Frequently Asked Questions
1. What is targeted resequencing?
Targeted resequencing is an application of next generation sequencing where you enrich regions of the genome that you are interested in sequencing.
2. Why do targeted resequencing over whole genome or exome sequencing?
The size of full genomes can be very large. Targeted resequencing lets you remove areas that you are not interested in knowing more about so that your initial target size is smaller. Since the output remains constant for a particular NGS platform and configuration, a smaller target size gives you the flexibility of multiplexing more samples into the same run or sequencing at a higher depth of coverage.
Increased ability to multiplex makes the project more cost-effective since you are sequencing more samples in a single run (significantly decreasing the per sample cost).
Higher depth of coverage gives the assay more sensitivity. This higher sensitivity allows you to detect low-frequency, rare mutations more effectively. Also, it allows for resolving more complex (e.g., GC- or AT-rich) genomic regions.
Exome sequencing is a form of targeted resequencing. However, the target size is significantly larger than most custom targeted assays. For this reason, the same benefits apply as compared to whole genome sequencing.
3. What types of targeted resequencing are available?
There are primarily two types of targeted resequencing: targeted enrichment and amplicon sequencing. Targeted enrichment captures regions of interests with baits following creation of the full genomic library. By contrast, amplicon sequencing amplifies the target regions directly from the unfragmented genomic DNA in a highly multiplexed PCR reaction. Further, there are multiple targeted enrichment and amplicon sequencing technologies designed by different companies, including Illumina, Agilent, and Life Technologies.
4. What are some advantages and disadvantages of all of these different types of targeted resequencing, and how do you choose which one to go with for a particular project?
The assay design process can range from relatively straightforward to extremely complex.
Some key elements of the design process include:
- Deciding between amplicon sequencing and targeted enrichment
- Deciding on the best amplicon or enrichment chemistry/technology
- Determining the best design for the particular regions/genes (e.g., a GC-rich or complex set of regions would be handled differently than a simple one)
GENEWIZ possesses extensive experience with targeted assay design, which has been demonstrated with the development of multiple in-house, proprietary panels optimized for specific applications (e.g., OncoGxOne™ Discovery cancer panels, which are optimized for cancer research).
5. What type of bioinformatics services are available for targeted resequencing projects?
We provide raw data as FASTQ files for all projects. We also have advanced bioinformatics capabilities to provide optional data analysis services, including:
- Standard DNA Analysis Package- includes mapping, SNP/INDEL detection, structural variation analysis
- CNV Discovery
6. Why choose GENEWIZ for targeted resequencing projects?
Some areas where GENEWIZ excels include but are not limited to:
- Proven experience with the complexities of assay design
- Expertise for project consultations and technical support
- Experience and availability of all major targeting technologies
- Proprietary, advanced bioinformatics pipelines to discover copy number variations (CNVs)
- Proprietary, advanced bioinformatics pipelines to discover gene rearrangements
7. What are some applications of targeted resequencing?
Some possible applications include but are not limited to:
- Discovery of common and rare genetic mutations, including point mutations, insertions/deletions (Indels), copy number variations (CNVs), and gene rearrangements.
- Characterization of genetic associations to a particular phenotype, such as a disease state or a drug response.
- Typing and classification of cell lines, including both eukaryotic and prokaryotic cells.
- Antibody discovery, including from both phage display libraries and in vitro selection.
- Genetic testing, such as pharmacogenomics or oncology assays.
8. How do I contact GENEWIZ for a technical consultation about my project?
GENEWIZ's NGS Team is composed of Ph.D. scientists who can help you optimize your project design and provide consultation to answer any questions. For any form questions that require support, contact the NGS Team at [email protected], toll-free at 877-436-3949 ext. 1, or directly at +1-908-222-0711 ext. 1.
9. Can GENEWIZ recommend the best data delivery option?
Yes, GENEWIZ will recommend the best data delivery option based on the platform and project details. Data delivery options include:
- Secure File Transfer Protocol (SFTP)
- Customer Cloud Account
- Hard Drive (additional charges may apply)
- Other (please explain in additional comments section of quote request form)