The DNA Sequencing Facility is a fee-for-service facility dedicated to providing access to technologies and methods that will keep University of Wisconsin on the forefront of research. The Facility evaluates the latest sequencing technologies, DNA library preparation methods, and DNA extraction methods to enable detection of large and small structural variants, base-specific methylation status, inter- and intra- chromosomal interactions, phased mutations across entire genes, and assembly of genomes and plasmids specific to a researcher’s study. The Facility is licensed to provide GBS/ddRAD/RAD-Seq library prep and sequencing for genotyping studies. Current evaluations include shotgun metagenomics and metatransciptomics using both long read and short read platforms with the goals of identifying all biological pathways in a microbiome sample and associate community-wide and species-specific expression.

The DNA Sequencing Facility resides within ca. 3,900 sq ft of laboratory and office space in the UW Biotechnology Center (UWBC), located at 425 Henry Mall, and is supported by ten full time scientists. The facility is directed by Dr. Joshua Hyman (PhD, 2001, The Pennsylvania State University). The facility offers DNA extraction, genotyping, and sequencing services to several hundred laboratories on the UW-Madison campus, biotechnology companies at the University of Wisconsin Research Park, and public and private laboratories across the United States and on six continents. An analysis of user fees over the last three years shows that 52% of current sequencing clients are NIH funded. The facility has an excellent long-standing relationship with researchers from the Wisconsin State Lab of Hygiene and collaborates with researchers from the UW School of Medicine and Public Health, and the UW Carbone Cancer Center on human whole genome, whole exome, and RNA-Seq studies. Directors of the DNA Sequencing Facility, the Bioinformatics Resource Center, and the Gene Expression Center work closely together to ensure all facets of the next generation sequencing workflow are seamlessly coordinated and we maintain relationships with next generation sequencing facilities at other Midwest institutions to share best practices and provide regional support. The Facility has twenty seven years of sound fiscal and operational management, with Dr. Hyman at the helm for the last eighteen years. All major equipment is covered by service contracts, and routine maintenance procedures are followed to keep downtime to a minimum.

The Facility has experienced increasing demand for next generation sequencing services since our first Illumina platform was installed in 2009, but is committed to keeping pace through equipment upgrades and purchases. Next generation sequencing projects are completed using a mix of Illumina NovaSeq and MiSeq sequencers for short read projects, and Pacific BioScience (2 Sequel IIs) and Oxford Nanopore (PromethION, GridION) sequencing platforms for long and short read projects. Facility staff have performed over 3,700 Illumina sequencing runs and hundreds of long read runs. Staff are experienced with the full range of next generation sequencing applications, often aiding UW researchers and local companies with beta-testing of kits and custom protocols. QC metrics are closely monitored to proactively detect and correct for reagent or machine failures, guaranteeing customers consistently high quality data. Illumina customers can purchase sequencing by the flow cell, by the lane, or by a partial lane with sequencing on a shared lane priced on a per million read basis. This provides access to low cost next generation sequencing to all customers, no matter the size of their project.

The Facility is upgrading its laboratory information management system (LIMS) and soon will be tracking all sample processing via Lockbox LIMS from Third Wave Analytics. Application- specific laboratory workflows are clearly defined prior to any sample processing and all workflow steps, QC data, and other relevant information is permanently associated with samples either as user input captured in the database or as attached files. Instrument run parameters and the location of the data generated are recorded for each sample. Each LIMS user is assigned a
secure login and password and made a member of a group having defined roles and access. Alterations to the information within the LIMS require a digital signature and role-based permission. The database and linked files, including the raw sequence data, are stored on a 500 terabyte storage server with scheduled backups to a remote location. The password protected data can be accessed 24/7 from any location.