According to the US News & World Report [1] there are 257 universities with biological sciences graduate programs in the US alone. Of these, fewer than a hundred [2] have genomics core facilities.  If you’re a researcher in an institution without a sequencing core facility you’ll obviously have to outsource your sequencing projects. We’ve also found that many researchers with access to their own local core facilities often choose to get their sequencing done  elsewhere, be it at other core facilities or commercial NGS providers. Here are some of the reasons why:

1. Shorter turnaround times

Depending on the volume of projects a core lab can handle at any given time, researchers are often faced with long queues before capacity opens up for their project. Even if a facility has plenty of capacity,  high-throughput instruments allow for multiple libraries to run simultaneously. For example the popular Illumina HiSeq 2000 sequencer has flow cells that have 8 lanes each. Reagent costs are largely independent of how many lanes are filled, so it makes sense for the facility manager to wait till there are enough projects to fill up all lanes before starting a new run. These are some of the factors that can lead to turnaround times as long as several weeks or even a few months. Especially when faced with tight publication deadlines it often makes sense for researchers to consider getting their sequencing done at a facility that can offer a shorter turnaround time for their project.

2. Access to instruments not available locally

Not all sequencing instruments are created equal. Typically the relevant parameters are total output per run, number of reads per run, read length, price per run and run duration.  Each sequencer is designed to strike a different balance between these parameters and there is no single sequencer that would be the optimal choice for all projects. Sometimes the right instrument for a project is simply not available at the local facility.

For example, applications such as de novo assemblies of novel genomes benefit from longer read lengths which will span more repeats and missing bases, closing gaps and simplifying finishing.  Going with an instrument like the PacBio RS whose average read length is currently ~4600 bp with some reads up to ~20,000 bp has become routine for those looking to completely assemble bacterial genomes. Long read lengths also allow you to uncover complex structural variations and identify where copy number variations have occurred relative to a reference genome. For transcriptome analysis, they help resolve RNA splicing patterns as long reads allow for a greater chance that the entire transcript is read, eliminating the need to infer isoforms.

3. Bioinformatics capabilities and expertise:

When it comes to analysis of sequencing data, there are typically three things to consider:

1. Expertise to design or select the right analysis pipeline for the given project
2. Access to and familiarity with the right software tools
3. Access to sufficient hardware resources, e.g. compute clusters.

It’s fairly common for researchers to not have all three available locally. Most NGS facilities can typically assist with one or more of these, but the vast majority of facilities have unique expertise and specializations.  For example, alignment of methylation sites using bisulfite-seq data differs from alignment of regular DNA sequence in that the conversion of unmethylated cytosines to uracil decreases the total amount of information available for alignment of sequenced reads against a reference genome. Some approaches align cytosines to reference genome cytosines and sequenced thymines to cytosines or thymines in the reference genome. An alternative method is to remove the bias toward the alignment of methylated reads at the cost of degrading the total information available for alignment. You will need to work with a provider who has experience with methylation analysis to determine which is the most appropriate for your study.

On the hardware resource front, while for example the E. Coli genome can be assembled in 15 minutes with a desktop computer equipped with 32GB of RAM, what about an organism that hasn’t been sequenced before? Will you be waiting on your core to setup a de novo pipeline? What if the analysis you need doesn’t fit a cookie cutter pipeline, does your core facility have the capacity to perform custom analysis services? These are all questions to think about when deciding where to get your NGS project done. 

4. Library preparation expertise

Properly designed libraries are probably the single most important part of a successful sequencing experiment. Library preparation is a relatively manual process, so experience matters and it will be reflected in your sequencing results. It is important to use facilities that have experience in the library preparation application you are looking for.

Each sequencing service facility usually has a core 3-4 library prep applications they are experts in. While almost every service facility you encounter has DNA-Seq and RNA-Seq in their “expert list”, if you’re looking for amplicon or targeted capture, it is important the facility has performed this type of work. Outside a core’s defacto 3-4 library prep applications, we recommend spending the time to  look for a facility experienced with your application.  Otherwise,  you may be just as successful by purchasing a kit and making your own libraries.

As a specific example, if you outsource chromatin immunoprecipitated or microRNA samples to a facility that hasn’t performed ChIP-Seq or Small RNA- Seq library prep, chances are you won’t be getting back anything that’s sequenceable. A fault of current small RNA library methodologies are adapter dimers that form during the preparation. An experienced provider will know to look for these and ensure that 50% of your reads are not wasted on meaningless sequence. ChIP-Seq or any low input library preparation methodology is prone to high duplication rates. Again, an experienced operator will know to perform qc checks and limit PCR cycles so that you achieve reads with high diversity. 

5. Cost

It’s needless to say that using the most efficient use of research funds is important. This is especially true given the recent tightening of government funding of life science research, at least in the US and Europe. Everything else being equal , it’s often wise to at least shop around to see whether there are facilities that can carry out your sequencing project at substantially lower prices. This used to be a very time consuming process but using Genohub you can now easily make apples-to-apples comparisons of NGS services with just a few clicks.

We’re here to help

Our job here at Genohub is to make it very easy for researchers to find NGS service providers and facilitate such collaborations. You can use our project matching page to compare very accurate information about NGS services from a wide variety of service providers and easily submit your project. We’d also love to hear from researchers directly and help identify the right sequencing solution and service provider. Just fill our free consultation form or email us at support@genohub.com.

References:

[1] US News& World Report Biological Sciences Graduate Programs

[2] http://omicsmaps.com/