Bioinformatics Analysis of Small RNAs in Plants Using Next Generation Sequencing Technologies

Author(s):  
Kan Nobuta ◽  
Kevin McCormick ◽  
Mayumi Nakano ◽  
Blake C. Meyers
2013 ◽  
Vol 2 (2) ◽  
pp. 104-111 ◽  
Author(s):  
Joakim Crona ◽  
Alberto Delgado Verdugo ◽  
Dan Granberg ◽  
Staffan Welin ◽  
Peter Stålberg ◽  
...  

BackgroundRecent findings have shown that up to 60% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are caused by germline or somatic mutations in one of the 11 hitherto known susceptibility genes: SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, HIF2A (EPAS1), RET, NF1, TMEM127 and MAX. This list of genes is constantly growing and the 11 genes together consist of 144 exons. A genetic screening test is extensively time consuming and expensive. Hence, we introduce next-generation sequencing (NGS) as a time-efficient and cost-effective alternative.MethodsTumour lesions from three patients with apparently sporadic PCC were subjected to whole exome sequencing utilizing Agilent Sureselect target enrichment system and Illumina Hi seq platform. Bioinformatics analysis was performed in-house using commercially available software. Variants in PCC and PGL susceptibility genes were identified.ResultsWe have identified 16 unique genetic variants in PCC susceptibility loci in three different PCC, spending less than a 30-min hands-on, in-house time. Two patients had one unique variant each that was classified as probably and possibly pathogenic: NF1 Arg304Ter and RET Tyr791Phe. The RET variant was verified by Sanger sequencing.ConclusionsNGS can serve as a fast and cost-effective method in the clinical genetic screening of PCC. The bioinformatics analysis may be performed without expert skills. We identified process optimization, characterization of unknown variants and determination of additive effects of multiple variants as key issues to be addressed by future studies.


2008 ◽  
Vol 18 (10) ◽  
pp. 1638-1642 ◽  
Author(s):  
D. R. Smith ◽  
A. R. Quinlan ◽  
H. E. Peckham ◽  
K. Makowsky ◽  
W. Tao ◽  
...  

2011 ◽  
Vol 16 (11-12) ◽  
pp. 512-519 ◽  
Author(s):  
Peter M. Woollard ◽  
Nalini A.L. Mehta ◽  
Jessica J. Vamathevan ◽  
Stephanie Van Horn ◽  
Bhushan K. Bonde ◽  
...  

2018 ◽  
Vol 46 (22) ◽  
pp. 11869-11882 ◽  
Author(s):  
Franziska Bonath ◽  
Judit Domingo-Prim ◽  
Marcel Tarbier ◽  
Marc R Friedländer ◽  
Neus Visa

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Daniela Barros-Silva ◽  
C. Marques ◽  
Rui Henrique ◽  
Carmen Jerónimo

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.


2021 ◽  
Author(s):  
Ahmed S Fahad ◽  
Cheng Yu Chung ◽  
Sheila N. Lopez Acevedo ◽  
Nicoleen Boyle ◽  
Bharat Madan ◽  
...  

Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. Here we developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale. To exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen- specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of human TCRs against diverse antigen targets associated with health, vaccination, or disease.


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