Building bioinformatics resources for the global community

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Building bioinformatics resources
for the global community
James Pettengill
james.pettengill@fda.hhs.gov
Biostatistics and...

CFSAN’s open-access peer reviewed methods for analyzing and differentiating
among samples based on WGS data.
Submitted 16 ...

Real-time pathogen detection in the era of whole-genome
sequencing and big data: K-mer and site-based methods for
inferrin...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

•  The adoption of whole-genome sequencing within the public health realm has
resulted in large databases being populated ...

NutButter Outbreak
?
http://www.cdc.gov/salmonella/braenderup-08-14/index.html
NCBI GenomeTrakr Tree

Efficient method
inter-category comparisons
intra-category comparisons
genetic distances
Experimental design: based on a c...

Experimental design:
Simulated data:

Experimental design:
Empirical data:
•  Analyze different distance methods on de novo assemblies of all Salmonella
samples...

Experimental design:
Empirical data: using cloud computing to perform assemblies on GenomeTrakr data
Assembly workflow:
Ob...

Assembly workflow:
Obtain latest metadata file
from NCBI pathogen database
Parse metadata and download raw data
Experiment...

Assembly workflow:
Obtain latest metadata file
from NCBI pathogen database
Parse metadata and download raw data
Quality fi...

Assembly workflow:
Obtain latest metadata file
from NCBI pathogen database
Parse metadata and download raw data
Quality fi...

Assembly workflow:
Obtain latest metadata file
from NCBI pathogen database
Parse metadata and download raw data
Quality fi...

1.  Obtain an assembly for each sample within GenomeTrakr
•  Use pilot of cloud computing to accomplish assemblies – “clou...

Site-based:
Sample1: ACCTAGTACC
Sample2: ACGTACTACC
Requires statements about homology/
sequence alignment
Kmer-based (L =...

Summary of methods used to infer the relationships among samples.
Class Method Description Exec. time (s)
Site-based
Nucme...

Classification of simulated data:
ROC curves identical across
different distance methods
* Simulated data is not complex/
...

Summary/Implications:
•  There are features (e.g., genomic, assembly, and contamination) that cause
k-mer based methods to...

Summary/Implications:
•  There are features (e.g., genomic, assembly, and contamination) that cause
k-mer based methods to...

Summary/Implications:
•  There are features (e.g., genomic, assembly, and contamination) that cause
k-mer based methods to...

Summary/Implications:
•  There are features (e.g., genomic, assembly, and contamination) that cause
k-mer based methods to...

Acknowledgements
FDA
•  Center for Food Safety and Applied Nutrition
•  Biostats/Bioinformatics staff – J. Baugher, H. Ran...

•  False negatives are primarily
due to failure to meet
consensus frequency
threshold
ConsensusFrequency<0.9
Coverage<8
X2...

Validation exercise of CFSAN SNP Pipeline key findings:
•  100× dataset
•  Recovered 98.9% of the introduced SNPs
•  False...

Building bioinformatics resources for the global community

Building bioinformatics resources for the global community

Building bioinformatics resources for the global community

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