Set cutoff for Sequenza cellularity

[EmreKocakavuk]

The distribution of Sequenza cellularity (tumor purity) values in the GLASS-dataset (n=680 samples) looks like this:

The number of samples with cellularity:

• <10% = 0
• <15% = 19
• <20% = 35
• <25% = 55
• <30% = 93
• <35% = 125
• <40% = 150

Questions at this point: What is the best cutoff for cellularity? Which low cellularity samples should be filtered out for further analyses? Or is it even necessary to set a cutoff?

__ The following plots show copy-number-plots of the 5 samples with the lowest cellularity

1. GLSS-DF-0007-R1-01D-WXS-C7TKYT (cellularity = 0.10)

   

2. GLSS-DF-0012-R1-01D-WXS-QGRYN1 (cellularity = 0.10)

   

3. GLSS-SM-R063-R1-01D-WXS-SF2PHH (cellularity = 0.10)

   

4. GLSS-SM-R069-TP-01D-WXS-EIPTR4 (cellularity = 0.11)

   

5. GLSS-SM-R099-R1-01D-WXS-I52D70 (cellularity = 0.12)

   

• [ ] Make a decision on setting a cutoff or not

[Kcjohnson]

Sequenza cellularity values and TITAN tumor purity values are now available for each tumor sample in the Synapse resource.