W. Tothill, Saman K. Halgamuge, Ian G. Campbell, Kylie L. Gorringe
2012 Computer applications in the biosciences : CABIOS  
easy integration with other next-generation sequencing analysis packages.  ...  Results: We present a method for CNV detection for TR data, including whole-exome capture data.  ...  We have developed a CNV detection tool called CONTRA (COpy Number Targeted Resequencing Analysis) for small-region TR, including data derived from exome capture.  ... 
doi:10.1093/bioinformatics/bts146 pmid:22474122 pmcid:PMC3348560 fatcat:wmlv6xl6ebc25hscsjhdjeqwze

Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens

Rui Zhong, Jimi Kim, Hyun Seok Kim, Minsoo Kim, Lawrence Lum, Beth Levine, Guanghua Xiao, Michael A. White, Yang Xie
2014 Nucleic Acids Research  
We developed a computational approach, deconvolution analysis of RNAi screening data, for automated quantitation of off-target effects in RNAi screening data sets.  ...  A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents.  ...  ACKNOWLEDGMENT R.Z. wishes to acknowledge his lab fellow Jessie Norris for thoughtfully reading the manuscript. FUNDING  ... 
doi:10.1093/nar/gku306 pmid:24972830 pmcid:PMC4117740 fatcat:fzt3c3guffb4llww6kpc62byey

DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution

Joshua J. Elacqua, Navpreet Ranu, Sarah E. Dilorio, Paul C. Blainey
2020 Genome Research  
DENT-seq produces a single deep sequence data set enriched for reads near nick sites and establishes a readily detectable mutational signal that allows for determination of the nick site and strand with  ...  There is currently a pressing need for methods to study off-target nicking activity genome-wide to evaluate the side effects of emerging genome editing tools on cells and organisms.  ...  This work was supported by start-up funds from the Broad Institute and a New Innovator Award from the National Institutes of Health (HL141005).  ... 
doi:10.1101/gr.265223.120 pmid:33355294 pmcid:PMC7849381 fatcat:zws6tygslfh63lleascn4x77za

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

Alok Jaiswal, Gopal Peddinti, Yevhen Akimov, Krister Wennerberg, Sergey Kuznetsov, Jing Tang, Tero Aittokallio
2017 Genome Medicine  
methods for inferring gene essentiality from shRNA level data.  ...  Importantly, by excluding shRNAs having higher propensity for off-target effects, based on their seed-sequence properties, one can remove noise from the genome-wide shRNA datasets.  ...  We thank the authors of Achilles, COLT-cancer, and BFG projects for making their data publicly available.  ... 
doi:10.1186/s13073-017-0440-2 pmid:28569207 pmcid:PMC5452371 fatcat:s44ewlztwvgi5gdnnwzs6nn4dy

Optimized targeted sequencing of cell-free plasma DNA from bladder cancer patients

Emil Christensen, Iver Nordentoft, Søren Vang, Karin Birkenkamp-Demtröder, Jørgen Bjerggaard Jensen, Mads Agerbæk, Jakob Skou Pedersen, Lars Dyrskjøt
2018 Scientific Reports  
generation sequencing (NGS).  ...  Next generation sequencing (NGS) approaches have been optimized to provide comparable technical performance, especially with the introduction of unique identifiers (UIDs).  ...  Acknowledgements The work was supported by grants from the Harboe Foundation, The Danish Cancer Society and the Novo Nordic Foundation.  ... 
doi:10.1038/s41598-018-20282-8 pmid:29382943 pmcid:PMC5789978 fatcat:nqhfgphd5vblzpttcytnjixhte
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