Sampling error

What we are reading

Gathered for the investigation and not yet written up. Each note says what the paper does and does not show.

1. Roh CK, Jung MJ. Laparoscopic excision for ectopic peritoneal paragonimiasis mimicking a gastric duplication cyst: A case report.Ann Med Surg (Lond) · 2021 · 69:10275410.1016/j.amsu.2021.102754 · PMID 34484726

   Their stated reason a fluke is missed on biopsy is not chemistry, it is arithmetic: 'insufficient amount'. And their recommendation is not a new reagent, it is a new habit — 'clinicians should bear in mind that an intra-abdominal mass may be related to a parasitic infection'. The barrier they name is the differential diagnosis, not the laboratory.

2. Tantrawatpan C, Intapan PM, Thanchomnang T, Sanpool O, Janwan P, Lulitanond V, Sadaow L, Maleewong W. Development of a PCR assay and pyrosequencing for identification of important human fish-borne trematodes and its potential use for detection in fecal specimens.Parasit Vectors · 2014 · 7:8810.1186/1756-3305-7-88 · PMID 24589167

   What is possible when somebody builds the assay. PCR plus pyrosequencing of a 46-nucleotide window in the 28S ribosomal gene distinguishes five fish-borne trematodes, and detects a SINGLE Opisthorchis viverrini or Clonorchis sinensis egg in 100 mg of stool. The authors note the reason it was needed: the eggs are 'difficult to differentiate MORPHOLOGICALLY ... even for experienced technicians'. The technology to name an organism from a few dozen bases has existed for over a decade. It is aimed at stool. It has not been aimed at tumors.

3. Matsunaga H, Arikawa K, Yamazaki M, Wagatsuma R, Ide K, Samuel AZ, Takamochi K, Suzuki K, Hayashi T, Hosokawa M, Kambara H, Takeyama H. Reproducible and sensitive micro-tissue RNA sequencing from formalin-fixed paraffin-embedded tissues for spatial gene expression analysis.Sci Rep · 2022 · 12(1):1951110.1038/s41598-022-23651-6 · PMID 36376423

   The arithmetic of the archive, and the change-my-mind study for the whole episode. A 100-micrometer punch, 10 micrometers thick — a few dozen cells — from six-year-old lung cancer blocks yielded usable sequence. The Hymenolepis case was solved by a broad eukaryotic PCR on FFPE tissue. Everything needed to ask 'is there non-human DNA in this tumor?' already exists and is already routine. Nobody has run it at scale.