bioinformatics platform options - aphl · began as primarily foodborne enteric bacterial pathogens...
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Bioinformatics platform options for Public Health Laboratories
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
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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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 $1,00
0
Moore’s Law
Adapted from NHGRI (https://www.genome.gov/sequencingcosts)
Sanger Sequencing Next‐Generation Sequencing
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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 characterization2. Enable new diagnostic methods to meet public health needs3. Support genomic and bioinformatics needs in the US public
health system4. Implement enhanced, sustainable, integrated information
systems5. Develop tools for prediction, modeling and early recognition
of emerging infectious threats
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Training lead only• GA PHL• WY PHL• MI PHL
Bioinformatics Resource lead only• 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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NGS Capacity in PHL (2013)
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NGS Capacity in PHL (2015)
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NGS Capacity in PHL (2016)
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NGS Capacity in PHL (2018)
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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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Bioinformatics resources accessed by PHLs
0.00%
10.00%
20.00%
30.00%
40.00%
50.00%
60.00%
Access tobioinformaticiansthrough external
partnership
Other stafftrained toperform
bioinformaticsanalysis
Regionalresource*
No access tobioinformaticians
Bioinformaticianson staff
Bioinformaticsfellow
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Pathogens PHLs are sequencing outside of Pulsenet
0.00%
5.00%
10.00%
15.00%
20.00%
25.00%
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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
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
www.aphl.org
Questions?Christin HaniganSr. Specialist, [email protected]
Office of Advanced Molecular Detection, CDCGreg ArmstrongTiki BarnesDuncan [email protected]
www.aphl.org
www.aphl.org
www.aphl.org
Input: DNA/RNASource:GenomicAmpliconWhole sample
Host/vector/pathogen/environment
…
Library
Output: InformationFrom Sequence Data
Comparative GenomicsIdentificationHigh res Straintyping/SubtypingCluster identificationMolecular evolutionGenotypic characterizationVirulence, AR, signaturesFunctional annotationDiagnostic dev/validationMinor populations, quasispeciesHost/pathogen expression
MetagenomicsPathogen identification/discoveryCulture‐independent diagnosticsMicrobial ecology/diversity
Data Info.
ACAATTTGTGCATAACATGTGGACAGTTTTAATCACATGTGGGTAAATAGTTGTCCACATTTGCTTTTTT TGTCGAAAACCCTATCTCATATACAAACGACGTTTTTAGGTTTTAAAATACGTTTCGTATAAATATACAT TTTATATTTATTAGGTTGTACATTTGTTGCGCAACCTTATTCTTTTACCATCTTAGTAAAGGAGGGACAC CTTTGGAAAATATCTCTGATTTATGGAATAGTGCCTTAAAAGAATTAGAAAAAAAGGTAAGCAAGCCTAG TTATGAAACATGGTTAAAATCAACAACGGCTCATAACTTGAAGAAAGACGTATTAACGATTACAGCTCCA AATGAATTTGCTCGTGACTGGCTAGAATCTCATTACTCAGAACTTATTTCGGAAACACTATACGATTTAA CAGGGGCAAAATTAGCAATTCGCTTTATTATTCCCCAAAGTCAATCGGAAGAGGACATTGATCTTCCTCC AGTTAAGCGGAATCCAGCACAAGATGATTCAGCTCATTTACCACAGAGCATGTTAAATCCAAAATATACA TTTGATACATTTGTTATCGGCTCTGGTAACCGTTTTGCCCATGCAGCTTCATTAGCTGTAGCCGAGGCGC CAGCTAAAGCGTATAATCCACTCTTTATTTATGGGGGAGTTGGGCTTGGAAAGACGCATTTAATGCACGC AATTGGTCATTATGTAATTGAACATAATCCAAATGCAAAAGTTGTATATTTATCATCAGAAAAATTCACG AATGAATTTATTAACTCTATTCGTGATAATAAAGCTGTTGATTTTCGTAATAAATATCGCAACGTAGATG
NGSWorkflow:PlatformsChemistryPerf. char.Labor/TaTExpertiseCost
BioinformaticsWorkflow:Hardware/softwareSpecialized skillsetsAlgorithms/pipelinesPathogen databasesData analysis/interpret/Integration/visualization
Increasingly Universal WorkflowsWorking 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 TargetRapidly 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/versioningValidated methods/databases
Process logging/audit
QA/QCSkills/proficiency
StandardsReporting
SecuritySample intakePrep/stagingExtraction
ConversionLibrary prepSequencing