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.

Genomics services, and where exome sequencing sits in them

Genomics services cover a ladder of breadth, and exome sequencing sits deliberately in the middle of it. A targeted panel reads tens to hundreds of genes deeply and cheaply, which suits a known question. An exome reads the coding fraction of every gene, around one to two per cent of the genome, at a depth that finds a coding variant nobody predicted. Whole genome adds the non-coding and structural picture and the data handling that comes with it. Choose by the variant class you need to detect and the depth it requires, then compare prices at that depth rather than per sample.

An exome panel, and how it differs from a gene panel

An exome captures the coding fraction of every gene, around one to two per cent of the genome, at a depth that finds a coding variant nobody predicted. A gene panel captures tens to hundreds of genes far more deeply and cheaply, which suits a known question and a degraded sample. The exome's own limits are real: capture is uneven across GC-rich exons, some genes are poorly covered by every commercial design, and a negative result is a negative for the captured regions rather than for the gene.

complete exome sequencing, and what complete means

Marketing uses complete to mean a design with broader capture, often including untranslated regions, promoters or additional annotated exons that older designs missed. It does not mean every base of every exon is read: coverage still depends on capture efficiency and on the depth ordered, and every commercial design has regions it covers poorly. Ask for the design's own coverage statistics at your ordered depth, and for the list of genes or regions the vendor knows to be problematic, because that list is what a clinical report has to disclose.

exome sequencing analysis, and the decisions that move a result

Alignment to a named reference build, duplicate marking, base recalibration, variant calling with a model that suits the depth, and then filtering and annotation against population frequencies and transcript sets: each step has versions that move borderline calls. Coverage reporting per target is part of the result, because a variant cannot be called where there were no reads, and a negative result is a negative for the covered regions only. Record the reference build and the annotation release with the data, since gene identities change between releases.

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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