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A survey of tools for variant analysis of next-generation genome sequencing data

S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, Z. Trajanoski
2013 Briefings in Bioinformatics  
Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and  ...  While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting  ...  Acknowledgements We thank the reviewers for their numerous constructive suggestions, which helped us to considerably improve the article.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq

Annotation and curation of human genomic variations: an ELIXIR Implementation Study

Alessia David, Valérie Barbié, Marcella Attimonelli, Roberto Preste, Enni Makkonen, Heidi Marjonen, Mats Lindstedt, Kati Kristiansson, Sarah E. Hunt, Fiona Cunningham, Ilkka Lappalainen, Michael J.E. Sternberg
2020 F1000Research  
and curating human genomic variants, including resources specific for next generation sequencing, research into mitochondria and protein structure.  ...  Methods: In 2018, ELIXIR commissioned an international survey on the usage of databases and tools for annotating and curating human genomic variants with the aim of improving ELIXIR resources.  ...  Next Generation Sequencing The next section of the survey focused on Next Generation Sequencing (NGS). 66 (72%) respondents worked with NGS and ranked 6 sequencing methods listed in Extended data: Table  ... 
doi:10.12688/f1000research.24427.1 fatcat:fvt6xtsvmnbr7o7cdnm2upboyq

The Challenge of Next Generation Sequencing in the Context of Neuromuscular Diseases

Monkol Lek, Daniel MacArthur
2014 Journal of Neuromuscular Diseases  
Here we survey the current literature on the application of new genomic technologies to the diagnosis of severe muscle diseases, with a focus on assessment of the approaches used for data processing, analysis  ...  New genomic technologies, such as exome, whole-genome and transcriptome sequencing, are transforming the genetic diagnosis of neuromuscular diseases and dramatically accelerating the discovery of new disease-associated  ...  The next is whole genome sequencing, which provides a relatively unbiased survey of the genome including non-coding variants and structural variants.  ... 
doi:10.3233/jnd-140032 fatcat:bb64556k3rckbkwud55zxb54gy

Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

Jamie M. Ellingford, Stephanie Barton, Sanjeev Bhaskar, Simon G. Williams, Panagiotis I. Sergouniotis, James O'Sullivan, Janine A. Lamb, Rahat Perveen, Georgina Hall, William G. Newman, Paul N. Bishop, Stephen A. Roberts (+6 others)
2016 Ophthalmology (Rochester, Minn.)  
Purpose: To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Design: Case series.  ...  Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing.  ...  and genomic diagnostics, as well as for other Mendelian disorders. 4 Next-generation DNA sequencing techniques permit the analysis of genetic variants across multiple areas of the genome in a single  ... 
doi:10.1016/j.ophtha.2016.01.009 pmid:26872967 pmcid:PMC4845717 fatcat:aasadotqr5gyniyoh5pxgpbadm

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

Marisa P. Dolled-Filhart, Michael Lee, Chih-wen Ou-yang, Rajini Rani Haraksingh, Jimmy Cheng-Ho Lin
2013 The Scientific World Journal  
It has become increasingly apparent that one of the major hurdles in the genomic age will be the bioinformatics challenges of next-generation sequencing.  ...  We provide an overview of a general framework of bioinformatics analysis.  ...  VARIANT (VARIant ANalysis Tool) (http://variant.bioinfo.cipf.es/) provides annotation of variants from next generation sequencing based on several different databases and repositories including dbSNP,  ... 
doi:10.1155/2013/730210 pmid:23365548 pmcid:PMC3556895 fatcat:7n6pbn3lqbf55pmugg3pwrjdkm

Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

Shilpa Nadimpalli Kobren, Undiagnosed Diseases Network, Dustin Baldridge, Matt Velinder, Joel B. Krier, Kimberly LeBlanc, Cecilia Esteves, Barbara N. Pusey, Stephan Züchner, Elizabeth Blue, Hane Lee, Alden Huang (+11 others)
2021 Genetics in Medicine  
Results We found that tools for processing genomic sequencing data can be grouped into four distinct categories.  ...  Purpose Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions.  ...  Aligning next-generation sequencing reads Aligning next-generation sequencing reads to a reference human genome is the necessary first step for all sequence analysis pipelines (Fig. 1g ); the ubiquity  ... 
doi:10.1038/s41436-020-01084-8 pmid:33580225 pmcid:PMC8187147 fatcat:s4mbmmxe7jhx5bn7fp5mv77iyu

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data

Jennifer D. Hintzsche, William A. Robinson, Aik Choon Tan
2016 International Journal of Genomics  
Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases.  ...  These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics.  ...  This work is partly supported by the National Institutes of Health P50CA058187, Cancer League of Colorado, the David F. and Margaret T.  ... 
doi:10.1155/2016/7983236 pmid:28070503 pmcid:PMC5192301 fatcat:qtlmgypwxjbv7ewg5wskhqxs4a

A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data

Shuoguo Wang, Jinchuan Xing
2013 Genomics & Informatics  
High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data.  ...  The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the  ...  Gary A. Heiman and Alexandra Nguyen for providing valuable comments and proofreading the manuscript and the anonymous reviewers for their constructive advice.  ... 
doi:10.5808/gi.2013.11.4.191 pmid:24465230 pmcid:PMC3897846 fatcat:polwfpfg3zbzpik5s44pzi7pw4

Genome interpretation and assembly—recent progress and next steps

H. Craig Mak
2012 Nature Biotechnology  
Some offer next-generation sequencing as a clinical diagnostic test (for example, Ambry or GeneDx).  ...  Anika Joecker: There is a lack of validated sequencing data-that is, not many public datasets are available for which all genomic variants are known.  ... 
doi:10.1038/nbt.2425 pmid:23138307 fatcat:w76ko3qes5fvbp4bp2wxyrhqaa

HomSI: a homozygous stretch identifier from next-generation sequencing data

Zeliha Görmez, Burcu Bakir-Gungor, Mahmut Şamil Sağıroğlu
2013 Computer applications in the biosciences : CABIOS  
Recently, the advent of next-generation sequencing enables the concurrent identification of homozygous regions and the detection of mutations relevant for diagnosis, using data from a single sequencing  ...  In this respect, we have developed a novel tool that identifies homozygous regions using deep sequence data.  ...  Alkuraya and Dr Fatih Bayraklı for sharing their datasets with them to test our program.  ... 
doi:10.1093/bioinformatics/btt686 pmid:24307702 fatcat:jeceriku2jckzn5wlcd6lhshz4

B1MG D3.1 - Quality metrics for sequencing

Ivo Gut, Lucia Estelles, Edwin Cuppen, Valtteri Wirta, Eivind Hovig, Pim Volkert, Gert Matthijs
2021 Zenodo  
Next Generation Sequencing (NGS) is becoming increasingly used in clinical settings for the genomic analysis of germline and cancer samples.  ...  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.  ...  Acknowledgements (not grant participants) Deliverable type Report Dissemination level Public Beyond One Million Genomes  ... 
doi:10.5281/zenodo.4889390 fatcat:sraqqmsbnvavpli2ysatswbn2a

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping

Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan
2021 PeerJ  
The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance  ...  Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.11724 fatcat:ffs53shbcjhsjd7czyb7txlhz4

The road from next-generation sequencing to personalized medicine

Manuel L Gonzalez-Garay
2014 Personalized Medicine  
A new technology, next-generation sequencing (NGS), has the potential to accelerate the early detection of disorders and to detect pharmacogenetics markers to customize treatments [2] .  ...  Next-generation sequencing (NGS) has the potential to accelerate the early detection of disorders and the identification of pharmacogenetics markers to customize treatments.  ...  Figure 2 . 2 Generic pipeline for the analysis of next-generation sequencing Figure 3 . 3 The road from next-generation sequencing to personalized medicine Per Med.  ... 
doi:10.2217/pme.14.34 pmid:26000024 pmcid:PMC4437232 fatcat:cqhj3rqrxvef5dzbck6vv5u6ke

A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record

Peter Tarczy-Hornoch, Laura Amendola, Samuel J. Aronson, Levi Garraway, Stacy Gray, Robert W. Grundmeier, Lucia A Hindorff, Gail Jarvik, Dean Karavite, Matthew Lebo, Sharon E. Plon, Eliezer Van Allen (+3 others)
2013 Genetics in Medicine  
Background on the six current CseR sites The six initial CSER sites 5 represent projects looking at the issue of generating and incorporating next-generation sequencing (NGS) data (WES and whole-genome  ...  whole-exome sequencing • Creating and testing novel ways of integrating next- generation sequencing data into the care of patients • Randomized controlled trial CHOP - PediSeq Pediatric patients  ... 
doi:10.1038/gim.2013.120 pmid:24071794 pmcid:PMC3951437 fatcat:s7j4rh3epjgsffm2xygh4d3bqu

Single-Nucleotide Polymorphism Bioinformatics: A Comprehensive Review of Resources

A. D. Johnson
2009 Circulation: Cardiovascular Genetics  
Genome-wide association studies (GWAS) based on largescale SNP genotyping have resulted in the generation and analysis of a previously unprecedented scale of data in the genetics literature, with Ͼ350  ...  The availability of homologous sequences and/or protein data bank structures can both limit and affect the potential for nSNP bioinformatics analysis.  ... 
doi:10.1161/circgenetics.109.872010 pmid:20031630 pmcid:PMC2789466 fatcat:hpihw32xhjbapibxxvggljvnum
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