Applications

Cell Free DNA (cfDNA)

Sequencing of cfDNA is an area of intense interest to the DNA sequencing community. Characterization of cfDNA from non-normal sources can provide diagnostic insight for pregnancies, cancer, and potentially other situations.

New research has shown that the cost of determining genetic conditions through sequencing can be improved through gel size selection that looks to recover cfDNA from non-normal tissues while excluding that from healthy, normal cells.  [citation #1: Underhill et al] [citation #2: Mouliere et al].

Coastal Genomics works with academic and clinical collaborators to realize the benefits of size selection for this application. Our latest undertaking with the Dr. Hunter Underhill at the University of Utah contributed to an enrichment of mutant allele fractions by an order of magnitude, while concurrently reducing the false-positive rate.

Metagenomics

Metagenomic sequencing of bacterial communities can involve so-called tagmentation approaches to library preparation. This process relies on the tight control of an enzymatic process that fragments larger DNA fragments into smaller pieces, the length of which cluster around a desired size.

Often, unavoidable deviations can lead to inconsistent fragment length profiles between different samples. This in turn can produce sequencing reads that are undesirably short, greatly limiting the data output of the sequencing run. Dr. Miguel Uyuguari-Diaz has leveraged Ranger® Technology to improve data output for his metagenomic research on antibiotic resistance genes [citation #1: Uyaguari-Diaz et al] [citation #2: Uyaguari-Diaz et al].

Small Nucleic Acid Work

The operating principle behind Ranger Technology was developed with the intent of recovering small nucleic acids while confidently rejecting adaptermers that were close in size to the target. Work with microRNA-SEQ experiments greatly benefits from size selection which can be accurately conducted at any scale with Ranger Technology.

Bioanalyzer 2100 (Agilent) electropherogram of proxy sample that was size selected using Ranger Technology

Bioanalyzer 2100 electropherogram of proxy sample post size selection with Ranger Technology

Overlay of Bioanalyzer 2100 electropoerograms of proxy sample input (pre size selection) and output (post size selection with Ranger Technology).

Large Fragment Isolation

The growing interest in sequencing of large DNA fragments has led to increased throughput requirements for selective exclusion of smaller DNA fragments that can cause problems for the application. Ranger Technology can process up to 96 samples in parallel for exclusive recovery of large DNA fragments. Size selections that reject fragments below a specific cutoff threshold can be conducted for samples up to 4 ug in total mass.

DNA Quality Control

Ranger Technology comes with the hardware complement that is necessary for it to act as a DNA quality control instrument. In addition to being compatible with Coastal Genomics reagent kits that enable high throughput fragment length analysis, the system can be used as a plate reader for the evaluation of solution-based fluorometric assays for the quantification of DNA. Data from both assays are combined with Ranger Technology software to improve upon the accuracy of concentration estimations from smear analyses. This in turn can improve balancing of libraries prior to multiplexed next generation sequencing.

Ranger Technology is compatible with numerous commercially-available fluorophores such Please contact us to discuss what viable options are.

Click here for an application note on the LightBench ability to evaluate solution-based fluorometric assays.

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