Phase Genomics Proximity-Ligation


Overview

The UMGC offers proximity ligation library prep and sequencing services for the Phase Genomics platforms. The quantitative linkage information obtained from proximity ligation (aka "Hi-C") data enables the quantification of chromosomal aberrations, and when combined with shotgun metagenomic sequencing data, it generates high-quality genome assemblies directly from complex microbial populations.  

Each Phase Genomics kit yields a dual-indexed proximity ligation library that is sequenced on either our NovaSeq or NextSeq instruments. The UMGC will purchase your kit from Phase Genomics using our bulk discount (15%).

CytoTerra Platform


The CytoTerra Platform leverages proximity ligation sequencing to characterize chromosome abnormalities in a single, ​​NGS-based assay. The technology combines the genome-wide structural and copy number variation detection power of traditional cytogenetics with the molecular-level detection precision of chromosomal microarrays and FISH. 

OncoTerra Platform


The OncoTerra Oncology Platform leverages cutting-edge genomic technology to expand the scope of precision oncology. It takes advantage of the unique properties of ultra-long-range sequencing to unlock the wealth of diagnostic and prognostic information contained in FFPE samples, in a cost-effective and scalable NGS-based assay.

ProxiMeta Platform


The ProxiMeta Metagenome Deconvolution Platform combines cost-effective proximity ligation data with shotgun sequencing data, to assemble high-quality metagenomes and associate mobile genetic elements with their hosts. Capture strain-level resolution without relying on 16S-based techniques, binning, or culturing. 

The ProxiMeta kits include free online ProxiMeta Metagenome Deconvolution analysis (see example sample reports). 

Proximo Platform


The Proximo Platform employs cost-effective proximity ligation data generated using in vivo Hi-C to orient and order contigs into chromosome-scale scaffolds, and generate reference-quality genome assemblies for virtually any organism. Five different kits, optimized for different sample types (human, animal, plant, fungi and microbes) ensure robust results across all organisms.

Customized Genome Scaffolding analysis is available through Phase Genomics for an additional fee. Additional computational services are also available.

Questions?


Contact us at next-gen@umn.edu for a Phase Genomics project quote, including library prep, sequencing, and the discounted kit. The UMGC’s library prep and sequencing services must be used in order to receive the kit discount.

Pricing

Expand all

Standard

 New 2022 proximity ligation library prep rates will be published in July. 

Guidelines

Expand all

Submission

How to order


Please contact next-gen@umn.edu for project specifications and a quote.

Samples can be dropped-off at one of our laboratory locations.

1-202 Nils Hasselmo Hall (Minneapolis campus)

1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)

20 Snyder Hall (St. Paul campus)

If shipping samples, the following address should be used.

Please send the tracking information to next-gen@umn.edu.

University of Minnesota Genomics Center
1475 Gortner Ave.
28 Snyder Hall
St. Paul, MN 55108
612-625-7736

Deliverables

Data Release


There are four options for transferring data from the UMGC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download from a secure website, 3) download with Globus, or 4) shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.

1. MSI storage

Internal clients have their data released to MSI's Shared User Resource Facility Storage (SURFS). Delivered data will be located in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/umgc). MSI does not charge for SURFS storage costs, but files expire and are removed one year after they've been delivered. Files should be copied to other MSI storage locations such as Tier2, Tier3, or your group's "shared" folder before they expire. 

2. Web download

Internal clients that opt-out of MSI storage and external clients can download their data from a secure website using either a web browser or a command-line download tool, complete instructions are provided in an email from the UMGC. The client’s data is available for download for 30 days, after which the data will be removed from the data download website and the client takes responsibility for storing the data.

3. Globus

Internal and External clients can use Globus to download their data. This is the recommended method for external clients to download large datasets.

4. Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client at a cost of $250 per hard drive.

Data Recovery


The UMGC archives most customer data for a year and some datasets are retained for 5 years or more. If you need a dataset re-delivered email a request to next-gen@umn.edu to initiate data recovery. The UMGC does not provide any guarantee that data can be successfully recovered from the archive.