Protocol 3: colonic biopsy preparation
Purpose
The biopsy provides the local methylation reference. Preparation must preserve DNA while retaining anatomical and pathological context: colon segment, lesion/inflammation status, sampling time, preservation method, tissue amount, and—where available—histology or cellular composition.
| Input | Laboratory handoff | Output |
|---|---|---|
| identified biopsy | controlled preservation and tissue preparation | extraction-ready tissue aliquot |
| location and pathology metadata | de-identified annotation | tissue context table |
| technical repeats/aliquots | replicate tracking | nested replicate records |
What can go wrong?
A biopsy mixes epithelium, immune cells, stroma, vessels, and possibly neoplastic cells. A methylation difference may therefore reflect regulation within cells, a different cell mixture, or both. Sampling a single area also cannot represent the entire colon.
QC gate
Record tissue integrity, input mass, preservation delay, contamination, extraction batch, and any deviation. Tissue DNA fragmentation happens downstream; native insert sizes from intentionally sheared tissue are not biological fragmentomics.
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