scholarly journals Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1713
Author(s):  
Mattia Zaghi ◽  
Federica Banfi ◽  
Edoardo Bellini ◽  
Alessandro Sessa
Keyword(s):  
Rare Diseases ◽  
Physiological Function ◽  
State Of The Art ◽  
Experimental Models ◽  
Biological Research ◽  
Chromatin Modifications ◽  
Cell Level ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and rare genomic variants and to perform detailed phenotypic characterizations of both physiological organs and experimental models. Recent years have seen the introduction of multiple techniques using NGS to profile transcription, DNA and chromatin modifications, protein binding, etc., that are now allowing us to profile cells in bulk or even at a single-cell level. Although rare and ultra-rare diseases only affect a few people, each of these diseases represent scholarly cases from which a great deal can be learned about the pathological and physiological function of genes, pathways, and mechanisms. Therefore, for rare diseases, state-of-the-art investigations using NGS have double valence: their genomic cause (new variants) and the characterize the underlining the mechanisms associated with them (discovery of gene function) can be found. In a non-exhaustive manner, this review will outline the main usage of NGS-based techniques for the diagnosis and characterization of neurodevelopmental disorders (NDDs), under whose umbrella many rare and ultra-rare diseases fall.

scholarly journals Characterization of Unknown Orthobunya-Like Viruses from India

Viruses ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 451 ◽  
Author(s):  
Shannon Whitmer ◽  
Pragya Yadav ◽  
Prasad Sarkale ◽  
Gouri Chaubal ◽  
Alicia Francis ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Febrile Illness ◽  
Geographic Region ◽  
Emerging Viruses ◽  
Simbu Serogroup ◽  
Isolation And Characterization ◽  
Karnataka State ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-generation sequencing (NGS) of agents causing idiopathic human diseases has been crucial in the identification of novel viruses. This study describes the isolation and characterization of two novel orthobunyaviruses obtained from a jungle myna and a paddy bird from Karnataka State, India. Using an NGS approach, these isolates were classified as Cat Que and Balagodu viruses belonging to the Manzanilla clade of the Simbu serogroup. Closely related viruses in the Manzanilla clade have been isolated from mosquitos, humans, birds, and pigs across a wide geographic region. Since Orthobunyaviruses exhibit high reassortment frequency and can cause acute, self-limiting febrile illness, these data suggest that human and livestock infections of the Oya/Cat Que/Manzanilla virus may be more widespread and/or under-reported than anticipated. It therefore becomes imperative to identify novel and unknown viruses in order to understand their role in human and animal pathogenesis. The current study is a step forward in this regard and would act as a prototype method for isolation, identification and detection of several other emerging viruses.

scholarly journals Unlocking the efficiency of genomics laboratories with robotic liquid-handling

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Houriiyah Tegally ◽  
James Emmanuel San ◽  
Jennifer Giandhari ◽  
Tulio de Oliveira
Keyword(s):  
Next Generation Sequencing ◽  
Sample Preparation ◽  
Return On Investment ◽  
State Of The Art ◽  
Cost Effective ◽  
Laboratory Automation ◽  
Liquid Handling ◽  
Do It Yourself ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract In research and clinical genomics laboratories today, sample preparation is the bottleneck of experiments, particularly when it comes to high-throughput next generation sequencing (NGS). More genomics laboratories are now considering liquid-handling automation to make the sequencing workflow more efficient and cost effective. The question remains as to its suitability and return on investment. A number of points need to be carefully considered before introducing robots into biological laboratories. Here, we describe the state-of-the-art technology of both sophisticated and do-it-yourself (DIY) robotic liquid-handlers and provide a practical review of the motivation, implications and requirements of laboratory automation for genome sequencing experiments.

scholarly journals Caracterización Molecular de la Diversidad Fúngica de los Bosques Llucud y Palictahua: Potencialidades en Control Biológico/Molecular Characterization of Diversity Fungic of the Llucud and Palictahua Forests: Potential in Biological Control

2020 ◽  
Author(s):  
N. S. Erazo Sandoval ◽  
J. C. Manzano Ocaña ◽  
B. D. Patiño Castillo
Keyword(s):  
Biological Control ◽  
Natural Ecosystem ◽  
Metarhizium Robertsii ◽  
Killer Activity ◽  
Pests And Diseases ◽  
Palabras Clave ◽  
Next Generation Sequencing Ngs ◽  
Chemical Pesticides ◽  
Generation Sequencing

Dentro de los microorganismos más abundantes que se pueden encontrar en formaciones ecosistémicas naturales como los bosques andinos del Ecuador se encuentran los hongos microscópicos, los cuales desempeñan funciones cruciales en dichos ecosistemas. Por lo cual el objetivo de esta investigación fue caracterizar molecularmente la diversidad de hongos presentes en los bosques nativos Llucud y Palictahua, estableciendo sus potencialidades de uso en el control biológico de plagas y enfermedades que afectan a los cultivos agrícolas y cuyo control en su mayoría se lo realiza con plaguicidas químicos. Mediante secuenciación de próxima generación (NGS por sus siglas en inglés) de las muestras compuestas de suelo tomadas del horizonte “A” (rizósfera) de cada bosque, se identificaron 56 especies de hongos en Palictahua y 38 en Llucud, presentándose en ambos bosques un total de 6 hongos con importantes potencialidades para su uso en el control biológico, dentro de las cuales se encontraron: Brachyphoris oviparasitica (nematófago), Simplicillium (entomopatógeno y micoparásito), Hamamotoa lignophila (levadura con actividad Killer) en Llucud, y Metarhizium robertsii (entomopatógeno), Brachyphoris oviparasitica (nematófago) y Paraphaeosphaeria parmeliae (micoparásito) en Palictahua. El Bosque Palictahua presentó mayor diversidad de hongos que el bosque Llucud, sin embargo es importante cuidar ambos bosques, pues poseen una gran riqueza microbiana con un sinnúmero de posibilidades de uso en la medicina, industria, biotecnología y otros campos. Among the most abundant microorganisms that can be found in natural ecosystem formations such as the Andean forests of Ecuador are microscopic fungi, which play crucial roles in these ecosystems. So that the objective of this research was to molecularly characterize the diversity of fungi present in the native forests Llucud and Palictahua, establishing their potential for use in the biological control of pests and diseases that affect agricultural crops and whose control is mostly carried out with chemical pesticides. Through next-generation sequencing (NGS for its acronym in English) of compound samples of soil took from “A” horizon (rhizosphere). 56 species of fungi were identified in Palictahua and 38 in Llucud, presenting in both forests a total of 6 fungi with significant potential for use in biological control, among which were found: Brachyphoris oviparasitica (nematophagous), Simplicillium sp. (entomopathogen and mycoparasite), Hamamotoa lignophila (yeast with Killer activity) in Llucud, and Metarhizium robertsii (entomopathogen), Brachyphoris oviparasitica (nematophagous) and Paraphaeosphaeria parmeliae (mycoparasite) in Palictahua. The Palictahua forest presented greater diversity of fungi than the Llucud forest, however it is important to take care of both forests, since they have a great microbial richness with a myriad of possibilities of use in medicine, industry, biotechnology and other fields. Palabras clave: Biodiversidad, Microbiota, Plaguicidas. Keywords: Biodiversity, Microbiota, Pesticides.

scholarly journals PAN2HGENE–tool for comparative analysis and identifying new gene products

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0252414
Author(s):  
Mônica Silva de Oliveira ◽  
Jorianne Thyeska Castro Alves ◽  
Pablo Henrique Caracciolo Gomes de Sá ◽  
Adonney Allan de Oliveira Veras
Keyword(s):  
Comparative Analysis ◽  
Genomic Sequence ◽  
Positive Impact ◽  
Biological Research ◽  
Gene Products ◽  
Original Genome ◽  
New Gene ◽  
Efficient Alternative ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software

scholarly journals Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny

2021 ◽  
Vol 12 ◽  
Author(s):  
Qiang Li ◽  
Lijiao Li ◽  
Huiyu Feng ◽  
Wenying Tu ◽  
Zhijie Bao ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Intron Loss ◽  
Gene Arrangement ◽  
Total Size ◽  
Next Generation Sequencing Ngs ◽  
Different Origins ◽  
Generation Sequencing

In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

scholarly journals PostSV: A Post–Processing Approach for Filtering Structural Variations

2020 ◽  
Vol 14 ◽  
pp. 117793221989295 ◽  
Author(s):  
Eman Alzaid ◽  
Achraf El Allali
Keyword(s):  
State Of The Art ◽  
Post Processing ◽  
Structural Variations ◽  
Sequencing Technologies ◽  
Structural Differences ◽  
Overall Performance ◽  
Next Generation Sequencing Ngs ◽  
Low Coverage ◽  
Ngs Data ◽  
Generation Sequencing

Genomic structural variations are significant causes of genome diversity and complex diseases. With advances in sequencing technologies, many algorithms have been designed to identify structural differences using next-generation sequencing (NGS) data. Due to repetitions in the human genome and the short reads produced by NGS, the discovery of structural variants (SVs) by state-of-the-art SV callers is not always accurate. To improve performance, multiple SV callers are often used to detect variants. However, most SV callers suffer from high false-positive rates, which diminishes the overall performance, especially in low-coverage genomes. In this article, we propose a post-processing classification–based algorithm that can be used to filter structural variation predictions produced by SV callers. Novel features are defined from putative SV predictions using reads at the local regions around the breakpoints. Several classifiers are employed to classify the candidate predictions and remove false positives. We test our classifier models on simulated and real genomes and show that the proposed approach improves the performance of state-of-the-art algorithms.

scholarly journals Advances in Omic Studies Drive Discoveries in the Biology of Anisakid Nematodes

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 801 ◽  
Author(s):  
Stefano D’Amelio ◽  
Fabrizio Lombardo ◽  
Antonella Pizzarelli ◽  
Ilaria Bellini ◽  
Serena Cavallero
Keyword(s):  
Diagnostic Tools ◽  
Parasitic Diseases ◽  
Pathogenic Potential ◽  
Marine Parasites ◽  
Causative Agents ◽  
Biological Aspects ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Anisakid Nematodes

Advancements in technologies employed in high-throughput next-generation sequencing (NGS) methods are supporting the spread of studies that, combined with advances in computational biology and bioinformatics, have greatly accelerated discoveries within basic and biomedical research for many parasitic diseases. Here, we review the most updated “omic” studies performed on anisakid nematodes, a family of marine parasites that are causative agents of the fish-borne zoonosis known as anisakiasis or anisakidosis. Few deposited data on Anisakis genomes are so far available, and this still hinders the deep and highly accurate characterization of biological aspects of interest, even as several transcriptomic and proteomic studies are becoming available. These have been aimed at discovering and characterizing molecules specific to peculiar developmental parasitic stages or tissues, as well as transcripts with pathogenic potential as toxins and allergens, with a broad relevance for a better understanding of host–pathogen relationships and for the development of reliable diagnostic tools.

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