Baseline Practices for the Application of Genomic Data Supporting Regulatory Food Safety

2017 ◽  
Vol 100 (3) ◽  
pp. 721-731 ◽  
Author(s):  
Dominic Lambert ◽  
Arthur Pightling ◽  
Emma Griffiths ◽  
Gary Van Domselaar ◽  
Peter Evans ◽  
...  
Keyword(s):  
Food Safety ◽  
Best Practices ◽  
Data Streams ◽  
Food Microbiology ◽  
Outbreak Detection ◽  
Genomic Information ◽  
Transfer Of Information ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Abstract The application of new data streams generated from next-generation sequencing (NGS) has been demonstrated for food microbiology, pathogen identification, and illness outbreak detection. The establishment of best practices for data integrity,reproducibility, and traceability will ensure reliable, auditable, and transparent processes underlying food microbiology risk management decisions. We outline general principles to guide the use of NGS data in support of microbiological food safety. Regulatory authorities across intra- and internationaljurisdictions can leverage this effort to promote the reliability, consistency, and transparency of processes used in the derivation of genomic information for regulatory food safety purposes, and to facilitate interactions and the transfer of information in the interest of public health.

scholarly journals Patient Derived Xenografts for Genome-Driven Therapy of Osteosarcoma

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 416
Author(s):  
Lorena Landuzzi ◽  
Maria Cristina Manara ◽  
Pier-Luigi Lollini ◽  
Katia Scotlandi
Keyword(s):  
Clinical Trials ◽  
Tumor Heterogeneity ◽  
Functional Studies ◽  
Ngs Data Analysis ◽  
The Many ◽  
Orthotopic Xenografts ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Somatic Copy Number Alterations

Osteosarcoma (OS) is a rare malignant primary tumor of mesenchymal origin affecting bone. It is characterized by a complex genotype, mainly due to the high frequency of chromothripsis, which leads to multiple somatic copy number alterations and structural rearrangements. Any effort to design genome-driven therapies must therefore consider such high inter- and intra-tumor heterogeneity. Therefore, many laboratories and international networks are developing and sharing OS patient-derived xenografts (OS PDX) to broaden the availability of models that reproduce OS complex clinical heterogeneity. OS PDXs, and new cell lines derived from PDXs, faithfully preserve tumor heterogeneity, genetic, and epigenetic features and are thus valuable tools for predicting drug responses. Here, we review recent achievements concerning OS PDXs, summarizing the methods used to obtain ectopic and orthotopic xenografts and to fully characterize these models. The availability of OS PDXs across the many international PDX platforms and their possible use in PDX clinical trials are also described. We recommend the coupling of next-generation sequencing (NGS) data analysis with functional studies in OS PDXs, as well as the setup of OS PDX clinical trials and co-clinical trials, to enhance the predictive power of experimental evidence and to accelerate the clinical translation of effective genome-guided therapies for this aggressive disease.

scholarly journals Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Molecules ◽  
2018 ◽  
Vol 23 (2) ◽  
pp. 399 ◽  
Author(s):  
Sima Taheri ◽  
Thohirah Lee Abdullah ◽  
Mohd Yusop ◽  
Mohamed Hanafi ◽  
Mahbod Sahebi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

scholarly journals The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data

2017 ◽  
Vol 2 ◽  
pp. 35 ◽  
Author(s):  
Shazia Mahamdallie ◽  
Elise Ruark ◽  
Shawn Yost ◽  
Emma Ramsay ◽  
Imran Uddin ◽  
...  
Keyword(s):  
Sequencing Data ◽  
Targeted Next Generation Sequencing ◽  
Negative Results ◽  
Targeted Ngs ◽  
Predisposition Genes ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Validation Series ◽  
Generation Sequencing ◽  
Dependent Probe

Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.

scholarly journals AbDiver - A tool to explore the natural antibody landscape to aid therapeutic design

2021 ◽  
Author(s):  
Jakub Mlokosiewicz ◽  
Piotr Deszynski ◽  
Wiktoria Wilman ◽  
Igor Jaszczyszyn ◽  
Rajkumar Ganesan ◽  
...  
Keyword(s):  
Rational Design ◽  
Therapeutic Antibody ◽  
Human Antibody ◽  
Use Case ◽  
Therapeutic Antibodies ◽  
Road Map ◽  
Antibody Sequence ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Motivation: Rational design of therapeutic antibodies can be improved by harnessing the natural sequence diversity of these molecules. Our understanding of the diversity of antibodies has recently been greatly facilitated through the deposition of hundreds of millions of human antibody sequences in next-generation sequencing (NGS) repositories. Contrasting a query therapeutic antibody sequence to naturally observed diversity in similar antibody sequences from NGS can provide a mutational road-map for antibody engineers designing biotherapeutics. Because of the sheer scale of the antibody NGS datasets, performing queries across them is computationally challenging. Results: To facilitate harnessing antibody NGS data, we developed AbDiver (http://naturalantibody.com/abdiver), a free portal allowing users to compare their query sequences to those observed in the natural repertoires. AbDiver offers three antibody-specific use-cases: 1) compare a query antibody to positional variability statistics precomputed from multiple independent studies 2) retrieve close full variable sequence matches to a query antibody and 3) retrieve CDR3 or clonotype matches to a query antibody. We applied our system to a set of 742 therapeutic antibodies, demonstrating that for each use-case our system can retrieve relevant results for most sequences. AbDiver facilitates the navigation of vast antibody mutation space for the purpose of rational therapeutic antibody de-sign and engineering. Availability: AbDiver is freely accessible at http://naturalantibody.com/abdiver

scholarly journals ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 50 ◽  
Author(s):  
Michael T. Wolfinger ◽  
Jörg Fallmann ◽  
Florian Eggenhofer ◽  
Fabian Amman
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Motif ◽  
Software Components ◽  
Sequencing Analysis ◽  
Next Generation ◽  
File Formats ◽  
Next Generation Sequencing Analysis ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods

2020 ◽  
Vol 9 (7) ◽  
pp. 2036
Author(s):  
Jaroslaw Bilinski ◽  
Mikolaj Dziurzynski ◽  
Pawel Grzesiowski ◽  
Edyta Podsiadly ◽  
Anna Stelmaszczyk-Emmel ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Fecal Microbiota ◽  
Dead Cell ◽  
Series Of Experiments ◽  
Multi Method Approach ◽  
The Stability ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing ◽  
Selection Of

Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find “super-donor” indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of “good” donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.

scholarly journals A Canadian guideline on the use of next-generation sequencing in oncology

2019 ◽  
Vol 26 (2) ◽  
Author(s):  
S. Yip ◽  
A. Christofides ◽  
S. Banerji ◽  
M. R. Downes ◽  
I. Izevbaye ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Best Practices ◽  
Sample Selection ◽  
Molecular Profile ◽  
Next Generation ◽  
Canadian Guideline ◽  
Molecular Tests ◽  
Management Guidance ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Rapid advancements in next-generation sequencing (ngs) technology have created an unprecedented opportunity to decipher the molecular profile of tumours to more effectively prevent, diagnose, and treat cancer. Oncologists now have the option to order molecular tests that can guide treatment decisions. However, to date, most oncologists have received limited training in genomics, and they are now faced with the challenge of understanding how such tests and their interpretation align with patient management. Guidance on how to effectively use ngs technology is therefore needed to aid oncologists in applying the results of genomic tests. The Canadian guideline presented here describes best practices and unmet needs related to ngs-based testing for somatic variants in oncology, including clinical application, assay and sample selection, bioinformatics and interpretation of reports performed by laboratories, patient communication, and clinical trials.

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