SBIR-STTR Award

Reference Standards for Quality Control and Data Validation in Microbiome Studies
Profile last edited on: 9/24/2022

Program
SBIR
Agency
NIH | NIGMS
Total Award Amount
$1,108,867
Award Phase
2
Principal Investigator
Raul J Cano
Activity Indicator

Company Information

(The) Biocollective LLC (AKA:TBC~The Biocollective LLC)

5650 North Washington Street Unit C9
Denver, CO 80216
   (720) 512-3923
   N/A
   www.thebiocollective.com
Multiple Locations:   
Congressional District:   07
County:   Douglas

Phase I

Phase I year
2019
Phase I Amount
$146,719
Significant advances in high-throughput sequencing and new tools for analyzing microbiomes as well as the demonstrated value of microbiome research in human health are driving rapid development in this field. This rapid and exponential increase in microbiome-related studies, however, employs a stochastic, non-standardized approach to microbiome research. As a consequence, a large volume of data has been gathered and interpreted in different ways, not readily comparable among laboratories and therefore, less useful. This must be remedied if microbiome science is to pay a central role in diagnosis and therapy of disease conditions. Because microbial community analysis can be biased by multiple technical factors, e.g., storage conditions, DNA extraction or PCR amplification, reference standards are essential to monitor and evaluate such variables as currently used in clinical chemistry and microbiology. We propose that well characterized, homogeneous and stable reference standards can be used as quality control to routinely monitor the laboratory process and to validate new methods. The results obtained during our Pilot Study indicate that it is feasible to construct a whole genome reference standard that can be homogenized to provide a well-defined microbiome composition that is statistically validated and useful for quality control of microbiome studies. From these results, the development of a reference standard is feasible, with high likelihood of success. We will develop an SOP, optimize the process and scale to commercial quantities the manufacturing of Microbiome Reference Standards (MRS). Each iteration of the manufacturing process will undergo internal validations to assess achieved homogeneity and stability during prolonged storage, as well as data reproducibility. The market for the proposed MRS is a new market in the field of microbiome research. We are not aware of any similar commercial product available. Our initial marketing efforts will be focused on developing key partnerships and developing products that will be sold and distributed through their existing sales channels. The proposed MRS products offers a solution for the unmet need for comprehensive microbiome quality control, addressing the need of the scientific community and NIH Human Microbiome Project. The MRS proposed here, prepared and made available at commercial scale, will provide microbiome practitioners with a much needed, and currently unavailable reference for quality control and validation of microbiomes and serve as gold standard for human microbiomes. Summary: AI 391812 1

Public Health Relevance Statement:
Contact PD/PI: Cano, Raul J. Company: The BioCollective, LLC • Application Identifier: 391812• FOA: PA-18-575 PROJECT NARRATIVE The goal is to develop and validate a manufacturing protocol and Standard Operating Procedure (SOP) for the production and characterization, in commercial quantities, of microbiome reference standards (MRS) from human sources that can be used to identify and quantify sources of bias in the measurements process; from DNA extraction to library preparation to NGS to bioinformatic interpretation as well as to benchmark the results in clinical and diagnostic efforts. These MRS could also be used as quality control material to routinely monitor the measurement process and identify run-to-run variation as well as for assessing and validating new protocols and methods. The BioCollective has the experience, expertise, and track record to develop a reference standard that will be useful and applicable in a wide range of microbiome-related applications and will fill this obvious and necessary void and be instrumental in improving the quality and value of future microbiome research and discovery efforts.

Project narrative:
AI 391812 1

NIH Spending Category:
Genetics; Human Genome; Microbiome

Project Terms:
Address; Area; Automobile Driving; Benchmarking; Bioinformatics; Clinical Chemistry; clinical diagnostics; Clinical Microbiology; Clinical Research; Collaborations; Communities; Consensus; Data; Data Analyses; Development; Diagnosis; diagnostic assay; Disease; DNA; Ensure; experience; Future; Goals; Gold; Guidelines; Health; High-Throughput Nucleotide Sequencing; Human; Human Microbiome; improved; Journals; Laboratories; Libraries; Life; manufacturing process; Marketing; Measurement; Methods; microbial community; microbiome; microbiome analysis; microbiome composition; microbiome research; Monitor; Outcome; Peer Review; Performance; Phase; Pilot Projects; Preparation; Procedures; Process; process optimization; Production; Protocols documentation; prototype; Publications; Publishing; Quality Control; Reagent; Reference Standards; Reproducibility; Role; Running; Sales; Sampling; scale up; Source; Specimen; success; symposium; Testing; tool; United States National Institutes of Health; Validation; Variant; web portal; whole genome

Phase II

Phase II year
2020 (last award dollars: 2021)
Phase II Amount
$962,148
Significant advances in high-throughput sequencing and new tools for analyzing microbiomes as well as the demonstrated value of microbiome research in human health are driving rapid development in this field. This rapid and exponential increase in microbiome-related studies, however, employs a stochastic, non-standardized approach to microbiome research. As a consequence, a large volume of data has been gathered and interpreted in different ways, not readily comparable among laboratories and therefore, less useful. This must be remedied if microbiome science is to pay a central role in diagnosis and therapy of disease conditions. Because microbial community analysis can be biased by multiple technical factors, e.g., storage conditions, DNA extraction or PCR amplification, reference standards are essential to monitor and evaluate such variables as currently used in clinical chemistry and microbiology. We propose that well characterized, homogeneous and stable reference standards can be used as quality control to routinely monitor the laboratory process and to validate new methods. The results obtained during our Pilot Study indicate that it is feasible to construct a whole genome reference standard that can be homogenized to provide a well-defined microbiome composition that is statistically validated and useful for quality control of microbiome studies. From these results, the development of a reference standard is feasible, with high likelihood of success. We will develop an SOP, optimize the process and scale to commercial quantities the manufacturing of Microbiome Reference Standards (MRS). Each iteration of the manufacturing process will undergo internal validations to assess achieved homogeneity and stability during prolonged storage, as well as data reproducibility. The market for the proposed MRS is a new market in the field of microbiome research. We are not aware of any similar commercial product available. Our initial marketing efforts will be focused on developing key partnerships and developing products that will be sold and distributed through their existing sales channels. The proposed MRS products offers a solution for the unmet need for comprehensive microbiome quality control, addressing the need of the scientific community and NIH Human Microbiome Project. The MRS proposed here, prepared and made available at commercial scale, will provide microbiome practitioners with a much needed, and currently unavailable reference for quality control and validation of microbiomes and serve as gold standard for human microbiomes.

Public Health Relevance Statement:
The goal is to develop and validate a manufacturing protocol and Standard Operating Procedure (SOP) for the production and characterization, in commercial quantities, of microbiome reference standards (MRS) from human sources that can be used to identify and quantify sources of bias in the measurements process; from DNA extraction to library preparation to NGS to bioinformatic interpretation as well as to benchmark the results in clinical and diagnostic efforts. These MRS could also be used as quality control material to routinely monitor the measurement process and identify run-to-run variation as well as for assessing and validating new protocols and methods. The BioCollective has the experience, expertise, and track record to develop a reference standard that will be useful and applicable in a wide range of microbiome-related applications and will fill this obvious and necessary void and be instrumental in improving the quality and value of future microbiome research and discovery efforts.

Project Terms:
Address; Area; Automobile Driving; Benchmarking; Bioinformatics; Clinical Chemistry; clinical diagnostics; Clinical Microbiology; Clinical Research; Collaborations; Communities; Consensus; Data; Data Analyses; Development; Diagnosis; diagnostic assay; Disease; DNA; Ensure; experience; Future; Goals; Gold; Guidelines; Health; High-Throughput Nucleotide Sequencing; Human; Human Microbiome; improved; Journals; Laboratories; Libraries; Life; manufacturing process; Marketing; Measurement; Methods; microbial community; microbiome; microbiome analysis; microbiome composition; microbiome research; Monitor; Outcome; Peer Review; Performance; Phase; Pilot Projects; Preparation; Procedures; Process; process optimization; Production; Protocols documentation; prototype; Publications; Publishing; Quality Control; Reagent; Reference Standards; Reproducibility; Role; Running; Sales; Sampling; scale up; Source; Specimen; success; symposium; Testing; tool; United States National Institutes of Health; Validation; Variant; web portal; whole genome