scholarly journals Strategies for Development of a Next-Generation Protein Sequencing Platform

2020 ◽  
Vol 45 (1) ◽  
pp. 76-89 ◽  
Author(s):  
Nicholas Callahan ◽  
Jennifer Tullman ◽  
Zvi Kelman ◽  
John Marino
Keyword(s):  
Protein Sequencing ◽  
Next Generation ◽  
Sequencing Platform

The mycobiome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-8
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Dna Sequencing ◽  
Fungal Species ◽  
Next Generation ◽  
Data Set ◽  
Next Generation Dna Sequencing ◽  
Sequencing Platform ◽  
The Family ◽  
Healthy Dogs

Abstract OBJECTIVE To investigate the mycobiome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS 51 dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The whole maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the internal transcribed spacer 2 region with a commercial sequencing platform. RESULTS Fungi were detected in all samples, with a total of 320 fungal species from 135 families detected in the data set. No single fungal species was found in all samples. The 3 most frequently found fungal species were Cladosporium sp (46/51 samples), Malassezia restricta (44/51 samples), and Malassezia arunalokei (36/51 samples). Certain fungi, specifically those of the family Didymellaceae, the family Irpicaceae, and the order Pleosporales, were significantly associated with different stages of periodontitis. Mycobial analysis indicated that Cladosporium sp could be considered part of the core oral cavity mycobiome. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that fungi are present in the oral cavity of dogs and are characterized by substantial species diversity, with different fungal communities associated with various stages of periodontal disease. The next-generation DNA sequencing used in the present study revealed substantially more species of fungi than previous culture-based studies.

A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data

2013 ◽  
Vol 2 (4) ◽  
pp. 86-98
Author(s):  
Chatzinikolaou Panagiotis ◽  
Makris Christos ◽  
Dimitrios Vlachakis ◽  
Sophia Kossida
Keyword(s):  
Next Generation Sequencing ◽  
Level Structure ◽  
Atomic Level ◽  
Protein Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Variant Analysis ◽  
Generation Sequencing

In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

scholarly journals Hi-C chromosome conformation capture sequencing of avian genomes using the BGISEQ-500 platform

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Marcela Sandoval-Velasco ◽  
Juan Antonio Rodríguez ◽  
Cynthia Perez Estrada ◽  
Guojie Zhang ◽  
Erez Lieberman Aiden ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Data Generation ◽  
Next Generation ◽  
Sequencing Data ◽  
Yield Data ◽  
Chromosome Conformation ◽  
Sequencing Platform ◽  
Sequencing Platforms ◽  
Generation Sequencing

Abstract Background Hi-C experiments couple DNA-DNA proximity with next-generation sequencing to yield an unbiased description of genome-wide interactions. Previous methods describing Hi-C experiments have focused on the industry-standard Illumina sequencing. With new next-generation sequencing platforms such as BGISEQ-500 becoming more widely available, protocol adaptations to fit platform-specific requirements are useful to give increased choice to researchers who routinely generate sequencing data. Results We describe an in situ Hi-C protocol adapted to be compatible with the BGISEQ-500 high-throughput sequencing platform. Using zebra finch (Taeniopygia guttata) as a biological sample, we demonstrate how Hi-C libraries can be constructed to generate informative data using the BGISEQ-500 platform, following circularization and DNA nanoball generation. Our protocol is a modification of an Illumina-compatible method, based around blunt-end ligations in library construction, using un-barcoded, distally overhanging double-stranded adapters, followed by amplification using indexed primers. The resulting libraries are ready for circularization and subsequent sequencing on the BGISEQ series of platforms and yield data similar to what can be expected using Illumina-compatible approaches. Conclusions Our straightforward modification to an Illumina-compatible in situHi-C protocol enables data generation on the BGISEQ series of platforms, thus expanding the options available for researchers who wish to utilize the powerful Hi-C techniques in their research.

Updated results from phase II study of guadecitabine for patients with higher risk myelodysplastic syndromes or chronic myelomonocytic leukemia.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 7020-7020 ◽  
Author(s):  
Guillermo Montalban-Bravo ◽  
Prithviraj Bose ◽  
Yesid Alvarado ◽  
Naval Guastad Daver ◽  
Farhad Ravandi ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Complete Response ◽  
Stopping Rules ◽  
Clinical Activity ◽  
Current Response ◽  
Complex Karyotype ◽  
Next Generation ◽  
Sequencing Data ◽  
Tp53 Mutations ◽  
Sequencing Platform

7020 Background: Improving the current response and survival outcomes of patients with higher risk MDS and CMML is fundamental. Guadecitabine is a next generation hypomethylating agent with increased length of exposure compared to decitabine and clinical activity in patients with MDS. Methods: Single arm phase 2 clinical trial of guadecitabine at a dose of 60mg/m2 sc daily for 5 days (days 1-5) every 28 days for patients with newly diagnosed MDS or CMML classified as Intermediate-2 or High risk by IPSS. Primary endpoint is complete response (CR). Responses were evaluated following the revised 2006 International Working Group criteria. Sequencing data was obtained at the time of pre-treatment evaluation by the use of a 28-gene next generation sequencing platform. Study included stopping rules for response and toxicity. Overall survival (OS) was censored at the time of transplant. Results: A total of 53 patients have been enrolled: 50 (94%) are evaluable for toxicity and 44 (83%) for response. Median age is 67 years (49-87). A total of 43 (86%) patients have MDS and 7 (14%) have CMML. A total of 21 (42%) have complex karyotype. Sequencing data was available in 48 (96%) patients with TP53 mutations being the most frequently detected in 36% patients. After a median of 6 treatment cycles (1-20), the ORR is 71% including 32% CR. Median best response occurred by 3 cycles (1-6). Seven (21%) out of 33 evaluable patients achieved a complete cytogenetic response. Ten (20%) subjects proceed to allogeneic stem cell transplantation. Median follow up was 6.3 months (0-23). Median OS is 14.1 months (CI 13.3-14.9 months) and median EFS is 8.4 months (CI 5.6-11.2 months). Forty-five (90%) patients experienced at least one AE during therapy. Most common grade 1-2 AEs included fatigue (66%), nausea (38%) and dyspnea (26%). Dose reductions due to cytopenias were required in 17 (34%) patients. Early 8-week mortality occurred in 3 (6%) patients. Conclusions: Guadecitabine is well-tolerated and active in patients with higher-risk MDS and CMML even in the presence of adverse biological features such as high frequency of complex karyotype, therapy related disease and TP53 mutations. Clinical trial information: NCT02131597.

scholarly journals Applications and data analysis of next-generation sequencing

2013 ◽  
Vol 37 (6) ◽  
Author(s):  
Ina Vogl ◽  
Anna Benet-Pagès ◽  
Sebastian H. Eck ◽  
Marius Kuhn ◽  
Sebastian Vosberg ◽  
...  
Keyword(s):  
Data Analysis ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
High Expectations ◽  
Sequencing Platform ◽  
Software Products ◽  
High Throughput Method ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Enrichment Methods

Abstract:Over the past 6 years, next-generation sequencing (NGS) has been established as a valuable high-throughput method for research in molecular genetics and has successfully been employed in the identification of rare and common genetic variations. Although the high expectations regarding the discovery of new diagnostic targets and an overall reduction of cost have been achieved, technological challenges in instrument handling, robustness of the chemistry, and data analysis need to be overcome. Each workflow and sequencing platform have their particular problems and caveats, which need to be addressed. Regarding NGS, there is a variety of different enrichment methods, sequencing devices, or technologies as well as a multitude of analyzing software products available. In this manuscript, the authors focus on challenges in data analysis when employing different target enrichment methods and the best applications for each of them.

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