Bioinformatics platform options for Public Health Laboratories - - PowerPoint PPT Presentation

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May 04, 2023 361 likes •573 views

Bioinformatics platform options for Public Health Laboratories Agenda Introductions Overview and background of bioinformatics Small group sessions Onsite server Commercial platform Webbased platform Discussion and

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Bioinformatics platform options for Public Health Laboratories

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www.aphl.org

Agenda

Introductions
Overview and background of bioinformatics
Small group sessions
On‐site server
Commercial platform
Web‐based platform
Discussion and re‐cap

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www.aphl.org

Introductions

Christin Hanigan, APHL
Kelly Oakeson, UT PHL
Joel Sevinsky, Thiagen, LLC
Kevin Libuit, VA DCLS
Logan Fink, CO PHL

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www.aphl.org

The Deep Impact of Next Generation Sequencing

100 1,000 10,000 100,000 1,000,000 10,000,000 100,000,000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015

Nucleotides per $1,000

Moore’s Law

Adapted from NHGRI (https://www.genome.gov/sequencingcosts)

Sanger Sequencing Next‐Generation Sequencing

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www.aphl.org

Advanced Molecular Detection (AMD)

2011: “Bioinformatics Blue Ribbon Panel” 2014: Advanced Molecular Detection and Response to Infectious Disease Outbreaks (AMD) budget initiative approved by Congress

$30M/yr public health laboratory innovation program
Focus on transformational laboratory tech & scientific computing

The AMD Program has five key objectives:

1. Improve pathogen detection and characterization
2. Enable new diagnostic methods to meet public health needs
3. Support genomic and bioinformatics needs in the US public

health system

4. Implement enhanced, sustainable, integrated information

systems

5. Develop tools for prediction, modeling and early recognition
f emerging infectious threats

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www.aphl.org

Training lead only

GA PHL
WY PHL
MI PHL

Bioinformatics Resource lead

nly
CO PHL
FL BPHL
WI SLH

Training and Bioinformatics resource

VA DCLS
MN PHL
MA PHL
WA PHL

Workforce Development and Bioinformatics Regional Resource support

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www.aphl.org

NGS Capacity in PHL (2013)

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www.aphl.org

NGS Capacity in PHL (2015)

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www.aphl.org

NGS Capacity in PHL (2016)

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www.aphl.org

NGS Capacity in PHL (2018)

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www.aphl.org

Bioinformatics platforms utilized by PHLs

0.00% 5.00% 10.00% 15.00% 20.00% 25.00% 30.00% 35.00% 40.00% 45.00%

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www.aphl.org

Bioinformatics resources accessed by PHLs

0.00% 10.00% 20.00% 30.00% 40.00% 50.00% 60.00% Access to bioinformaticians through external partnership Other staff trained to perform bioinformatics analysis Regional resource* No access to bioinformaticians Bioinformaticians

n staff

Bioinformatics fellow

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www.aphl.org

Pathogens PHLs are sequencing outside of Pulsenet

0.00% 5.00% 10.00% 15.00% 20.00% 25.00%

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www.aphl.org

All 50 states have at least 1 sequencer in-house.

Began as primarily foodborne enteric bacterial pathogens

Network-driven initiative
Surveillance and outbreak detection
Transitioning from PFGE to WGS since 2014
Heavy reliance on federal partners for bioinformatics analysis

Growing dependence on WGS data

PulseNet: Complete transition to WGS for national surveillance of

major foodborne pathogens by January of 2019

Bioinformatics capacity and support continues to be one of the biggest challenges in the growth of NGS

NGS in PHL

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www.aphl.org

Agenda

Introductions
Overview and background of bioinformatics
Small group sessions
On‐site server
Commercial platform
Web‐based platform
Discussion and re‐cap

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www.aphl.org

Questions?

Christin Hanigan

Sr. Specialist, AMD

Christin.Hanigan@aphl.org Office of Advanced Molecular Detection, CDC Greg Armstrong Tiki Barnes Duncan MacCannell

amd@cdc.gov

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www.aphl.org

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www.aphl.org

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www.aphl.org

Input: DNA/RNA

Source: Genomic Amplicon Whole sample Host/vector/ pathogen/ environment …

Library

Output: Information From Sequence Data

Comparative Genomics Identification High res Straintyping/Subtyping Cluster identification Molecular evolution Genotypic characterization Virulence, AR, signatures Functional annotation Diagnostic dev/validation Minor populations, quasispecies Host/pathogen expression Metagenomics Pathogen identification/discovery Culture‐independent diagnostics Microbial ecology/diversity

Data Info.

ACAATTTGTGCATAACATGTGGACAGTTTTAATCACATGTGGGTAAATAGTTGTCCACATTTGCTTTTTT TGTCGAAAACCCTATCTCATATACAAACGACGTTTTTAGGTTTTAAAATACGTTTCGTATAAATATACAT TTTATATTTATTAGGTTGTACATTTGTTGCGCAACCTTATTCTTTTACCATCTTAGTAAAGGAGGGACAC CTTTGGAAAATATCTCTGATTTATGGAATAGTGCCTTAAAAGAATTAGAAAAAAAGGTAAGCAAGCCTAG TTATGAAACATGGTTAAAATCAACAACGGCTCATAACTTGAAGAAAGACGTATTAACGATTACAGCTCCA AATGAATTTGCTCGTGACTGGCTAGAATCTCATTACTCAGAACTTATTTCGGAAACACTATACGATTTAA CAGGGGCAAAATTAGCAATTCGCTTTATTATTCCCCAAAGTCAATCGGAAGAGGACATTGATCTTCCTCC AGTTAAGCGGAATCCAGCACAAGATGATTCAGCTCATTTACCACAGAGCATGTTAAATCCAAAATATACA TTTGATACATTTGTTATCGGCTCTGGTAACCGTTTTGCCCATGCAGCTTCATTAGCTGTAGCCGAGGCGC CAGCTAAAGCGTATAATCCACTCTTTATTTATGGGGGAGTTGGGCTTGGAAAGACGCATTTAATGCACGC AATTGGTCATTATGTAATTGAACATAATCCAAATGCAAAAGTTGTATATTTATCATCAGAAAAATTCACG AATGAATTTATTAACTCTATTCGTGATAATAAAGCTGTTGATTTTCGTAATAAATATCGCAACGTAGATG

NGS

Workflow: Platforms Chemistry

Perf. char.

Labor/TaT Expertise Cost

Bioinformatics

Workflow: Hardware/software Specialized skillsets Algorithms/pipelines Pathogen databases Data analysis/interpret/ Integration/visualization

Increasingly Universal Workflows

Working to establish standardized sequencing workflows for a wide range of pathogens.

Many results from a single dataset. Faster and cheaper than serial tests. A Moving Target

Rapidly evolving technology space. Changing hardware and COTS/OSS capabilities. Lots of choice, but lack of consistent standards. BIG

DATA. New workforce and skillset is

required.

Pathogen‐ and application‐specific, standard and/or compliant assays

File hashes/versioning Validated methods/databases Process logging/audit QA/QC Skills/proficiency Standards Reporting Security Sample intake Prep/staging Extraction Conversion Library prep Sequencing