In the new age of genomics, researching specific genes within a genome has become a common focal point of interest. This is prevalent in bacterial research fields primarily because it provides deep insight into specific functions and attributes of the organism.
Researchers across multiple fields are finding great value in honing in on specific gene functions. For example, researchers in biologic drug development may introduce specific mutations in order to create a certain gene function. Genome sequencing in this case is highly useful for identifying gene stability through multiple passages. Conversely, in plant pathology researchers are looking at antibiotic resistant genes in order to produce new antibiotics.
To target specific genes in bacteria, there is a method for both downstream and upstream of sequencing. How do you know which one is right for you?
Downstream of Sequencing:
The downstream option is to perform whole genome sequencing on the bacteria which produces a full genome data set. From there, researchers can use bioinformatics to scope in on the genes of interest to perform data evaluations, such as SNP analysis and dataset comparison.
One of the key benefits of whole genome sequencing is that the sequencing kits are already created and significantly cheaper than targeted sequencing. If you ever need the additional data from the rest of the genome you’ll have it in your back pocket without the need to go back and resequence.
The downside to this method is that it produces a significantly higher volume of data which is more costly to store over the course of a year. This cost can be anywhere from 10-12x what you will pay for when doing targeted sequencing. Since you’re dealing with more data, the bioinformatics analysis can become unwieldy. It requires more data quality control, manipulation, and management which inherently increases time to insight and raw computation power.
Who Does this Work Best For?
This type of sequencing works great for researchers who foresee their research and investigations expanding in the future. By performing this type of sequencing, the researchers gain the benefits of always having access to the data. Additionally, researchers who have steady funding (even on a smaller budget) will benefit best from this method when they plan on retaining the data for longer periods of time.
Upstream of Sequencing:
The upstream option is to create a targeted sequencing kit that hones in on only the genes that you need. This route produces only the data for the genes that the researcher needs.
Sequencing data output through targeted sequencing will be significantly less than whole genome sequencing. This, in return, reduces your long term data storage costs by a significant factor – sometimes up to 6x when dealing with higher quantities of samples. Additionally, the bioinformatics analysis is typically more manageable since you’re dealing with far less data. Tasks like data set comparisons, searching, filtering, and more take significantly less time and computing power.
The downsides to this route are that custom targeted sequencing panels are more expensive than the prebuilt whole genome sequencing panels. You’re paying a premium to scope in on only the genes that you need which requires kit customization. This will increase your upfront cost making the barrier to entry for sequencing higher. If you ever need a different aspect of data from the organism you’ll need to go back and re-sequencing the samples incurring an additional sequencing run cost.
Who Does this Work Best For?
This method works very well for researchers who know that they are only going to be performing research on specific genes and nothing more. Additionally, if the researchers have a higher short term budget and don’t plan on retaining the data for long periods of time then this option is great.
The Bottom Line
What it really comes down to between the two options is what you’re researching. If you are confident that you won’t need any of the extra data and you’re willing to pay an upfront premium, then targeted sequencing may be the best option.
Conversely, if you may need the extra data in the future (perhaps for something like pathway analysis) and you are trying to focus on steady costs, then whole genome sequencing is the way to go.
For bacterial research we personally recommend whole genome sequencing even if researchers are only looking at specific genes. The reason being is that the kits are much more cost effective, especially if you’re planning on running a high amount of samples (multiplex run). We find that after the first round of sequencing, researchers get insights into their initial hypothesis which leads to new questioning about the organism. By performing whole genome sequencing, they have the ability to further explore their new questions off of the same data set.
Effectively, whole genome sequencing provides more mileage on your research for the best bang for your buck, regardless of the long term costs. It’s much easier to manipulate already sequenced data than go back and re-sequence. Computationally, searching data is much more cost effective than physical data manipulation in the lab.
Still have questions about which method is best for your needs? Get in touch for a free consultation.