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Getting Started in NGS With the Illumina MiniSeq™

Allison Yunghans, MPH, Research Associate I, Illumina Core Applications Group
| Jan 11, 2016

Today, the world learned about a new Illumina sequencer called MiniSeq, designed for researchers who need a simple and affordable, yet powerful solution for targeted sequencing. However, I have had my hands on this little box for a few months since joining the Illumina Core Applications group. My background is in general biology and public health, and while I have worked as a research associate in both academic and industrial labs, I had no previous experience with next-generation sequencing (NGS). Despite the challenges of coming up to speed on technology and applications critical to my job, I was able to get experiments up and running on it with relative ease. From the very beginning, MiniSeq was conceived with novice NGS users like me in mind, including features to guide everything from run setup to analysis.

One of my responsibilities is to support Illumina library preparation products, including TruSeq® Targeted RNA, an amplicon-based method for simultaneous gene expression profiling of dozens to thousands of genes. After library preparation, I would sequence my libraries on the MiSeq®, which has been the workhorse Illumina desktop sequencing system for a few years now, and analyze the data on BaseSpace®. Although MiSeq systems are user-friendly, when I started working with MiniSeq, I was surprised to find even more helpful and easy to use features which are derived from the best ideas from the MiSeq and NextSeq® systems. The MiniSeq flow cell is packaged dry, eliminating the preparation time needed for MiSeq flow cells which are shipped in liquid. The MiniSeq integrated reagent cartridge design saves both time and space in the lab. A further improvement introduced with the MiniSeq is that the reagent cartridge is all-inclusive and contains all the wash buffers, so there is no need to purchase and track multiple reagent buffers or parts for each run. And at 18 x 19 inches, the MiniSeq system has the smallest footprint of Illumina’s desktop sequencing systems, leaving more space on the lab bench for other tasks.

Set-up time for a MiniSeq run is minimal; final library preparation for sequencing takes less than 10 minutes. Instrument setup is a breeze, with on-screen, animated step-by-step instructions to guide me through the process of loading the reagent tray and the flow cell. After a few system checks, the instrument is ready to go. MiniSeq completes 2 x 150 bp sequencing runs in about 24 hours, making planning the next run on the next day easier. The instrument also displays an estimate of when the run will be complete.

Figure 1 (Click to enlarge): Screenshot of the MiniSeq Control Software during a run showing the estimated completion time.

MiniSeq launches straight into wash when the run completes, like NextSeq, so there is no need to return to the machine until the next run is planned. MiniSeq systems also include the option to automatically purge the reagent cartridge of all reagents into the waste bottle after the run, aiding safe disposal of the used reagent cartridge.

Like other Illumina sequencing systems, MiniSeq is fully compatible with BaseSpace. But here’s the best part of MiniSeq: the system includes Illumina’s new Local Run Manager. This on-instrument software tracks runs and automates data analysis. I had assumed all NGS analysis had an absolute requirement for a large computer system or a cloud analysis environment like BaseSpace (and you can still use these for analysis), but Local Run Manager is different – all analysis is done automatically on the MiniSeq.

Run setup through Local Run Manager is simple, and operates through a standard web browser. The first step is to select the pre-programmed applications. Local Run Manager opens up a predefined template for selecting your run parameters to accommodate the desired read lengths and sample indexing configuration and entering sample information.

Figure 2 (Click to enlarge): TruSeq Targeted RNA Run Setup in Local Run Manager

I like the ability to cut and paste library and sample information right into the setup screen, or import with a simple template. The Local Run Manager run template will also allow you to select options for your analysis. Following run setup and completion, Local Run Manager will automatically perform analysis and generate reports summarizing the sequencing results for the run.

Shown here are some of the results generated from my Targeted RNA libraries using the Local Run Manager Targeted RNA workflow. Again, all of this occurs on the MiniSeq itself – no big computer system and no connection to the cloud needed. This will really be a great benefit to labs that can’t use cloud-based computing, or as an automated first-pass analysis of the run before the data undergoes more extensive analysis by a bioinformatician.

Figure 3 (Click to enlarge): TruSeq Targeted RNA results as displayed in Local Run Manager. The plot and table show gene expression count data between two technical replicates of Human Brain Reference RNA (HBRR). Selecting the EGFR gene in the table highlights the specific data point (red) on the scatterplot.

I’ve enjoyed working with the Illumina team to bring MiniSeq and Local Run Manager to life. I think researchers who have been wanting to get into NGS but were worried about operating complicated equipment or not having enough IT and bioinformatics support are going to be pleasantly surprised with how MiniSeq performs in your hands.

Explore MiniSeq Applications:

Tumor Profiling Application Note
Germline Testing Application Note
miRNA Discovery & Profiling Application Note
Expression Profiling Application Note