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.
People
Daryl Gohl, PhD – Innovation Lab Group Leader, Assistant Research Professor, Department of Genetics, Cell Biology, and Developmental Biology
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.
Microbiome
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.
Research collaborations
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.
Applying genomic tools to respond to the COVID-19 pandemic
UMGC Innovation Lab scientists aided the University of Minnesota's and the UMGC's response to the COVID-19 pandemic. In March, the Innovation Lab contributed to the development and clinical validation of a COVID-19 diagnostic assay in just five days. Innovation Lab scientists also helped lead R&D efforts to address supply chain bottlenecks of critical testing reagents, including developing and validating a customized RNA extraction method. Leveraging our experience in NGS methods development, the Innovation Lab also developed a rapid and low-cost tailed amplicon method for sequencing the SARS-CoV-2 genome, which is being used broadly for genomic viral surveillance and epidemiology.
Technology Commercialization
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.
