scholarly journals NGS Screening for Identification of Novel Pexophagy-Related Mutation in Arabidopsis thaliana

Proceedings ◽  
2020 ◽  
Vol 76 (1) ◽  
pp. 7
Author(s):  
Katarzyna Sieńko ◽  
Kacper Żukowski ◽  
Kenji Yamada ◽  
Shino Goto-Yamada
Keyword(s):  
Arabidopsis Thaliana ◽  
Sequence Data ◽  
Bioinformatic Analysis ◽  
Mapping Method ◽  
Eukaryotic Cells ◽  
Causative Gene ◽  
Biochemical Pathways ◽  
Conventional Mapping ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Peroxisomes are the type of organelles in eukaryotic cells that are involved in different biochemical pathways depending on the type of cell. We have isolated a number of peroxisome unusual positioning (peup) mutants, which display the accumulation of abnormal peroxisomes, and demonstrated that autophagy is involved in removing damaged organelles. These peup mutants also show defects of other autophagy-related processes, such as the recovery from dark-senescence, and also failed to induce vacuole-related vesicle formations during microautophagy under nutrient deprivations. The aim of this study was to identify the causative gene of the peup33 mutant using next-generation sequencing (NGS) as a tool. Identification of mutations with NGS will allow us to save time compared to the conventional mapping method. Here, we present the workflow of the experiment, the procedure of bioinformatic analysis and the software applied to the sequence data produced by NGS.

scholarly journals Next Generation Sequencing Identifies Five Novel Mutations in Lebanese Patients with Bardet–Biedl and Usher Syndromes

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1047 ◽  
Author(s):  
Lama Jaffal ◽  
Wissam H Joumaa ◽  
Alexandre Assi ◽  
Charles Helou ◽  
George Cherfan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Usher Syndrome ◽  
Bioinformatic Analysis ◽  
Next Generation ◽  
Novel Mutations ◽  
Pathogenic Variants ◽  
Whole Exome ◽  
Targeted Ngs ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Aim: To identify disease-causing mutations in four Lebanese families: three families with Bardet–Biedl and one family with Usher syndrome (BBS and USH respectively), using next generation sequencing (NGS). Methods: We applied targeted NGS in two families and whole exome sequencing (WES) in two other families. Pathogenicity of candidate mutations was evaluated according to frequency, conservation, in silico prediction tools, segregation with disease, and compatibility with inheritance pattern. The presence of pathogenic variants was confirmed via Sanger sequencing followed by segregation analysis. Results: Most likely disease-causing mutations were identified in all included patients. In BBS patients, we found (M1): c.2258A > T, p. (Glu753Val) in BBS9, (M2): c.68T > C; p. (Leu23Pro) in ARL6, (M3): c.265_266delTT; p. (Leu89Valfs*11) and (M4): c.880T > G; p. (Tyr294Asp) in BBS12. A previously known variant (M5): c.551A > G; p. (Asp184Ser) was also detected in BBS5. In the USH patient, we found (M6): c.188A > C, p. (Tyr63Ser) in CLRN1. M2, M3, M4, and M6 were novel. All of the candidate mutations were shown to be likely disease-causing through our bioinformatic analysis. They also segregated with the corresponding phenotype in available family members. Conclusion: This study expanded the mutational spectrum and showed the genetic diversity of BBS and USH. It also spotlighted the efficiency of NGS techniques in revealing mutations underlying clinically and genetically heterogeneous disorders.

scholarly journals Pharmacogenomics in Children: Advantages and Challenges of Next Generation Sequencing Applications

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
O. M. Vanakker ◽  
A. De Paepe
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Next Generation ◽  
Clinical Implementation ◽  
Ethical Aspects ◽  
Number Of Genes ◽  
Working Groups ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Single Reaction

Pharmacogenetics is considered as a prime example of how personalized medicine nowadays can be put into practice. However, genotyping to guide pharmacological treatment is relatively uncommon in the routine clinical practice. Several reasons can be found why the application of pharmacogenetics is less than initially anticipated, which include the contradictory results obtained for certain variants and the lack of guidelines for clinical implementation. However, more reproducible results are being generated, and efforts have been made to establish working groups focussing on evidence-based clinical guidelines. For another pharmacogenetic hurdle, the speed by which a pharmacogenetic profile for a certain drug can be obtained in an individual patient, there has been a revolution in molecular genetics through the introduction of next generation sequencing (NGS), making it possible to sequence a large number of genes up to the complete genome in a single reaction. Besides the enthusiasm due to the tremendous increase of our sequencing capacities, several considerations need to be made regarding quality and interpretation of the sequence data as well as ethical aspects of this technology. This paper will focus on the different NGS applications that may be useful for pharmacogenomics in children and the challenges that they bring on.

scholarly journals Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Biology ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 295
Author(s):  
Girum Fitihamlak Ejigu ◽  
Jaehee Jung
Keyword(s):  
Next Generation Sequencing ◽  
Genome Annotation ◽  
Sequence Data ◽  
Genetic Disorders ◽  
Next Generation ◽  
Functional Annotations ◽  
General Aspects ◽  
Tools And Techniques ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation.

Novel splice variants of the human kallikrein-related peptidases 11 (KLK11) and 12 (KLK12), unraveled by next-generation sequencing technology

2018 ◽  
Vol 399 (9) ◽  
pp. 1065-1071 ◽  
Author(s):  
Panagiotis G. Adamopoulos ◽  
Christos K. Kontos ◽  
Andreas Scorilas
Keyword(s):  
Next Generation Sequencing ◽  
Serine Proteases ◽  
Splice Variants ◽  
Bioinformatic Analysis ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Normal Tissues ◽  
Rapid Amplification ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractTissue kallikrein, kallikrein-related peptidases (KLKs), and plasma kallikrein form the largest group of serine proteases in the human genome, sharing many structural and functional characteristics. In this study, we describe the molecular cloning of four novel splice variants of the humanKLK11andKLK12genes, discovered by combining 3′ rapid amplification of cDNA ends (3′ RACE), next-generation sequencing (NGS) technology, advanced bioinformatic analysis and Sanger sequencing. Expression analysis of these new transcripts in cell lines originating from 17 cancerous and two normal tissues revealed the expression pattern of each transcript. These novelKLK11andKLK12splice variants represent new potential cancer biomarkers.

Endometrial Liquid Biopsy Provides a miRNA Roadmap of the Secretory Phase of the Human Endometrium

2019 ◽  
Vol 105 (3) ◽  
pp. 877-889 ◽  
Author(s):  
Alessia Grasso ◽  
Roser Navarro ◽  
Nuria Balaguer ◽  
Inmaculada Moreno ◽  
Pilar Alama ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Ribonucleic Acid ◽  
Liquid Biopsy ◽  
Bioinformatic Analysis ◽  
Endometrial Receptivity ◽  
Mirna Signature ◽  
Secretory Phase ◽  
Messenger Ribonucleic Acid ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Context Endometrial liquid biopsy (ELB) is a minimally invasive alternative for research and diagnosis in endometrial biology. Objective We sought to establish an endometrial micro ribonucleic acid (miRNA) roadmap based on ELB during the secretory phase of the menstrual cycle in both natural and hormonal replacement therapy (HRT) cycles. Design Human ELB samples (n = 58) were obtained from healthy ovum donors undergoing a natural and an HRT cycle consecutively. miRNA profiles were identified using next-generation sequencing (NGS). For functional analysis, messenger ribonucleic acid targets were chosen among those reported in the endometrial receptivity analysis. Results The human endometrial secretory phase is characterized by a dynamic miRNA secretion pattern that varies from the prereceptive to the receptive stages. No differences in miRNA profiles were found among natural versus HRT cycles in the same women, reinforcing the similarities in functional and clinical outcomes in natural versus medicated cycles. Bioinformatic analysis revealed 62 validated interactions and 81 predicted interactions of miRNAs differentially expressed in the HRT cycle. Annotation of these genes linked them to 51 different pathways involved in endometrial receptivity. Conclusion This NGS-based study describes the miRNA signature in human ELB during the secretory phase of natural and HRT cycles. A consistent endometrial miRNA signature was observed in the acquisition of endometrial receptivity. Interestingly, no significant differences in miRNA expression were found in natural versus HRT cycles reinforcing the functional clinical similarities between both approaches.

scholarly journals An archaeogenetic approach to identify the remains of the Hungarian Kings. Working Plan

2021 ◽  
Vol 1 (2) ◽  
pp. 333-342
Author(s):  
Gergely I. B. Varga ◽  
Kitti Maár ◽  
Alexandra Ginguta ◽  
Bence Kovács ◽  
Balázs Tihanyi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Analysis ◽  
Genetic Information ◽  
Sequence Data ◽  
Rapid Development ◽  
Personal Identification ◽  
Library Preparation ◽  
Working Plan ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

The Royal Basilica of Székesfehérvár was the burial place of fifteen Hungarian kings. Unfortunately, the anthropological findings excavated at the site of the Basilica were mixed up during the tumultuous centuries of Hungary, hence the royal remains still lie unidentified in a charnel-house. The appearance and rapid development of archaeogenetics now allows the personal identification of the royal skeletons from among the remains of the Basilica. The genetic information necessary for the identification of the Árpád dynasty members is accessible, while sequence data of the non-Árpádian kings’ relatives still need to be obtained by further genetic analysis. Here we provide an outline of the investigation for the identity of the royal skeletons: we sketch the process of sample preparation and DNA extraction, the steps of library preparation for next-generation sequencing (NGS) and give a brief report of the current progressions.

scholarly journals A New Binning Method for Metagenomics by One-Dimensional Cellular Automata

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Ying-Chih Lin
Keyword(s):  
Sequence Data ◽  
Taxonomic Diversity ◽  
Similar Species ◽  
One Dimensional ◽  
Space Experiments ◽  
Data Volume ◽  
Multiple Species ◽  
The One ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

More and more developed and inexpensive next-generation sequencing (NGS) technologies allow us to extract vast sequence data from a sample containing multiple species. Characterizing the taxonomic diversity for the planet-size data plays an important role in the metagenomic studies, while a crucial step for doing the study is thebinningprocess to group sequence reads from similar species or taxonomic classes. The metagenomic binning remains a challenge work because of not only the various read noises but also the tremendous data volume. In this work, we propose an unsupervised binning method for NGS reads based on the one-dimensional cellular automaton (1D-CA). Our binning method facilities to reduce the memory usage because 1D-CA costs only linear space. Experiments on synthetic dataset exhibit that our method is helpful to identify species of lower abundance compared to the proposed tool.

scholarly journals SNP Mining in Functional Genes from Nonmodel Species by Next-Generation Sequencing: A Case of Flowering, Pre-Harvest Sprouting, and Dehydration Resistant Genes in Wheat

2016 ◽  
Vol 2016 ◽  
pp. 1-10
Author(s):  
Zhong-Xu Chen ◽  
Mei Deng ◽  
Ji-Rui Wang
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Data ◽  
Low Cost ◽  
Functional Genes ◽  
Accurate Information ◽  
Next Generation ◽  
Polynomial Fitting ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

As plenty of nonmodel plants are without genomic sequences, the combination of molecular technologies and the next generation sequencing (NGS) platform has led to a new approach to study the genetic variations of these plants. Software GATK, SOAPsnp, samtools, and others are often used to deal with the NGS data. In this study, BLAST was applied to call SNPs from 16 mixed functional gene’s sequence data of polyploidy wheat. In total 1.2 million reads were obtained with the average of 7500 reads per genes. To get accurate information, 390,992 pair reads were successfully assembled before aligning to those functional genes. Standalone BLAST tools were used to map assembled sequence to functional genes, respectively. Polynomial fitting was applied to find the suitable minor allele frequency (MAF) threshold at 6% for assembled reads of each functional gene. SNPs accuracy form assembled reads, pretrimmed reads, and original reads were compared, which declared that SNPs mined from the assembled reads were more reliable than others. It was also demonstrated that mixed samples’ NGS sequences and then analysis by BLAST were an effective, low-cost, and accurate way to mine SNPs for nonmodel species. Assembled reads and polynomial fitting threshold were recommended for more accurate SNPs target.

scholarly journals Compartmentalized Replication of SARS-Cov-2 in Upper vs. Lower Respiratory Tract Assessed by Whole Genome Quasispecies Analysis

2020 ◽  
Vol 8 (9) ◽  
pp. 1302 ◽  
Author(s):  
Martina Rueca ◽  
Barbara Bartolini ◽  
Cesare Ernesto Maria Gruber ◽  
Antonio Piralla ◽  
Fausto Baldanti ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Lower Respiratory Tract ◽  
Bioinformatic Analysis ◽  
Whole Genome ◽  
Significant Difference ◽  
Minority Variants ◽  
Selection For ◽  
Next Generation Sequencing Ngs ◽  
Quasispecies Evolution ◽  
Generation Sequencing

We report whole-genome and intra-host variability of SARS-Cov-2 assessed by next generation sequencing (NGS) in upper (URT) and lower respiratory tract (LRT) from COVID-19 patients. The aim was to identify possible tissue-specific patterns and signatures of variant selection for each respiratory compartment. Six patients, admitted to the Intensive Care Unit, were included in the study. Thirteen URT and LRT were analyzed by NGS amplicon-based approach on Ion Torrent Platform. Bioinformatic analysis was performed using both realized in-house and supplied by ThermoFisher programs. Phylogenesis showed clade V clustering of the first patients diagnosed in Italy, and clade G for later strains. The presence of quasispecies was observed, with variants uniformly distributed along the genome and frequency of minority variants spanning from 1% to ~30%. For each patient, the patterns of variants in URT and LRT were profoundly different, indicating compartmentalized virus replication. No clear variant signature and no significant difference in nucleotide diversity between LRT and URT were observed. SARS-CoV-2 presents genetic heterogeneity and quasispecies compartmentalization in URT and LRT. Intra-patient diversity was low. The pattern of minority variants was highly heterogeneous and no specific district signature could be identified, nevertheless, analysis of samples, longitudinally collected in patients, supported quasispecies evolution.

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