scholarly journals Transcriptional Identification of Related Proteins in the Immune System of the Crayfish Procambarus clarkii

2018 ◽  
Vol 7 (3) ◽  
pp. 26 ◽  
Author(s):  
Gabina Calderón-Rosete ◽  
Juan González-Barrios ◽  
Manuel Lara-Lozano ◽  
Celia Piña-Leyva ◽  
Leonardo Rodríguez-Sosa
Keyword(s):  
Immune System ◽  
De Novo ◽  
Procambarus Clarkii ◽  
Freshwater Crayfish ◽  
Future Studies ◽  
Consensus Sequences ◽  
Next Generation Sequencing Ngs ◽  
Related Proteins ◽  
Generation Sequencing

The freshwater crayfish Procambarus clarkii is an animal model employed for physiological and immunological studies and is also of great economic importance in aquaculture. Although it is a species of easy husbandry, a high percentage of its production is lost annually as a result of infectious diseases. Currently, genetic information about the immune system of crustaceans is limited. Therefore, we used the abdominal nerve cord from P. clarkii to obtain its transcriptome using Next Generation Sequencing (NGS) to identify proteins that participate in the immune system. The reads were assembled de novo and consensus sequences with more than 3000 nucleotides were selected for analysis. The transcripts of the sequences of RNA were edited for annotation and sent to the GenBank database of the National Center for Biotechnology Information (NCBI). We made a list of accession numbers of the sequences which were organized by the putative role of the immune system pathway in which they participate. In this work, we report on 80 proteins identified from the transcriptome of crayfish related to the immune system, 74 of them being the first reported for P. clarkii. We hope that the knowledge of these sequences will contribute significantly to the development of future studies of the immune system in crustaceans.

scholarly journals HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intra-Host Viral Populations

2020 ◽  
Author(s):  
Matthew L Bendall ◽  
Keylie M Gibson ◽  
Margaret C Steiner ◽  
Uzma Rentia ◽  
Marcos Pérez-Losada ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
De Novo ◽  
Consensus Sequence ◽  
Haplotype Reconstruction ◽  
Consensus Sequences ◽  
Genome Wide ◽  
Genomic Regions ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract Deep sequencing of viral populations using next generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about the intra-host viral molecular epidemiology. Furthermore, existing analytical pipelines may only analyze genomic regions involved in drug resistance, thus are not suited for full viral genome analysis. Here we present HAPHPIPE, a HAplotype and PHylodynamics PIPEline for genome-wide assembly of viral consensus sequences and haplotypes. The HAPHPIPE protocol includes modules for quality trimming, error correction, de novo assembly, alignment, and haplotype reconstruction. The resulting consensus sequences, haplotypes, and alignments can be further analyzed using a variety of phylogenetic and population genetic software. HAPHPIPE is designed to provide users with a single pipeline to rapidly analyze sequences from viral populations generated from NGS platforms and provide quality output properly formatted for downstream evolutionary analyses.

scholarly journals CSF3R T618I, SETBP1 G870S, SRSF2 P95H, and ASXL1 Q780* tetramutation co-contribute to myeloblast transformation in a chronic neutrophilic leukemia

2021 ◽  
Author(s):  
Yi Qian ◽  
Yan Chen ◽  
Xiaoming Li
Keyword(s):  
Alpha Interferon ◽  
Past Medical History ◽  
Variant Allele Frequency ◽  
Significant Past Medical History ◽  
Chronic Neutrophilic Leukemia ◽  
Hypercellular Marrow ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Stat Pathway

AbstractChronic neutrophilic leukemia (CNL) is a rare but serious myeloid malignancy. In a review of reported cases for WHO-defined CNL, CSF3R mutation is found in about 90% cases and confirmed as the molecular basis of CNL. Concurrent mutations are observed in CSF3R-mutated CNL patients, including ASXL1, SETBP1, SRSF2, JAK2, CALR, TET2, NRAS, U2AF1, and CBL. Both ASXL1 and SETBP1 mutations in CNL have been associated with a poor prognosis, whereas, SRSF2 mutation was undetermined. Our patient was a 77-year-old man and had no significant past medical history and symptoms with leukocytosis. Bone marrow (BM) aspirate and biopsy revealed a markedly hypercellular marrow with prominent left-shifted granulopoiesis. Next-generation sequencing (NGS) of DNA from the BM aspirate of a panel of 28 genes, known to be pathogenic in MDS/MPN, detected mutations in CSF3R, SETBP1, and SRSF2, and a diagnosis of CNL was made. The patient did not use a JAK-STAT pathway inhibitor (ruxolitinib) but started on hydroxyurea and alpha-interferon and developed pruritus after 4 months of diagnosis and nasal hemorrhage 1 month later. Then, the patient was diagnosed with CNL with AML transformation and developed intracranial hemorrhage and died. We repeated NGS and found that three additional mutations were detected: ASXL1, PRKDC, MYOM2; variant allele frequency (VAF) of the prior mutations in CSF3R, SETBP1, and SRSF2 increased. The concurrence of CSF3RT618I, ASXL1, SETBP1, and SRSF2 mutation may be a mutationally detrimental combination and contribute to disease progression and AML transformation, as well as the nonspecific treatment of hydroxyurea and alpha-interferon, but the significance and role of PRKDC and MYOM2 mutations were not undetermined.

Role of Ancillary Techniques in Biliary Cytopathology Specimens

2019 ◽  
Vol 64 (1-2) ◽  
pp. 175-181 ◽  
Author(s):  
Lester Layfield
Keyword(s):  
Mutational Analysis ◽  
Diagnostic Sensitivity ◽  
Individual Gene ◽  
Duct Systems ◽  
Brushing Cytology ◽  
Standard Of Practice ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Biliary brushing cytology has become the standard of practice for the investigation of strictures of the biliary and pancreatic duct systems. The methodology however has a limitation in that it has low diagnostic sensitivity when only cytologic evaluation is used. A number of testing methodologies have been applied to brushing specimens in an attempt to improve overall sensitivity without loss of specificity. These have included DNA ploidy analysis, immunocytochemistry, individual gene mutational analysis, fluorescence in-situ hybridization (FISH), and next generation sequencing (NGS). Currently, FISH coupled with routine cytology appears to be the method of choice for improving diagnostic sensitivity. NGS shows significant promise for improvement of diagnostic sensitivity.

scholarly journals The effect of variant interference on de novo assembly for viral deep sequencing

2019 ◽  
Author(s):  
Christina J. Castro ◽  
Rachel L. Marine ◽  
Edward Ramos ◽  
Terry Fei Fan Ng
Keyword(s):  
Deep Sequencing ◽  
De Novo ◽  
Gc Content ◽  
Read Length ◽  
Viral Genomes ◽  
Minor Variant ◽  
Main Driver ◽  
Next Generation Sequencing Ngs ◽  
Viral Sequences ◽  
Generation Sequencing

AbstractViruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approach has surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. Our results from >15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten most used de novo assemblers, and occurs independent of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs. These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.

scholarly journals Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3982 ◽  
Author(s):  
RuiJuan Feng ◽  
Xin Wang ◽  
Min Tao ◽  
Guanchao Du ◽  
Qishuo Wang
Keyword(s):  
Genome Size ◽  
Aquatic Plant ◽  
Nuclear Dna ◽  
De Novo ◽  
Repetitive Sequences ◽  
Nuclear Dna Content ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.

scholarly journals Genetic predisposition to neural crest-derived tumors: revisiting the role of KIF1B

2020 ◽  
Vol 9 (10) ◽  
pp. 1042-1050
Author(s):  
Catherine Cardot Bauters ◽  
Emmanuelle Leteurtre ◽  
Bruno Carnaille ◽  
Christine Do Cao ◽  
Stéphanie Espiard ◽  
...  
Keyword(s):  
Germline Variant ◽  
Whole Exome ◽  
Familial Cancers ◽  
Heterozygous Variant ◽  
Unknown Significance ◽  
Next Generation Sequencing Ngs ◽  
Design And Methods ◽  
Generation Sequencing

Objective We previously described a family in which predisposition to pheochromocytoma (PCC) segregates with a germline heterozygous KIF1B nucleotide variant (c.4442G>A, p.Ser1481Asn) in three generations. During the clinical follow-up, one proband’s brother, negative for the KIF1B nucleotide variant, developed a bilateral PCC at 31 years. This prompted us to reconsider the genetic analysis. Design and methods Germline DNA was analyzed by next-generation sequencing (NGS) using a multi-gene panel plus MLPA or by whole exome sequencing (WES). Tumor-derived DNA was analyzed by SnapShot, Sanger sequencing or NGS to identify loss-of-heterozygosity (LOH) or additional somatic mutations. Results A germline heterozygous variant of unknown significance in MAX (c.145T>C, p.Ser49Pro) was identified in the proband’s brother. Loss of the wild-type MAX allele occurred in his PCCs thus demonstrating that this variant was responsible for the bilateral PCC in this patient. The proband and her affected grandfather also carried the MAX variant but no second hit could be found at the somatic level. No other pathogenic mutations were detected in 36 genes predisposing to familial PCC/PGL or familial cancers by WES of the proband germline. Germline variants detected in other genes, TFAP2E and TMEM214, may contribute to the multiple tumors of the proband. Conclusion In this family, the heritability of PCC is linked to the MAX germline variant and not to the KIF1B germline variant which, however, may have contributed to the occurrence of neuroblastoma (NB) in the proband.

scholarly journals Potentially Actionable Targets: Evidence Standards for Credible Next Generation Sequencing Technology Assessment Claims

2017 ◽  
Vol 8 (3) ◽  
pp. 9
Author(s):  
Paul C Langley
Keyword(s):  
Next Generation Sequencing ◽  
Technology Assessment ◽  
Critical Issue ◽  
Evidence Base ◽  
Cost Of Care ◽  
Next Generation ◽  
Next Generation Sequencing Technology ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Despite considerable resources devoted to developing databases to support competitive credible claims for next generation sequencing (NGS) claims, we have yet to meet the standards required in health technology assessment to support such claims. The purpose of this commentary is to consider options open in establishing claims for NGS recommendations. Although NGS platforms offer potential promise in improving clinical outcomes, supporting cost-effectiveness and reducing the overall cost of care in target populations, this has yet to be demonstrated on a scale that is likely to satisfy reimbursers and health care decision makers. Issues addressed include (i) the importance of credible, evaluable and replicable claims from individual NGS platforms; (ii) the difficulties in moving beyond broad-brush claims for improved survival; (iii) the standards required for an NGS evidence base; (iv) protocol designs in establishing the independent contribution of NGS actionable therapy recommendations to outcomes claims; (v) the role of NGS registries; and (vi) protocols to support ongoing credible, evaluable and replicable claims in target patient populations. The critical issue is not analytical and clinical validity but clinical utility. This has yet to be demonstrated.   Type: Commentary

scholarly journals A cloud-based learning environment for comparing RNA-seq aligners

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 888
Author(s):  
Elizabeth Baskin ◽  
Peter DeFord ◽  
Allison F. Dennis ◽  
Ian Misner ◽  
Frederick J. Tan ◽  
...  
Keyword(s):  
Rna Seq ◽  
Data Intensive ◽  
Data Analyst ◽  
Analysis Process ◽  
Wet Lab ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Machine Image ◽  
Made In

The rapid rise of high-throughput, data intensive experimental techniques has thrust many biologists into the role of data analyst – a role many biologists feel ill equipped to fill. Novices often struggle to find the resources and expertise they need to analyze their experimental results in a wet-lab environment. To fill this need, we developed an educational resource as part of a National Center for Biotechnology Information (NCBI) hackathon. Using RNA-seq as a model, our tutorial guides new users through the steps of data analysis, while placing an emphasis on understanding the motivation behind choices made in the process. To advance the goal of providing a deeper understanding of the analysis process, we developed a new tool, bamDiff. bamDiff allows users to compare the performance of multiple RNA-seq aligners, allowing users to select the most appropriate aligner for the data in question and experimental end-goal. Our tutorial is accessible via a GitHub wiki, with associated data and software provided on an Amazon Machine Image (AMI), which can be completed at no cost to the user through the Amazon Educate Program. Following the hackathon, our tutorial was integrated into the October 2015 offering of NCBI NOW (Next Generation Sequencing (NGS) Online Workshop) a free online experience targeting individuals new to NGS analysis.

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