"Bacterial Pathogen Genomics at NCBI" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Dr. Bill Klimke.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Applications of Whole Genome Sequencing (WGS) to Food Safety – Perspective fr...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management- United Kingdom. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Web applications for rapid microbial taxonomy identification ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Web applications for rapid microbial taxonomy identification. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...Nathan Olson
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Applications of Whole Genome Sequencing (WGS) to Food Safety – Perspective fr...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management- United Kingdom. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Development of FDA MicroDB: A Regulatory-Grade Microbial Reference DatabaseNathan Olson
"Development of FDA MicroDB: A Regulatory-Grade
Microbial Reference Database" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Heike Sichtig, PhD from the FDA and Luke Tallon from IGS UMSOM.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Web applications for rapid microbial taxonomy identification ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Web applications for rapid microbial taxonomy identification. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Dr. Ben Hause - Pathogen Discovery Using Metagenomic SequencingJohn Blue
Pathogen Discovery Using Metagenomic Sequencing - Dr. Ben Hause, College of Veterinary Medicine, Kansas State University, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Progress report 2016: GMI proficiency testing: Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for surveillance of foodborne infections in Den...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management - Denmark. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
This presents a number of case studies on the application on high-throughput sequencing (HTS), next generation sequencing (NGS), to biological problems ranging from human genome sequencing, identification of disease mutations, metagenomics, virus discovery, epidemic, transmission chains and viral populations. Presented at the University of Glasgow on Friday 26th June 2015.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
Dr. Ben Hause - Pathogen Discovery Using Metagenomic SequencingJohn Blue
Pathogen Discovery Using Metagenomic Sequencing - Dr. Ben Hause, College of Veterinary Medicine, Kansas State University, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Building bioinformatics resources for the global communityExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Building bioinformatics resources for the global community. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Progress report 2016: GMI proficiency testing: Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for surveillance of foodborne infections in Den...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management - Denmark. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
"Microbial Genomics @NIST" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Nathan Olson from NIST.
"Bacterial Pathogen Genomics at NCBI" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by the National Institute for Standards and Technology October 2014 by Dr. Bill Klimke.
Automation in microbiology, changing concept and defeating challengesAyman Allam
A presentation about the automation in microbiology presented in 24th conference of the Egyptian Society of Medical Microbiology and immunology, 4/2017.
Dr. Jianqiang Zhang - Improvement of PRRSV Isolation from Clinical Samples Us...John Blue
Improvement of PRRSV Isolation from Clinical Samples Using a ZMAC Cell Line - Dr. Jianqiang Zhang, Veterinary Diagnostic Lab, Iowa State University, from the 2018 Aptimmune Pre-AASV Symposium, March 2, 2018, San Diego, CA, USA.
More presentations at http://www.swinecast.com/2018-aptimmune-symposium-aasv
An overview of reverse genetic approaches to enhanced FMD vaccines in Africa ...EuFMD
The European Commission for the Control of Foot-and-Mouth Disease (EuFMD), one of FAO’s oldest Commissions, came into being on the 12th June 1954, with the pledge of the sixth founding member state to the principles of a coordinated and common action against Foot-and-mouth Disease.
Unveiling the Potential of your AAV Gene Therapy: Orthogonal methods to under...Merck Life Sciences
Watch the presentation of this webinar here: https://bit.ly/3pCCjPF
Ensure your Adeno-Associated Virus (AAV) is safe throughout its entire drug development journey. Learn methods that will help you speed to clinic, potentially treating diseases sooner and with greater effectiveness.
The potential of gene therapies to cure previously untreatable diseases has spurred the development of novel drugs, including those based on Adeno-Associated Virus (AAV). As with all biopharmaceuticals, it is important to identify and monitor the critical quality attributes (CQAs) of these products to ensure their safety and efficacy.
In this webinar, we will present a range of orthogonal methods to understand and define the CQAs of AAV products. These include assays for the confirmation of capsid protein identity and quantity, as well as the characterization of important product-related impurities, such as aggregates. Together these methods represent a comprehensive analytical testing package to support the characterization and lot release of AAV products.
In this webinar, you will learn:
• How to identify and monitor the critical quality attributes (CQAs) of your AAV therapy
• What assays to utilize to confirm capsid protein identity and quantity
• Why you need look to product characterization to identify and remove important product-related impurities
Unveiling the Potential of your AAV Gene Therapy: Orthogonal methods to under...MilliporeSigma
Watch the presentation of this webinar here: https://bit.ly/3pCCjPF
Ensure your Adeno-Associated Virus (AAV) is safe throughout its entire drug development journey. Learn methods that will help you speed to clinic, potentially treating diseases sooner and with greater effectiveness.
The potential of gene therapies to cure previously untreatable diseases has spurred the development of novel drugs, including those based on Adeno-Associated Virus (AAV). As with all biopharmaceuticals, it is important to identify and monitor the critical quality attributes (CQAs) of these products to ensure their safety and efficacy.
In this webinar, we will present a range of orthogonal methods to understand and define the CQAs of AAV products. These include assays for the confirmation of capsid protein identity and quantity, as well as the characterization of important product-related impurities, such as aggregates. Together these methods represent a comprehensive analytical testing package to support the characterization and lot release of AAV products.
In this webinar, you will learn:
• How to identify and monitor the critical quality attributes (CQAs) of your AAV therapy
• What assays to utilize to confirm capsid protein identity and quantity
• Why you need look to product characterization to identify and remove important product-related impurities
Each year the CPT and the HCPCS code sets undergo significant changes, and your staff needs to be aware of the changes in order to ensure a smooth transition into 2023. Join us for a discussion of the new, deleted and revised CPT codes and associated guidelines for 2023. This is part one in a three part series.
During these complimentary webinars, we will empower you to correctly apply the new and revised codes and discuss the rationale behind this year’s changes. This presentation will be geared towards hospital staff with a focus on the non-surgical sections of the CPT book.
Learning Objectives:
Evaluation of the CPT code changes for the radiology, laboratory and medicine sections of the code book
Discussion regarding changes to guidelines and instructional notes affecting these sections of the code book
Review of the rationale behind the identified code changes
Presentation of coding examples related to the new codes for 2023
Optimized Design of Broadly Detecting qPCR Primers and Probes Using a Conserv...Kate Barlow
Jonas Blomberg, Emeritus Professor of Clinical Virology, Uppsala University, Sweden
Design of broadly detecting qPCRs is a challenge. It requires both an accurate analysis of sequence conservation and of how primers and probes interact with their targets. Hybridization prediction has gone from a simple reliance on GC content to more precise algorithms. Nearest neighbour analysis relies on short distance prediction. We developed an algorithm for longer nucleotide distances, NucZip. It allows design of long primers and probes, using wobble positions and inosine. A computer program which embodies both conservation analysis and hybridization prediction, ConSort, was developed. We used it for development of qPCRs for Orthomyxo-, Corona-, Entero-, Retro- and Noroviruses. Different aspects of the design process will be discussed.
SNP marker development in a QTL region associated with drought tolerance trai...ICRISAT
Drought is a major abiotic stress greatly limiting chickpea production, resulting in up to 50% yield loss. To understand the genetic complexity and mechanism of drought tolerance in chickpea, extensive phenotyping for drought tolerance traits and genotyping using SSR markers was peformed on the ICC 4958 ICC 1882 recombinant inbred line (RIL) population.
24 June 2014
Global germplasm collections: sure benefits without seedborne diseasesCIAT
The Genetic Resources Program is the germplasm bank of CIAT which conserves the collections of bean and tropical forage seeds, and the collection of cassava "in vitro" for a total of approximately 67,500 different accessions. The conservation of these collections allows the benefit of the distribution of germplasm of approximately 6,000 samples of genetic material per year, at national and international level. To minimize the risks associated with the movement of germplasm, especially the transport of pathogens of quarantine interest, it is required a process of laboratory tests certifying the plant quality. This process is carried out in the Germplasm Health Laboratory of the GRP, where also research is developed to improve the effectiveness of the detection, testing reliability and efficiency of operations.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
3. FDA, USDA, CDC State, Local and
Foreign Public Health Agencies
Industry/Academia Additional
DATA ANALYSIS
DATA ASSEMBLY AND
STORAGE and Analysis
DATA ACQUISITION
NCBI, EMBL DDBJ (INDIS)
(Public Access Database)
Our Current Model – Publicly available data
National Network of SequencersIntrenational Network of Sequencers
4. Automated Bacterial Assembly
SRA Reads
sample 1
Trim reads
(Ns, adaptor)
Reference
Distance tree
Find closest reference genome(s)
ArgoCA (Combined Assembly)
De novo assembly panel
Argo (Reference
assisted
assembly)
SOAP denovo
GS-assembler
(newbler)
MaSuRCA
Celera
Assembler
Reads remapped to combined assembly
Contig fasta
Read placements (bam)
Quality profile
SPAdes
5. WGS & Epidemiologically Relevant Distance (ERD)
• WGS allows high resolution genotypic comparison of
pathogen isolates
• What is the epidemiological relevance of genotypic
distance?
• Many methods to compute – we need some common
principles…
6. Since all approaches start with sequence reads, we must
retain for independent confirmation
0
0.2
0.4
0.6
0.8
1
0 500 1000 1500
Millions
FDA-CFSAN: microbial foodborne pathogen
research
SRA format bytes per sequenced base versus
number of bases in MiSeq runs
With Quality Without Qualities
0
0.2
0.4
0.6
0.8
0 200 400 600 800 1000 1200
Millions
OXFORD University: Population Genomics of
Mycobacterium tuberculosis
SRA format bytes per sequenced base versus
number of bases in MiSeq and HiSeq runs
With Quality Without Quality
Storage is manageable…
7. Reliable, transparent, high throughput, high
resolution ERDs?
Major challenge is to distinguish independent
events (SNPs) from single events that generate
multiple nucleotide differences
i.e. collapsed repeats and other artifacts,
alignment errors (reference-based alignments),
sequence quality, & recombination
11. Table: Samples currently processed (as of Sept 5, 2014) in NCBI Pathogen Pipeline
Organisms
Center Listeria Salmonella E. coli Total
CDC 903 903
FDA + State Partners* 858 6129 307 7294
100K 565 34 599
FERA 14 14
Total 1775 6694 341 8810
Processing Status
12. How to measure the system?
need the raw data (sequence reads) in unprocessed form
any read trimming/filtering along with the assembly can be regenerated
13. Assembly metrics
map the reads back to the assembly and generate a profile of each position
(coverage, alleles, qualities)
compare the assembly against other assemblies of the same organism (genus,
species) and check the expected genome size, or similarity to related genomes
annotation metrics such as frameshifted proteins
14. What is the actual measurement for sequence
similarity?
the number of pairwise SNPs between two genomes
What is the threshold?
a pairwise distance (an observationally determined cutoff below which a cluster of 2
or more isolates are considered significantly close enough to warrant further investigation)
15. Sensitivity vs. Specificity
sequence clustering
sensitivity – measure of isolates which belong to the cluster within epidemiologically
relevant distance
(true positives) / true positives + false negatives (not correctly identified)
specificity – measure of isolates which are excluded from a cluster within
epidemiologically relevant distance
(true negatives) / true negatives + false positives
29. Assembly for sample SAMN02727350
Type
Number of
contigs
Sum of contig
lengths
Full assembly 667 5251272
contigs with Listeria hits 37 3031650
contigs with Staphylococcus
hits 630 2203573
34. Table: Assembly stats for SAMN02693748
measurement result
num_input_reads 4212706
aligned_reads 4040070
assembly_num_bases 3180478
assembly_num_contigs 50
assembly_N50 2817733
poor_quality_support_bases 132321
35.
36.
37.
38.
39.
40. Organism Biosample SRA Run Similarity to:
Listeria monocytogenes IEH-NGS-LIS-00100 SAMN02567873 SRR1207486 Listeria SLCC7179
SRR1220750 Listeria J0161
Salmonella enterica Enteritidis MDH-2014-
00798 SAMN02741943 SRR1553852
Schwarzengrund str.
CVM19633
SRR1272871 Enteritidis str. P125109
Salmonella enterica Fluntern MDH-2013-
00153 SAMN02378158 SRR1067624
Javiana and
Schwarzengrund
SRR1395304 Cubana and Agona
41.
42. Proficiency Testing
• Replicate results (phylogeny, SNPs) from published studies
• Resequencing
same isolate on multiple platforms
same isolate in multiple libraries
same isolate in multiple labs
• Blinded submissions
already-characterized isolates
mixed sample isolates
metagenomic isolates
• Corner cases
Extreme coverage
Duplicates
Sample mixups
43.
44.
45.
46.
47. Acknowledgements
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
Richa Agarwala
Azat Badretdin
Slava Brover
Joshua Cherry
Vyacheslav Chetvernin
Robert Cohen
Michael DiCuccio
Mike Feldgarden
Dan Haft
William Klimke
Arjun Prasad
Edward Rice
Kirill Rotmistrovskyy
Stephen Sherry
Sergey Shiryev
Martin Shumway
Tatiana Tatusova
Igor Tolstoy
Chunlin Xiao
Leonid Zaslavsky
Alexander Zasypkin
Alejandro A. Schaffer
Lukas Wagner
Aleksandr Morgulis
David Lipman
James Ostell
NCBI
• This research was supported by the Intramural
Research Program of the NIH, National Library of
Medicine. http://www.ncbi.nlm.nih.gov
CDC
FDA/CFSAN
NIHGRI
UC-Davis
USDA
Vendors: PacBio, Illumina, Roche
