Dr. Douglas Marthaler - Use of Next Generation Sequencing for Whole Genome Analysis of Pathogens
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Using Next Generation Sequencing for Whole Genome Analysis of Pathogens Douglas Marthaler, PhD Assistant Professor University of Minnesota Veterinary Diagnostic Laboratory Fangzhou Chen, Matthew Jarvis, Ham Lam, and Todd Knutson Leman Conference September 19 th , 2016 St. Paul, Minnesota
Transcript of Dr. Douglas Marthaler - Use of Next Generation Sequencing for Whole Genome Analysis of Pathogens
Using Next Generation Sequencing for Whole Genome
Analysis of PathogensDouglas Marthaler, PhD
Assistant ProfessorUniversity of Minnesota Veterinary Diagnostic Laboratory
Fangzhou Chen, Matthew Jarvis, Ham Lam, and Todd Knutson
Leman ConferenceSeptember 19th, 2016St. Paul, Minnesota
NGS platformsNGS, Amplified Single Molecule Sequencing• 454 Sequencing-Roche
– GS Junior System– GS FLX+ System
• Illumina-Solexa– HiSeq– Miseq
• Applied Biosystems-Thermo– SOLiD 5500 systems
• Ion Torrent –Thermo– Personal Genome Machine
(PGM)– Proton
Third Generation Sequencing, Single Molecule Sequencing• Helicos• Pacific Biosciences• Oxford Nanopore
Technologies– GridlON System– MinION
Amplified Single Molecule Sequencing
Third Generation Sequencing, Single Molecule Sequencing
Multiplexing
Genome Assembly: ConceptComplete genome sequences don’t come flying out
of the sequencing machines, instead,Tiny genome “pieces” are produced.Must “stitch” the pieces together.This is known in genomics as “Assembly”.
Genome Assembly Tools: HardwareMinnesota Supercomputing Institute
Multi-processors workstations
Connected to MSI network
Supercomputers
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Whole genome comparison of PEDV strains
Song D, Park B. Virus Genes. 2012 Apr;44(2):167-75. doi: 10.1007/s11262-012-0713-1. Epub 2012 Jan 22. Review.PubMed PMID: 22270324.
Regions of diversity
• NSP2 and NSP3 function is ambiguous, but might play a role in host antagonist activities
Recombination within US strains
PRRS investigations
Can whole genome sequencing answer all the industries question?
Will WG sequencing solve all the problems?
• Neurological case of PRRS– Virus was introduced from another system– ORF5 =100% nucleotide identity– WG = 99.33% nucleotide identity (~100 nt and 19 aa changes)
• What’s causing neurological signs? – Undiscovered protein, amino acid changes, ect? – More basic research is needed to understand this relationship!
Will WG sequencing solve all the problems?
• PRRS break in non-immunized herd– Severe clinical signs in piglets (Ct values = 6-11)– ORF5 =99.17% nucleotide identity to vaccine strain– WG = 99.6% nucleotide identity (61 nt changes)
• Revertant from the vaccine strain • Any PRRS strain can cause abortions and mortality during late
gestation!
AcknowledgementsSwine veterinarians for sending the samples and allowing me to assist with trying to solve the problem. THANK YOU!
• My apologizes for the lengthy duration to receive results
Meet the research team and learn more about other research projects
Marthalerlab.org
