Welcome to the very first podcast of Seqing Knowledge, a genomics podcast from The Sequencing Center. Our goal for this show is to provide our listeners with quick episodes centered around genome sequencing. These episodes will be filled with general sequencing information, tips and tricks to get great sequencing results, and explore innovative applications of genome sequencing across various industries.
We invited our CEO and founder Richard Casey to guide us through this week’s topic “What kind of sequencing do I need?”. The Sequencing Center frequently receives requests for whole genome sequencing, but after further discussions, it turns out our clients might actually benefit more from targeted resequencing. Do you know the difference and pros and cons of each?
What is whole genome sequencing?
Whole genome sequencing (WGS) is a comprehensive method that produces the entire genome sequence for any organism. The scale at which one talks about a whole genome varies in size, for example, humans have about 3 billion base pairs versus microbes with often have between 5-20 million base pairs.
Why do whole genome sequencing?
Whole genome sequencing produces deep genomic data and can be best utilized in the following cases:
- You are looking to understand the genomic structure of a novel organism,
- You don’t know which genes are affecting your research and need a comprehensive view to determine root cause,
- For smaller genomes around <3MB, such as microbes, it’s often more cost-effective to do whole genome sequencing compared to other types of sequencing.
Reasons not to do whole genome sequencing
- WGS produces a high volume of data which can be very slow to transmit over some networks,
- Data can be complex bioinformatically and computationally and be challenging to process and interpret,
- WGS often produces data that is not directly relevant to your research focus and become cumbersome to extract meaningful information,
- WGS can be overkill for researchers focused on examining small gene sets for protein coding, or researchers looking for mutations in particular genes.
What is targeted resequencing?
Targeted resequencing is the sequencing of an isolated region of interest such a specific gene, gene set, or exome.
Reasons to do targeted re-sequencing
Compared to the wide-spanning coverage of whole genome sequencing, targeted resequencing provides a more concise and manageable data set relevant to a targeted region. It is often a preferable choice for researchers in the following cases:
- You want to sequence a small region of interest such as a specific gene or gene set,
- You are interested in examining the number of promoters and enhancers present and what their structure looks like for gene regulation purposes,
- You are interested in SNPs or small indels such as insertion and deletion,
- You want to re-evaluate an older sequence for better clarity on newer technology,
- You are interested in just the exome of an organism.
What Kind of Sequencing Do You Need?
Both whole genome sequencing and targeted resequencing can deliver valuable data to researchers, so we hope by illuminating the benefits and differences of each our clients can make the choices right for their particular research. As you prepare to gather samples and place a sequencing order we recommend you ask yourself the following questions to confirm you know what you hope to gain from sequencing.
Ask Yourself These Questions
- Am I researching a novel organism?
- Do I know which genes are affecting my research?
- Am I looking at a particular gene or gene set?
- How large is my organism of interest (in mega bases)?
- Will I be able to store and examine the volume of data I’ll receive?
If you have questions about which type is best for you or need a quote for your next project please contact our sequencing experts at email@example.com.