Introduction to DNA sequencing
DNA sequencing identifies genomic variation and comes generally in two varieties: 1. Whole-genome sequencing (WGS) surveys coding and noncoding regions across the entire genome. 2. Whole-exome sequencing (WES) uses target enrichment to focus primarily on protein-coding regions.
Use WGS when broad genomic coverage, noncoding variation, or genome-wide structural information is important. Use WES when the primary interest is coding variation and a compatible exome panel provides an efficient way to focus sequencing on those regions.
WES is not equivalent to WGS: it does not comprehensively interrogate noncoding regions and may not reliably detect every structural or copy-number event. Standard short-read WGS may also be insufficient for some repeat expansions, complex
structural variants, phasing questions, or applications that require long reads. Neither assay should be selected until the required variant types, sensitivity, and coverage are defined.
Compatible sample types
Projects typically begin with purified genomic DNA that meets project-specific quantity, concentration, purity, and integrity requirements. Other DNA materials, including amplicons or DNA from enrichment experiments, may require a different library design and should be discussed separately. In some cases the Genomics CoLab may be able offer DNA extraction from standardized tissue or cellular sources.
Genomics CoLab offerings
Illumina DNA Preperation: DNA library preparation without exome enrichment for broad sequencing of the genome.
Illumina DNA Preperation with whole-exome enrichment: DNA library preparation followed by compatible exome enrichment to concentrate sequencing in targeted coding regions.
Other DNA library preparation: Library preparation from compatible amplicon or enriched DNA may be possible after review but should not be assumed to be WGS or WES.
See our DNA sequencing pricing.
Design considerations
When you start your project you will discuss with Genomics CoLab term the following items to assure we can meet your project needs:
- Variant types the study must detect: single-nucleotide variants, small insertions
and deletions, copy-number changes, structural variants, or low-frequency variants.
- Organism, genome size, reference assembly, and exome-panel compatibility.
- Desired mean coverage and minimum acceptable coverage in regions of interest.
- Germline versus somatic study design, matched controls, sample purity, and expected
variant allele frequency.
- DNA quality, fragmentation, extraction method, and sample number.
- Data-storage, transfer, security, and downstream analysis requirements.
What the CoLab performs
The CoLab may perform DNA quality review, library preparation, exome enrichment when selected, library quality control, pooling, sequencing coordination, and agreed-upon primary data processing. In certain cases the Genomics CoLab can preform DNA extractions from standardized tissue/cellular sources utilizing our Kingfisher Flex and Zymo Quick-DNA Magbead extraction kits. Please inquire for more details about what may be possible.
What the investigator supplies
The investigator supplies DNA, sample metadata, organism and reference information, the study design, relevant matched samples, and a clear description of the variant types and detection sensitivity required.
Data and analysis delivered
Deliverables include raw sequencing data, and may be extended to aligned files, sequencing and coverage quality-control summaries, and other agreed primary outputs. Variant calling, annotation, interpretation, and specialized structural-variant analyses are project-dependent and must be defined before work begins.
Pricing and sequencing considerations
Sequencing is a major component of DNA-sequencing cost. WGS usually requires far more sequencing per sample than WES, while somatic or low-frequency variant detection may require greater depth than standard germline studies. Estimates should state the assumed genome or target size, coverage goal, library preparation, enrichment, sequencing allocation, data processing, and optional analysis separately.
To start a project
Please download our project description form, fill it in with the as much detail as you can and then send it along with a consultation request to the [email protected] email address.