Sample #170 Breast tumor (breast cancer)

Overview


Overview

This sample had limited amount of tissue, thus only 6 consecutive 12μm microtome slides were placed on membrane suitable for laser capture microdissection (LCMD). A grid of 96 (~25000 μm2) circles was used as a template for the laser capture microdissection on each membrane slide. This sample has corresponding lymph node and liver metastases. An attempt was also made to insert a guide object (plastic string) that could be followed through the tissue (click on the picture for enlargement).



Descriptive statistics of mutant fraction found in each LCMD sample.
MF_histogram

Marker P1F1Prime tumor
Liver metLymph node
N524708571
Min (%)000
Max (%)86.889.689.2
Mean (%)34.922.350.8
First Quantile (%)26.014.247.5
Median (%)36.420.553.1
Third Quantile (%)44.327.458.6

 

 

Links to 3 different approaches to visualizing the mutant fraction in the3D volume.

 

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

P1F1Non-mutatedMutated

 

Isosurfaces of mutant fractions from 5% to 95% in 5% points increments.

 

 35%70%
5%40%75%
10%45%80%
15%50%85%
20%55% 
25%60% 
30%65% 

 

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

 Bubble plot

 

 
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