Biomarker discovery and clinical samples
Cohort and clinical work asks a different question from mapping: not where a mark sits, but whether its level separates the groups being compared. These studies start with a screen across the sample set and then narrow to the candidates that move.
01The question behind these studies
Biomarker discovery work asks whether a modification level differs between groups of samples — cases against controls, responders against non-responders, one clinical stage against another — and whether that difference is consistent enough to follow up.
The answer is a statement about the sample set, so it is usually asked of many samples at once. That is a different constraint from mapping work: rather than the highest resolution on a single sample, the design needs a comparable measurement on every sample in the comparison.
When a comparison does produce candidates, the question changes again — to where the difference sits on the transcript, and whether it survives an independent measurement. Screening and confirmation are therefore planned as two steps from the outset rather than added at the end.
02Which service line fits
Cohort work rarely uses only one line. A screen across the sample set narrows the field, and the targets that move are taken further.
RNA Modification RIP-Sequencing
Enrichment-based profiling across conditions and cohorts, for comparisons between groups rather than resolved positions.
Many samplesprofile SCREEN_02RNA Modification Arrays
Modification levels for a defined transcript set, read in parallel, for studies that already know which targets they care about.
Defined setscreening RESOLVESingle-Base RNA Modification Sequencing
Takes the candidates that moved and reports the individual site on each transcript, with its modification level.
Site-levelconfirmation BEFORESample submission guide
Quality thresholds, storage and shipping notes for clinical material, checked before the sample set is committed to a workflow.
QC firstlogistics03What the project gets back
- Profiles across the whole set. Enrichment-based modification profiles for every sample in the comparison, measured the same way on each one.
- Group comparison tables. Differential modification between the groups under study, with the direction and size of each change alongside its significance.
- Array readouts. Modification levels for the transcripts on the array, sorted so the targets that changed are visible before any site-level work begins.
- Site tables for the candidates. Position, host gene and modification ratio for the targets taken into a single-base method.
- An independent readout where the level carries the conclusion. LC-MS on the fraction of interest measures nucleoside content by a route that does not share the assumptions of enrichment or sequencing.
A screening result is a level, not a position. Where a conclusion names a nucleotide, it has to come from a single-base method: the enrichment and array lines show what is worth resolving, and the single-base line says where it is.
04How a project is set up
- Fix the comparison before the samples are run — the groups, the sample type and the mark — so the design is not revised after the data arrive.
- Check the material against the quality thresholds: OD 260/280 at or above 1.8 and RIN at or above 7, with no visible degradation.
- Collect blood in EDTA tubes. Heparin is not compatible with the downstream procedure, so a heparin collection cannot be rescued later.
- Run the screen across the whole set rather than in separate rounds, so a difference between groups is not carried by a difference in how the samples were handled.
- Take the candidates that moved into a single-base method, or into an independent readout, depending on what the conclusion needs to claim.
| Need | Request Quote |
|---|---|
| Modification screening across a sample set | |
| Clinical sample suitability check before shipping | |
| Site-level confirmation of a candidate |
05FAQ
Can a cohort study report positions rather than levels?
Through a single-base method, yes. The enrichment and array lines report modification levels for transcripts and regions, so a study that needs a nucleotide position takes its candidates into single-base sequencing and reports the screen and the resolved positions together.
Which sample types can clinical material be submitted as?
Total RNA, cells, tissue or blood, with blood collected in EDTA tubes because heparin interferes with the downstream procedure. Every sample is checked against the quality thresholds — OD 260/280 at or above 1.8 and RIN at or above 7 — before the workflow starts, and a sample that fails is flagged rather than carried into the comparison.
Do we need a target list before starting?
No — working without one is the point of a screen, which is designed to find targets rather than test them. A study that already knows its targets can start on the array line, or go straight to a single-base method if positions are what the conclusion needs, and the screen itself returns levels rather than positions.
How is a candidate confirmed independently?
LC-MS measures nucleoside content directly, so it does not depend on enrichment or on sequencing, and it is used where a level change is the finding and has to stand on its own. Where the candidate is a position rather than a level, the independent check is a single-base method instead, run on the same candidate set.