De-risking Microbiome Research and Clinical Discoveries: Robust At-home Methods for Sample Collection, Storage and Transport
Date: May 20, 2020
Time: 1:00 PM CDT
Collection and storage of fecal material are the first steps in processing samples for evaluating microbiome composition and function via high-throughput shotgun sequencing. If samples are not handled and stored correctly, the risk of introducing unwanted variation into the analysis is high. Sample storage at -80°C immediately after sample collection is considered best-practice, or “gold standard”, in microbiome sample preservation. However, access to this storage condition is a major challenge, especially when sample collection occurs away from a research or clinical site. Changes affecting samples can occur rapidly, within days, yet many studies rely on cold chain or collection methods that do not rapidly freeze, or otherwise stabilize the sample. We sought to evaluate the changes in microbiome profile over short durations (1 to 7 days) using collection and storage conditions at room temperature, in an insulated foam container with ice packs, and using the OMNIgene®·GUT collection and stabilization device. Changes over time, and between start and end timepoints were compared to show that unstabilized fecal samples do not represent the originally collected sample. These changes have significant impact on the representation of the taxonomic and functional gene composition.
The presenters will discuss implications of unwanted variation for downstream data analysis, and how the OMNIgene·GUT collection device combined with high quality sequencing and analysis provided by Diversigen’s BoosterShot shallow shot gun approach can help generate more stable and reproducible results, and provide opportunities for home collection while mitigating the need for cold-chain transfer. This is true more so now than ever, allowing research and clinical discoveries to continue during these unprecedented times.
Jean Macklaim is a Bioinformatics Scientist at DNA Genotek, where she is developing and implementing bioinformatics and analytics approaches to sequence data. These R&D efforts are focused on deriving consistent, stable, and meaningful results from metagenomic, metatranscriptomic, and other omics data from a variety of human sample types including stool, oral, and urogenital.
She completed her Ph.D at Western University, Canada with a research focus on computational biology approaches for understanding microbiome function and composition. Her postdoctoral work contributed to developing compositional data analysis tools and methods for differential analysis in metatranscriptomic and high-throughput sequencing data for a number of human health, agriculture, in vitro, and environmental applications.
Christina Fragel is a Bioinformatics Scientist at DNA Genotek where she is developing and implementing bioinformatics and analytics approaches to sequence data. These R&D efforts are centered around statistical analysis and data visualization of the microbial composition in human-derived samples.
She received her Master’s degree in Bioinformatics from the University of Guelph, Ontario, Canada with a focus on machine learning techniques for assessing genetic diversity of invasive insect species.