Development and characterization of NIST candidate microbial genomic DNA reference material presentation given at BERM14

1. NIST Microbial Genomic Reference Materials
Characterization of Bacterial
Genomic Reference Materials
Nathan D. Olson
National Institute of Standards and Technology
Biosystems and Biomaterials Bioforum
October 2015
Opinions expressed in this paper are the authors and do not necessarily reflect the policies and views of NIST or affiliated venues. Certain commercial
equipment, instruments, or materials are identified in this paper only to specify the experimental procedure adequately. Such identification is not intended to
imply recommendation or endorsement by the NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for
the purpose. Official contribution of NIST; not subject to copyrights in USA.

2. NIST Microbial Genomic Reference Materials
Why Bacterial
Genomic RMs?

3. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Quality Control

4. NIST Microbial Genomic Reference Materials
RM Selection

5. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Material Selection and Acquisition
Strain Selection

6. NIST Microbial Genomic Reference Materials
RM
Characterization

7. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

8. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

9. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

10. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

11. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

12. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

13. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

14. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials

15. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Pipeline for Evaluating Prokaryotic References

16. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
● S. enterica and S. aureus preliminary results
○ Characterization of Bacterial Genomic Reference Materials.
■ http://dx.doi.org/10.6084/m9.figshare.1451417
● Bioinformatic Pipeline
○ Manuscript Pre-Print Coming Soon https://peerj.com/preprints/
Characterization Results

17. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Computational Reproducibility
Code EnvironmentData

18. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Computational Reproducibility
Data
● Sequence data NIH SRA
○ Bioproject PRJNA252728 http://www.ncbi.nlm.nih.
gov/bioproject/PRJNA252728
● Optical Mapping and Genome Assembly
○ https://github.com/nate-d-olson/NIST_Micro_Genomic_RM_Data

19. Background Material Selection Characterization
NIST Microbial Genomic Reference Materials
Computational Reproducibility
● Bioinformatic Pipeline
○ https://github.com/usnistgov/pepr
○ https://hub.docker.com/r/natedolson/pepr/
○ https://hub.docker.com/r/natedolson/docker-pathoscope/
● Data Analysis and Reporting
○ https://github.com/usnistgov/peprr
Code

20. NIST Microbial Genomic Reference Materials
Conclusions
● Microbial genomic RMs characterized:
○ Genome Assembly
○ Base Level Purity
○ Genomic Contaminants
● RMs and associated data will help validate sequencing and
bioinformatic processes.
● Reproducible and transparent characterization

21. NIST Microbial Genomic Reference Materials
Acknowledgements
FDA:
○ Heike Sichtig
○ Marc Allard
○ Tim Muruvanda
○ Shashi Sharma
○ Nagarajan Thirunavukkarasu
NIST:
○ Marc Salit
○ Justin Zook
○ Scott Jackson
○ Nancy Lin
○ Jenny McDaniel
○ Lindsay Vang
○ David Catoe
○ Steven Lund
This work was supported by the Department of Homeland Security (DHS) Science and Technology
Directorate under the Interagency Agreement HSHQPM-12-X-00078 with NIST and by two interagency
agreements with the FDA.