Targeted gene panels vs. whole exome sequencing


One frequent question we hear on Genohub is, ‘should I make a custom panel for this gene set, or not bother and do whole exome sequencing?’. While whole genome sequencing approaches can capture all possible mutations, whole exome or targeted gene panel sequencing are cost-effective approaches for capturing phenotype altering mutations. We go into the advantages of WGS vs. WES in an earlier blog post. A remaining question however is, among targeting approaches, which is best. We attempt to address this here:

Advantages of targeting all exons – whole exome sequencing (WES)

If your study is discovery based, in other words you don’t know what genes you need to target, WES is the obvious choice.

  • Better for discovery based applications where you’re not sure what genes you should be targeting.
  • Exome panels are commercially available, they don’t need to be customized or designed.
  • Exome sequencing services are fairly standard, costs range between $550-800 for 100-150x mean on target coverage.

Advantages of targeted gene panels (amplicon-seq or targeted hybridization methods)

Targeted gene panels are ideal for analyzing specific mutations or genes that have suspected associations with disease.

  • Focusing on individual genes or gene regions allows you to sequence at a much higher depth than exome-seq, e.g. 2,000-10,000x as opposed to 200x which is typical with exome-seq.
  • High depth sequencing enables the identification of rare variants
  • Can be customized for different samples types, e.g. FFPE, cf/ctDNA, degraded samples.
  • Lower input amounts can be used with targeted gene panels (1 ng vs. 100 ng with whole exome sequencing).
  • Gene panels can be customized to only include genomic regions of interest. Why sequence everything when you don’t need that extra information?
  • Panels can be easily designed for non-human species. Designing a non-human exome is much more laborious.
  • Gene panel workflows are a lot simpler and time to results is often as little as 1-2 days.
  • You can process thousands of samples on a single sequencing run. Targeted gene panels can be run at a higher throughput and are often more cost-effective than whole exome sequencing.

By focusing on genes likely to be involved with disease, you can reduce expense and focus sequencing resources on your targeted region. However, if you only have a few samples that you need to sequence at a low depth of coverage, consider whether it’s worth designing a panel vs. performing whole exome sequencing using an existing commercial panel.

If you’re interested in designing a custom gene panel or already have an existing panel you’d like to sequence, submit a request describing your project or view several of the existing commercially available panels here.

Guides to improve your next generation sequencing project

read length, output and instrument recommendations for next generation sequencing

If you’re new to next generation sequencing or if you’re simply looking for tips to improve your next project, we recommend you take some time to look at the guides available on Genohub. As researchers order sequencing services it’s completely normal for there to be numerous questions related to nucleic acid extraction, library prep and best practices for loading a sequencing instrument. Over the years, we’ve curated these questions and published guides to help those embarking on their next NGS project. Topics covered include: library prep applications, batch effects, optimal cluster densities, read lengths and instrument output.

Next generation sequencing is a tool that can be applied to answer any number of questions related to the genome, transcriptome or epigenome. Regardless of the organism being sequenced or the library method used to prepare nucleic acid from that organism, the fundamentals of how a sequencing platform works, is similar across all samples. There are currently four main sequencing platforms that researchers regularly use. These include Illumina, Ion, PacBio and Oxford Nanopore. The guides below tend to be Illumina focused because that’s the platform most people are currently using today. Despite that, we review the read throughput of each available instrument and discuss hybrid methodologies where short and long reads are combined from two different instruments to improve assemblies.

Guides for sequencing

  1. Designing a sequencing project
  2. Recommended coverage by library preparation application
  3. Comparison of instrument read lengths and read outputs

Guides for preparing your samples

  1. Best practices for shipping tissue and nucleic acid 
  2. Library preparation kits and tips

Guides by application

  1. Transcriptome and mRNA-Seq
  2. Genome sequencing and re-sequencing
  3. Exome
  4. Metagenomics 
  5. Small RNA (microRNA)
  6. WGS vs. WES

Tips and considerations for commonly used sequencing instruments

  1. HiSeq X
  2. HiSeq 3000/4000
  3. Nextseq and low diversity

These are evolving guides, meaning our goal is to continuously improve them. If you have any feedback or would like to contribute please send us a message. We hope these guides will be helpful in designing your next NGS run. If you have technical questions related to an upcoming NGS project, feel free to submit them on our consultation page.