Sample #5 Testicular tumor (Leydig cell tumor)

 Overview of tissue

 Overview

The sample was snap-frozen in liquid nitrogen within 10 minutes of removal from the patient. The sample was mounted and cut in a cryotome.  24 microtome slices, of 12 μm thickness, were placed on membrane suitable for laser capture microdissection (LCMD). 18 of the 24 slices were subjected to LCMD. A grid of 96 (~25000 μm2) circles was used as a template for the laser capture microdissection on each slide. Pictures of slices and LCMD cuts can be found at the following link.

 

Descriptive statistics of mutant fraction found in each LCMD sample.

Comparison MF

 P2F1 (M1) 
P2F2 (M2)
N1484 1606
Min (%)0 0
Max (%)100 100
Mean (%)28.1 22.9
First Quantile (%)0 0
Median (%)8.2 5.4
Third Quantile (%)46.8 27.8

 

 

 

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.

P2F1 (M1)Non-mutatedMutated
P2F2 (M2)Non-mutatedMutated

 

Isosurfaces of mutant fractions from 0% to 100% in 5% points increments.

ISO MF90

 

3D bubble plot of wild type and mutant fractions.

Marker 1 (P2F1)

 Bubble plot M1

 Marker 2 (P2F2)

Bubble marker 2