Sample #231 Bladder tumor

Overview of tissue



This sample was a tiny tissue piece that had dried in the -70°C freezer. Attempts were made to rehydrate the tissue prior to sectioning in the cryotome. The reason for this deviation from the standard protocol was that a matching lymph node (in good condition) was available. Consequently thicker slices had to be taken. 9 microtome slices, of 20 μm thickness were obtained, where  4 slices were subjected to laser capture microdissection (LCMD). The same grid of 96 (~25000 μm2) circles was used as a template for the laser capture microdissection on each slide.

Descriptive statistics of mutant fraction found in each LCMD sample.

Comparison MF

  P2F6 (M1)  
P5F6 (M2)
N 286 228
Min (%) 1.5 4.4
Max (%) 93.8 93.7
Mean (%) 25.5 35.1
First Quantile (%) 8.24 9.7
Median (%) 11.5 18.7
Third Quantile (%) 25.0 59.3

Links to 3 different approaches to visualizing the mutant fraction in the 3D volume.


Isosurface of a random spread of homoplasmic cells (wild-type and/or mutant) in each LCMD volumes.

P2F6 (M1) Non-mutated Mutated
P5F6 (M2) Non-mutated Mutated


No isosurfaces of mutant fractions were created for the two markers due condition of the tissue and the sampling. 



3D bubble plot of wild-type and mutant fractions.

Marker 1 (P2F6)

Bubble plot M1

Marker 2 (P5F6)

Bubble marker 2