Whole exome sequencing services: specifying capture, depth and coverage uniformity, and agreeing what the provider actually delivers

Specifying the run

1. The capture kit defines the exome. Different capture designs target different regions, so two providers can both deliver an exome and cover different parts of your gene of interest. Ask which kit is used and check your genes of interest against its target definition before ordering rather than after.
2. Depth is a mean, uniformity is the truth. A mean depth figure conceals whether coverage is even. Ask for the proportion of the target covered above your required threshold, which is the specification that determines whether a variant can be called in the regions you care about.
3. Input quality and quantity. Providers state DNA input requirements and quality thresholds, and fixed tissue, degraded material and low-input samples each need a different library route. Declare the sample type honestly at quoting rather than letting it fail at the laboratory.
4. What analysis is included. Establish whether the price covers raw reads, alignment, variant calling, annotation or interpretation, and in which file formats. Bioinformatics is where quotes diverge most, and a cheap sequencing price with no analysis is not cheaper once somebody has to do the analysis.
5. Data delivery and retention. Agree how raw and processed data is delivered, how long the provider retains it, and what it costs to have it again. Sequencing data is large, and a provider that deletes after a short window is a risk if your storage plan is not ready.

Exome or genome

Exome sequencing covers the coding regions at high depth for a fraction of the cost of a genome, which suits variant discovery in genes. It misses regulatory and intronic variation, structural variants and anything outside the capture design, and those absences are invisible in the results.

Where the question could involve non-coding variation or structural change, a genome at lower depth frequently answers more for a comparable spend. Decide this from the biological question rather than from the price list.

Human samples carry obligations

Sequencing human samples engages consent, data protection and, where results could be clinically relevant, a policy on incidental findings. Establish before sequencing what happens if something medically significant appears, because deciding afterwards is far harder.

Confirm where data is processed and stored and whether that satisfies the obligations attached to your samples. Data location is a contractual question that is easy to ask and awkward to unwind.

Common questions

What should I specify for exome sequencing?

The capture kit and its target definition checked against your genes of interest, the depth and the proportion of target covered above your threshold, the sample type and input, what analysis is included, and how data is delivered and retained.

Is mean depth a useful specification?

Only partly. A mean conceals uneven coverage, so ask instead for the proportion of the target covered above the threshold you need, which is what determines whether variants can be called where it matters.

Exome or whole genome sequencing?

Exome covers coding regions deeply and cheaply but misses non-coding, regulatory and structural variation entirely. Where the question could involve those, a genome at lower depth often answers more for similar spend.

What analysis is normally included?

It varies widely, from raw reads only to full annotation and interpretation. Establish the scope and the file formats explicitly, because bioinformatics is where apparently similar quotes differ most.

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