Pilot samples before a large cohort

A pilot and a cohort answer different questions, and they are easy to buy as if they were the same purchase. The pilot is allowed to decide whether the method and the logistics work on a small number of samples. It is not allowed to decide whether a treatment changed a biological measurement, or whether a difference in a population is real. This page compares those two decisions so a quotation can be checked against the smaller one. Writing the lines is how to write a laboratory sourcing enquiry. The study around them is commissioning a sequencing or proteomics study. Send the file through laboratory procurement.

Sample handling classes sit with sample preparation. Sequencing as a research application is genomics research. Neither page means a sequencing service is being operated from this site. A method can be discussed. The decision about what the pilot may conclude stays in your statement of work. University groups can start from academic research. The quotation page and the contact page carry the specification.

Two decisions that look like one

You are specifying a small run before you commit samples, labour, and a larger design. Commercial intent means the quotation should say it is a pilot and should list the decisions it supports. If the quotation reads like the cohort, you are buying the wrong scope even when the kit names are right.

The control is a sentence you can show a colleague who was not in the meeting: "This pilot may change our method. It may not be cited as the biological result." If that sentence is missing, the branch is to write it before anyone extracts the first sample. A surprising band or a surprising count in three tubes is a reason to inspect the method. It is not a result.

What a pilot is allowed to decide

A pilot is a rehearsal with real material and a narrow conclusion. It may decide that the extraction works on this matrix, that a library meets the QC checks you wrote down, and that the physical path from bench to the next handoff can be repeated. It uses the same classes of reagent and plastic you intend for the cohort, so the rehearsal is honest. It uses too few samples, and often the wrong statistical role, to estimate an effect.

Write the allowed decisions as lines in the statement of work. Each line names the observation and the threshold your laboratory already uses. Do not paste a universal pass mark from a brochure. Public method collections such as protocols.io and Addgene show how workflows are described. Your threshold is the one in your SOP or the one you agree in the commissioning document.

Extraction yield

Yield asks whether this tissue, this blood tube, this culture, or this environmental matrix gives nucleic acid or protein you can take forward, using the extraction class you specified. The pilot may decide to change lysis conditions, input mass, or the kit class before the cohort. It may decide that the matrix is unsuitable for the method. Those are method decisions.

The observation is a quantity and a purity or integrity measure your SOP already names. Record the measure and the instrument or assay class. A single high yield does not prove the cohort will yield the same, and a single failure does not prove the biology. It proves that this attempt, on this input, with this chemistry, did what it did. The branch when yield is unusable: stop, change one variable, and pilot again. Do not proceed to a large cohort on a method you have not seen succeed once under the conditions you will actually use.

Library QC

If the pilot includes a library, QC asks whether the library looks like a library your statement of work would accept. Typical checks, always as defined in that document and the manufacturer's protocol, include a concentration method, a size profile, and a look at adapter dimer or other artefacts the SOP names. The pilot may decide that fragmentation, input amount, or the cleanup must change. It may decide that the index plan is impractical.

It may not decide that a gene is differentially expressed, that a variant is real in the population, or that a pathway is "up". Those words need the cohort, the contrasts, and the analysis rules set out in commissioning a sequencing or proteomics study. A beautiful library from three treated samples and no controls is a methods success and a biological anecdote. Label it that way in the file so a figure does not escape into a report.

The branch when QC fails: the pilot has done its job. It has refused the current method. Revise the method line and run another pilot, or stop. Do not relabel the failed QC as a biological finding because the samples were precious.

A logistics rehearsal

The third allowed decision is operational. Can the laboratory extract, store, pack, and hand off a practice shipment so that temperature evidence, documents, and identity survive? This is a rehearsal of your process. It is not a claim about a sequencing provider's performance, and it is not a claim that this website runs that work. Dry ice packing for sample shipments and storing biological samples from fridge to freezer are the handling references. IATA's dangerous goods programme is the public transport reference when dry ice or other regulated materials are involved.

The pilot may decide that labels were inadequate, that a logger was omitted, that the time from extraction to the freezer was too long for your SOP, or that two sample identities were nearly confused. Those findings should change the cohort's logistics lines. They should not be filed only in someone's memory. Write them next to the pilot conclusion: method acceptable or not; logistics acceptable or not; biology not assessed.

What a pilot cannot decide

A biological effect is a comparison with a design: controls, a stated contrast, a sample size chosen for that contrast, and an analysis that was not invented after the numbers appeared. A pilot is usually too small, and it is often unblinded and exploratory, so it cannot carry that conclusion. It also cannot decide safety or efficacy in a clinical sense. This page is not medical advice and not a diagnostic method.

If the pilot samples are the first human or animal specimens, ethics and biosafety decisions are still outside the product quotation. They are not waived because the run is small. A small unapproved collection is still a collection. See the institution's rules before the tubes exist, not after the library looks fine.

The branch when someone wants the pilot to "see if the effect is there": rewrite the aim. Either it is a method pilot, and the effect language comes out, or it is a study with a design, and it is no longer a pilot in the sense this page uses. Mixing the two in one quotation is how three samples become a claim.

When a pilot is asked to do the cohort's job

The failure is a sentence in the report that outruns the file. The file says "pilot, n as chosen for yield". The report says the treatment worked. The repair is in the statement of work, written before the run: allowed conclusions listed, forbidden conclusions listed. A quotation that offers "full biological interpretation" on the pilot scope is offering a different study. Mark it as an exception or refuse it.

A second failure is changing many method variables and then treating the one success as the cohort's standard operating procedure without writing down which variable moved. The pilot may change the method. It has to say which change.

A third failure is ordering the cohort's full reagent quantity "since we are piloting anyway". That spends the cohort's material on an unfixed method. Specify pilot quantities as pilot quantities. The cohort order waits until the allowed decisions are actually recorded.

Ethics, biosafety, and research use

A pilot is still research on whatever material you use. Human material, animal work, and clinical-adjacent samples need the institution's ethics decision even when the tube count is small. Biosafety is a separate institutional decision. The WHO Laboratory Biosafety Manual is a public biosafety reference, not a permit for your samples. This page does not approve a study and does not give medical advice.

Reagents in the pilot are for the research use you named. A QC metric is not a diagnosis. Do not put clinical performance language into the pilot quotation to make the small run sound more important.

Rehearsing the handoff in the heat

Include the season you will actually face. A logistics rehearsal in a hot, humid week tells you whether labels survive, whether a coolant pack is still cold at the dock, and whether a power cut between centrifuge and freezer leaves you without a temperature note. A rehearsal done only in an air-conditioned hour can miss the failure the cohort will hit. Write the dock and the storage place into the pilot's logistics lines. The finding is allowed to change packing and timing. It is not allowed to be narrated as a biological difference between samples that thawed and samples that did not. Those are handling losses. Record them as handling losses.

The enquiry

State that the request is a pilot. List the three decisions it may support: extraction yield against your threshold, library QC against the checks in the commissioning document, and a logistics rehearsal. List the decisions it may not support, including the biological effect. Give sample type, count, and matrix without turning the count into a population. Specify reagent classes, documents, temperature evidence, and acceptance. Say the cohort is out of scope.

Put that file on the quotation page or send it through the contact page. Keep it beside the commissioning document so a later reader can see which conclusions were purchased and which were not.