Flicker Effect Analysis in Human Subjects: New Noninvasive Method for Next-Generation Flickermeter

Abstract Background: Microbiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms. Results: The total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species. Conclusion: NGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

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Next generation sequencing in psychiatric research: what study participants need to know about research findings

The International Journal of Neuropsychopharmacology ◽

10.1017/s1461145713000527 ◽

2013 ◽

Vol 16 (9) ◽

pp. 2119-2127 ◽

Cited By ~ 9

Author(s):

Ghislaine Mathieu ◽

Iris Jaitovich Groisman ◽

Beatrice Godard

Keyword(s):

Next Generation Sequencing ◽

Human Subjects ◽

Consent Process ◽

Psychiatric Research ◽

Return Of Results ◽

Next Generation ◽

Research Participants ◽

Research Findings ◽

The Impact ◽

Generation Sequencing

Abstract The use of next generation sequencing (NGS) technologies in psychiatric genetics research and its potential to generate individual research results will likely have far reaching implications for predictive and diagnostic practices. The extent of this impact may not be easily understood by psychiatric research participants during the consent process. The traditional consent process for studies involving human subjects does not address critical issues specific to NGS research, such as the return of results. We examined which type of research findings should be communicated, how this information should be conveyed during the consent process and what guidance is required by researchers and IRBs to help psychiatric research participants understand the peculiarities, the limits and the impact of NGS. Strong standards are needed to ensure appropriate use of data generated by NGS, to meet participants' expectations and needs, and to clarify researchers' duties regarding the disclosure of data and their subsequent management. In the short term, researchers and IRBs need to be proactive in revising current consent processes that deal with the disclosure of research findings.

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GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets

Briefings in Bioinformatics ◽

10.1093/bib/bbaa033 ◽

2020 ◽

Author(s):

Alba Gutiérrez-Sacristán ◽

Carlos De Niz ◽

Cartik Kothari ◽

Sek Won Kong ◽

Kenneth D Mandl ◽

...

Keyword(s):

Next Generation Sequencing ◽

Web Application ◽

Large Scale ◽

Human Subjects ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Phenotypic Data ◽

Data Repositories ◽

Generation Sequencing

Abstract Precision medicine promises to revolutionize treatment, shifting therapeutic approaches from the classical one-size-fits-all to those more tailored to the patient’s individual genomic profile, lifestyle and environmental exposures. Yet, to advance precision medicine’s main objective—ensuring the optimum diagnosis, treatment and prognosis for each individual—investigators need access to large-scale clinical and genomic data repositories. Despite the vast proliferation of these datasets, locating and obtaining access to many remains a challenge. We sought to provide an overview of available patient-level datasets that contain both genotypic data, obtained by next-generation sequencing, and phenotypic data—and to create a dynamic, online catalog for consultation, contribution and revision by the research community. Datasets included in this review conform to six specific inclusion parameters that are: (i) contain data from more than 500 human subjects; (ii) contain both genotypic and phenotypic data from the same subjects; (iii) include whole genome sequencing or whole exome sequencing data; (iv) include at least 100 recorded phenotypic variables per subject; (v) accessible through a website or collaboration with investigators and (vi) make access information available in English. Using these criteria, we identified 30 datasets, reviewed them and provided results in the release version of a catalog, which is publicly available through a dynamic Web application and on GitHub. Users can review as well as contribute new datasets for inclusion (Web: https://avillachlab.shinyapps.io/genophenocatalog/; GitHub: https://github.com/hms-dbmi/GenoPheno-CatalogShiny).

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1201. Sarcoidosis Candidate Microbes Identified by Next Generation Sequencing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.1386 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S622-S622

Author(s):

John D Kriesel ◽

Emily Eckman ◽

Lyska Emerson ◽

Marybeth Scholand ◽

John Hoidal ◽

...

Keyword(s):

Lymph Nodes ◽

Human Subjects ◽

Positive Control ◽

Negative Control ◽

Experimental Sample ◽

Mediastinal Lymph Nodes ◽

Next Generation ◽

Control Subjects ◽

False Discovery Rate Method ◽

Negative Controls

Abstract Background Sarcoidosis is an autoimmune disease characterized by granulomatous lung disease with very prominent mediastinal adenopathy. Acid-fast bacteria, fungi, and viruses have been considered as possible causes of sarcoidosis. We used next-generation or deep sequencing to characterize the microbial content of diseased mediastinal lymph nodes from 10 sarcoidosis patients compared to a set of 10 negative-controls. Methods RNA was extracted from fixed paraffinized mediastinal lymph nodes (MLN) from 12 diseased specimens taken from 10 sarcoidosis patients and 2 positive control subjects (TB, MAI), and normal appearing MLN from 10 negative-control subjects (mostly cancer patients). The extracted RNA was sequenced on the Illumina 2500, yielding 125-bp paired-end reads. These reads were aligned to the human genome, human transcriptome, and a nonredundant panmicrobial database. Each experimental sample were compared against the set of 10 negative-controls using the false discovery rate method (q-value). Directed qPCR was performed on all the samples. Results 100-153 million read-pairs were obtained from the 24 sequenced samples (12 sarcoidosis, 10 negative-control, 2 positive-control). Among these, 0.01-1.32% of the reads were microbial, with a trend towards fewer microbial reads in the sarcoidosis group compared to controls (means 66K vs. 457K, p=0.09). Mycobacterial sequence was significantly enriched (q< 0.05) in the MAI but not the TB sample compared to the negative-controls. Among the 12 sarcoidosis samples, sequence mappings were significantly enriched (q< 0.05) for the following genera: fungal, Magnaporthe (N=4 samples) and Debaromyces (1); bacteria, Odoribacter (1) and Granulicella (1); and viral, Roseolovirus (6) and Mardivirus (6). Further metagenomic analysis eliminated Magnaporthe as a candidate. qPCR confirmed the presence of Odoribacter in 2 specimens and Debaromyces in 1. Roseolovirus (HHV6) could not be detected by qPCR in any of the samples. Conclusion We conclude that sequencing is a feasible method for identifying candidate microbes that might trigger sarcoidosis in human subjects. Further research is required to establish or refute the pathogenicity of these organisms in patients with sarcoidosis. Disclosures All Authors: No reported disclosures

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Application of next generation sequencing for discovery of novel miR-based candidate biomarkers in human subjects

Toxicology Letters ◽

10.1016/j.toxlet.2016.07.173 ◽

2016 ◽

Vol 259 ◽

pp. S68

Author(s):

J. Krauskopf ◽

F. Caiment ◽

T.M. De Kok ◽

K.J. Johnson ◽

R.L. Warner ◽

...

Keyword(s):

Next Generation Sequencing ◽

Human Subjects ◽

Next Generation ◽

Generation Sequencing

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Genomic characterization of fecal microbial communities in severely sick humans and broiler chickens using next generation sequencing

10.21203/rs.2.21973/v1 ◽

2020 ◽

Author(s):

Ome Kalsoom Afridi ◽

Johar Ali ◽

Jeong Ho Chang

Keyword(s):

Next Generation Sequencing ◽

Microbial Communities ◽

Broiler Chickens ◽

Human Subjects ◽

Fecal Microbiota ◽

Next Generation ◽

Microbial Association ◽

Taxonomic Profiling ◽

Microbial Dysbiosis ◽

Generation Sequencing

Abstract BackgroundMicrobiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms.ResultsThe total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species.ConclusionNGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

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Elevated level of circulatory sTLT1 induces inflammation through SYK/MEK/ERK signalling in coronary artery disease

Clinical Science ◽

10.1042/cs20190999 ◽

2019 ◽

Vol 133 (22) ◽

pp. 2283-2299

Author(s):

Apabrita Ayan Das ◽

Devasmita Chakravarty ◽

Debmalya Bhunia ◽

Surajit Ghosh ◽

Prakash C. Mandal ◽

...

Keyword(s):

Risk Factors ◽

Coronary Artery Disease ◽

Coronary Artery ◽

Chronic Inflammation ◽

Ex Vivo ◽

Human Subjects ◽

Critical Role ◽

Atherosclerotic Cardiovascular Disease ◽

Tnf Α ◽

Artery Disease

Abstract The role of inflammation in all phases of atherosclerotic process is well established and soluble TREM-like transcript 1 (sTLT1) is reported to be associated with chronic inflammation. Yet, no information is available about the involvement of sTLT1 in atherosclerotic cardiovascular disease. Present study was undertaken to determine the pathophysiological significance of sTLT1 in atherosclerosis by employing an observational study on human subjects (n=117) followed by experiments in human macrophages and atherosclerotic apolipoprotein E (apoE)−/− mice. Plasma level of sTLT1 was found to be significantly (P<0.05) higher in clinical (2342 ± 184 pg/ml) and subclinical cases (1773 ± 118 pg/ml) than healthy controls (461 ± 57 pg/ml). Moreover, statistical analyses further indicated that sTLT1 was not only associated with common risk factors for Coronary Artery Disease (CAD) in both clinical and subclinical groups but also strongly correlated with disease severity. Ex vivo studies on macrophages showed that sTLT1 interacts with Fcɣ receptor I (FcɣRI) to activate spleen tyrosine kinase (SYK)-mediated downstream MAP kinase signalling cascade to activate nuclear factor-κ B (NF-kB). Activation of NF-kB induces secretion of tumour necrosis factor-α (TNF-α) from macrophage cells that plays pivotal role in governing the persistence of chronic inflammation. Atherosclerotic apoE−/− mice also showed high levels of sTLT1 and TNF-α in nearly occluded aortic stage indicating the contribution of sTLT1 in inflammation. Our results clearly demonstrate that sTLT1 is clinically related to the risk factors of CAD. We also showed that binding of sTLT1 with macrophage membrane receptor, FcɣR1 initiates inflammatory signals in macrophages suggesting its critical role in thrombus development and atherosclerosis.

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