The UMGC Innovation Lab is a research group that operates within the University of Minnesota Genomics Center and develops novel tools and technologies for genomics research. Current areas of focus are improving microbiome measurements, development of synthetic standards for NGS applications, tool development for functional genomics, and long read and single cell sequencing applications.
Daryl Gohl, PhD – Innovation Lab Group Leader, Assistant Research Professor, Department of Genetics, Cell Biology, and Developmental Biology
Ben Auch, MSc – Research Scientist
Genomics Technology Development
The Innovation Lab aims to improve the accuracy and expand the scope, scale, and resolution of genomic measurements. We have developed methods for accurate and high-resolution microbiome profiling (see below), methods for large-scale transposable element mapping, and a novel method (REcount) which allows for PCR-free quantification of engineered constructs using Illumina sequencing. We have used REcount to quantify size biases across different Illumina sequencing platforms.
Illumina size standards allow measurement of sequencer-specific size biases. Top) Design of REcount-based Illumina size standard constructs. Each standard construct contains a normalization barcode, as well as a barcode associated with a variable size standard that can be liberated by MlyI digestion and directly sequenced. Left) Raw abundance data for all 30 size standards and normalization barcodes from a MiSeq run. Right) Size bias profiles of the MiSeq (n=6 flow cells), NextSeq (n=4 flow cells), and NovaSeq (n=1 flow cell, 1 lane) sequencers.
- Measuring sequencer size bias using REcount: a novel method for highly accurate quantification of engineered genetic constructs
Gohl, D.M., Magli, A., Garbe, J., Becker, A., Johnson, D.M., Anderson, S., Auch, B., Billstein, B., Froehling, E., McDevitt, S.L., Beckman, K.B. 2019. Genome Biology, 20(1). 85.
- Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF
Dale, J.L., Beckman, K.B., Willett, J.L.E., Nilson, J.L., Palani, N.P., Baller, J.A., Hauge, A., Gohl, D.M., Erickson, R., Manias, D.A., Sadowsky, M.J., Dunny, G.M. 2018. mSystems. 3(5): e00062-18.
- Large-scale mapping of transposable element insertion sites using digital encoding of DNA sample identity
Gohl, D.M.*, Freifeld, L.*, Silies, M., Hwa, J.J, Horowitz, M., Clandinin, T.R. 2014. Genetics. 196(3) 615-623.
The microbiome plays a critical role in human health and disease, as well as the health of our planetary ecosystem. The UMGC Innovation Lab has been working to improve the accuracy and resolution of microbiome measurements. Our contributions include uncovering mechanistic insights into several forms of error and bias in amplicon-based microbiome studies. In these experiments, we also discovered an unexpected phenomenon, editing of the amplification primers during PCR, which can be exploited to expand the set of taxa that can be detected.
In addition, the UMGC Innovation Lab contributed to the development of a highly scalable shallow shotgun sequencing approach for high-throughput metagenomic sequencing, which allows species or strain-level resolution of a microbial community to be obtained for a fraction of the cost of conventional deep shotgun sequencing, enabling dense sampling and increased power and resolution in large-scale microbiome studies.
An optimized protocol for amplicon-based microbiome profiling. Comparison of the Earth Microbiome Project (EMP) protocol (left) and the UMGC-developed protocol (right). Plots show mean abundance +/- SEM of each organism in the HM-276D even mock community. Expected abundances are indicated with the dashed line.
- Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T.J., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D., Beckman, K.B. 2016.. doi:10.1038/nbt.3601.
- Evaluating the Information Content of Shallow Shotgun Metagenomics
Hillmann, B., Al-Ghalith, G.A., Shields-Cutler, R., Zhu, Q., Gohl, D.M., Beckman, K.B., Knight, R., Knights, D. 2018. mSystems. 3(6) DOI:10.1128/mSystems.00069-18.
- Run-to-Run Sequencing Variation Can Introduce Taxon-Specific Bias in the Evaluation of Fungal Microbiomes
Song, Z., Schlatter, D., Gohl, D.M., Kinkel, L.L. 2018. Phytobiomes. 2(3):165-170.
- DNA Template Dilution Impacts Amplicon Sequencing-Based Estimates of Soil Fungal Diversity
Castle, S.C., Song, Z., Gohl, D.M., Gutknecht, J.L.M., Rosen, C.J., Sadowsky, M.J., Samac, D.A., Kinkel, L.L. 2018. Phytobiomes. 2(2):100-107.
- Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome
Belda, E., Coulibaly, B., Fofana, A., Beavogui, A.H., Traore, S.F., Gohl, D.M., Vernick, K.D, Riehle, M.M. 2017. Scientific Reports. 7:3421.
- Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery
Baldwin, E.A., Walther-Antonio, M., MacLean, A.M., Gohl, D.M., Beckman, K.B., Chen, J., White, B., Creedon, D.J., Chia, N. 2015. PeerJ 3:e1398.
The UMGC Innovation Lab also enters into research collaborations which involve the development or application of genetic or genomic technologies to answer important biological questions. One such collaboration was the sequencing of the zebra mussel genome together with University of Minnesota scientists at MAISRC and MSI.
Left) Zebra mussels (D. polymorpha). Photo by N. Blinick. Right) Plot of long (>25 kb) Oxford Nanopore (red) and PacBio (grey) reads supporting the proposed 67 kb circular D. polymorpha mitogenome structure.
- The Genome of the Zebra Mussel, Dreisena polymorpha: A Resource for Invasive Species Research
McCartney, M.A., Auch, B., Kono, T., Mallez, S., Zhang, Y., Obille, A., Becker, A., Abrahante, J., Garbe, J., Badalamenti, J., Herman, A., Mangelson, H., Liachko, I., Sullivan, S., Sone, E.D., Koren, S., Silverstein, K., Beckman, K., Gohl, D.M. 2019. bioRxiv 696732; doi: 10.1101/696732
- Genome-wide assessment of Mycobacterium tuberculosis conditionally essential metabolic pathways
Minato, Y., Gohl D.M., Thiede, J.M., Chacón, J.M., Harcombe, W.R., Maruyama, F., Baughn, A.D. 2019. mSystems. 4:e00070-19.
- Single-strand consensus sequencing reveals that HIV type but not subtype significantly impacts viral mutation frequencies and spectra
Rawson, J.M.O., Gohl, D.M., Landman, S.R., Roth, M.E., Meissner, M.E., Peterson, T.S., Hodges, J.S., Beckman, K.B., Mansky, L.M. 2017. Journal of Molecular Biology. 429 (2017) 2290-2307.
- FlpStop, a tool for conditional gene control in Drosophila
Fisher Y.E., Yang, H.H, Isaacman-Beck, J., Xie, M., Gohl, D.M., Clandinin, T.R. 2017. eLife. 6:e22279.
In addition to research and education, it is the mission of the University of Minnesota to apply our knowledge and discoveries to benefit the people of the state, the nation, and the world. One way that we do this is through technology commercialization. UMGC Innovation Lab scientists have filed multiple patent applications on new genomics technologies that have been developed at the University of Minnesota and have also worked to translate discoveries through company formation.
Technology commercialization activities
- Founded CoreBiome, Inc., a microbiome services company, which was acquired by OraSure Technologies.
- ANALYTICAL STANDARDS AND METHODS OF USING SAME (application number 62/332,879, international application number PCT/US17/31271). Inventors: Kenneth Beckman and Daryl Gohl.
- SIZE STANDARDS FOR NEXT-GENERATION SEQUENCING (application number 62/630,463). Inventors: Kenneth Beckman and Daryl Gohl.