Custom Library Creation

Next-generation sequencing methodologies and techniques have rapidly evolved over the past few years and new methods are continually being published and commercialized. With such rapid proliferation of new genomic methods, the UMGC has expanded our custom service options to enable researchers to capitalize on the potential of these emerging applications. 

Given the number of these new, non-routine protocols that may only be used by a few research labs, the UMGC is not able to offer all possible methods as part of our standard services. By offering researchers a custom option, it serves as a catch-all for projects requiring specialized attention, higher complexity, optimization, kit customization, method testing, or all of the above. Essentially, custom services give researchers the ability to “Build Your Own Service” when an option isn’t found through our standard services. 

Parameters and expectations are different for custom vs standard services. Each custom project will have a unique set of requirements, yielding different outcomes, costs, and deliverables; unlike standard services with fixed prices and established expectations for turnaround and performance.

Custom Table

Below are examples of custom projects we have worked on or plan to work on. This is not an exhaustive list of options; please reach out (next-gen@umn.edu) to discuss a specific method or protocol not found on our website.

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Commercialized kits

TwinStrand Duplex Sequencing

Duplex sequencing is an ultra-high accuracy sequencing method that overcomes the limitations of next-generation sequencing by independently tracking both strands of individual DNA molecules. Duplex sequencing capitalizes on the naturally-occurring complementarity between strands of the DNA double-helix. Each strand of each original molecule is uniquely labeled such that both can be tracked throughout amplification and sequencing for subsequent error correction. The paired sequences are compared to eliminate errors.

Phase Genomics Ultra-long-range Sequencing

Phase Genomics’ ultra-long-range sequencing technology (enabled by proximity ligation) and computational tools enable researchers to generate direct, quantitative evidence of the spatial relationships between DNA sequences in vivo. The quantitative linkage information obtained from proximity ligation (aka "Hi-C") data enables deeper insights into the architecture, variation, function, and complexity of genomes, epigenomes, and metagenomes.

NEBNext Enzymatic Methyl-Seq (EM-Seq)

NEBNext Enzymatic Methyl-seq (EM-seq) is a new method for identification of 5mC and 5hmC. The highly effective enzymatic conversion minimizes damage to DNA and produces high-quality libraries that enable superior detection of 5mC and 5hmC from fewer sequencing reads. The EM-seq method results in the same converted sequence as WGBS and so the same analysis pipelines can be used.

PacBio Multiplexed Arrays Sequencing (MAS-Seq)

MAS-Seq for 10X 3’ Concatenation kit by PacBio is a kitted solution leveraging 10x Genomics’ Single Cell Gene Expression technology to enable cost-effective long-read single-cell RNA sequencing for a more complete interrogation of the transcriptome. MAS-Seq enables single-cell researchers to better identify and characterize novel isoforms, mutations, and cancer fusion genes, which are particularly relevant in the fields of cancer research and neurodegenerative diseases.

Additional Commercialized Kits

Published methods

Transposon Insertion Sequencing (Tn-seq)

Large-scale transposon mutagenesis coupled with next-generation sequencing (Tn-Seq) is a method to simultaneously assess the essentiality of all genes under experimental conditions. Researchers submit purified DNA for library preparation using NEBNext Ultra II FS DNA Library Prep, followed by PCR enrichment of transposon insertions. The location of each insertion mutation and the number of bacteria with that mutation is determined by sequencing. We are able to customize for different transposons sequences, like Mariner, Tn5, Sleeping Beauty, Piggybac.

Panel design

Custom Sequence Capture

While many off-the-shelf options exist, it is often desirable or necessary to develop a custom capture for a specific target or organism. The UMGC has significant experience working with vendors (Twist, Agilent, IDT) to develop baits for these custom projects. We can coordinate and carry out your entire project, from the design phase through data delivery.

Questions?

Contact us at next-gen@umn.edu with a general description of your project needing custom services, and we will contact you for a project consultation.