Summer 2020 Newsletter

summar 2020 newsletter

 

To help researchers at the University of Minnesota, the state of Minnesota, and elsewhere combat the To help researchers at the University of Minnesota, the state of Minnesota, and elsewhere combat the COVID-19 pandemic, we have developed a high-throughput amplicon-based service for SARS-CoV-2 sequencing


WE'VE REOPENED

The UMN Genomics Center has received permission to resume regular operations at all four of our locations (Snyder, NHH, CCRB, and off-campus at UEL). We will continue to work on projects that were paused during the University's reduced operations, and we are now accepting new non-COVID projects and samples.

We will continue to have significant involvement in Minnesota’s COVID-19 testing effort, and following the University's Sunrise Plan, we have taken measures to stagger staff at our sites to facilitate social distancing. With these factors in mind, turnaround times may initially be longer than we have traditionally been able to provide.

Please reach out to a service manager for service-specific turnaround times. Clients should make arrangements ahead of time to drop off samples as clients are no longer permitted to enter UMGC labs as a public health precaution. Masks are required to enter buildings.

Note: Our Do-It-Yourself (DIY) Service will remain suspended.


SERVICE NEWS & UPDATES

sars cov

SARS-CoV2-Strain Sequencing 

UMGC Launches SARS-CoV-2 Strain Sequencing Service

The UMGC has developed a PCR amplicon-based SARS-CoV-2 strain sequencing service that leverages protocols developed by the ARTIC Network. Our published methodology reduces costs and increases throughput and achieves virtually complete genomic assembly.

To help accelerate the fight against COVID-19, we are offering this service to both UMN and external researchers at cost recovery rates. This service includes QC, library creation, sequencing, genomic assembly and annotation relative to the reference, and optional upload to NextStrain.

Contact next-gen@umn.edu to discuss input requirements.

 

sars cov

Next-generation Sequencing

Lower NovaSeq S4 rate for UMN

We’ve lowered our NovaSeq S4 rate to $6,872 per lane for UMN researchers! Thanks to  a considerable decrease in reagent costs from Illumina, we were able to lower our S4 lane costs by over $1,800 (21%), effective immediately, giving external researchers cost-effective, high-capacity sequencing for popular applications, including RNA Sequencing, Whole-genome and Exome Sequencing, Metagenomic Sequencing, and Genotyping-by-sequencing. 

Clients are encouraged to contact our NGS team at next-gen@umn.edu to discuss via email (or to set up a Zoom consult) your experimental design, library creation methods, and sequencing options.

 

sars cov

Spatial Genomics

GeoMX DSP has arrived!

Thanks to a successful Minnesota Partnership for Biotechnology and Medical Genomics Infrastructure grant awarded to Dr. Laura Niedernhofer (UMN Institute on the Biology of Aging) and Dr. Nathan LeBrasseur (Mayo Clinic), the University of Minnesota will be installing NanoString’s GeoMX Digital Spatial Profiler (DSP).

Available this summer, the GeoMX DSP will enable researchers to rapidly and quantitatively assess the biological implications of the heterogeneity within tissue samples. For the latest on all of our spatial platforms, contact spatialomics@umn.edu

 

sars cov

Long-read Sequencing

New PacBio Sequel II has been installed

In our continuing commitment to assess and acquire emerging genomic technologies, we have advanced our long-read sequencing service by installing the PacBio Sequel II.

With the Sequel II System, UMN researchers will see longer reads with greater accuracy and generate more HiFi data per SMRT Cell 8M. It will enable sequencing of larger inserts (15-20 kb), characterization of a whole transcriptome in a single SMRT Cell 8M, multiplexing up to 48 microbial samples per SMRT Cell 8M, and more.

Contact next-gen@umn.edu for project support.


 


ANNOUNCEMENTS

Congrats to our Illumina NovaSeq S2 Flow Cell awardees! To assist UMN researchers in exploring the NovaSeq’s capabilities and preparing grant applications that take advantage of its power, the UMGC and Illumina partnered on a university-wide grant opportunity to support deep next-generation sequencing projects. PIs awarded S2 flow cells: 
 

Daniel Schmidt, Ph.D. | CBS Genetics, Cell Biology, and Development
The Grammar of Protein Domain Recombination

Nathan Schuldt, Ph.D. | 
Medical School Department of Pediatrics
Comprehensive temporal analysis of insulin-reactive T cells through disease in the non-obese diabetic model of Type 1 diabetes.


RECENT PUBLICATIONS

A Rapid, Cost-Effective Tailed Amplicon Method for Sequencing SARS-CoV-2
Daryl M. Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H. B. Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe, Kenneth B. Beckman. bioRxiv 088724 (2020 May 11). DOI: 10.1101/2020.05.11.088724

Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods
Andrew C. Nelson, Benjamin Auch, Matthew Schomaker, Daryl M. Gohl, Patrick Grady, Darrell Johnson, Robyn Kincaid, Kylene E. Karnuth, Jerry Daniel, Jessica K. Fiege, Elizabeth J. Fay, Tyler Bold, Ryan A. Langlois, Kenneth B. Beckman, Sophia Yohe. bioRxiv 022186 (2020 April 5). DOI: 10.1101/2020.04.02.022186

Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer 
Yingming Li, Rendong Yang, Christine Henzler, Yeung Ho, Courtney Passow, Benjamin Auch, Suzanne Carreira, Daniel Nava Rodrigues, Claudia Bertan, Tae Hyun Hwang, David Quigley, Ha Dang, Colm Morrissey, Michael Fraser, Stephen Plymate, Christopher Maher, Felix Feng, Johann de Bono and Scott Dehm. Clin Cancer Res. (2020 Jan 13). DOI: 10.1158/1078-0432.CCR-19-3023.


WEBINAR

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