Interpretation of (negative) in-vitro results

[fantasy121]

@wwjvdsande I think this question has been asked before in a meeting but I can't trace back the answer. Making a new GHI for this for future reference.

The quoted in vitro results are growth of mycetoma at 100 uM of a compound. If the growth is negative, how should I interpret this result? Is a more negative result better or is a negative growth considered "zero"? For instance, if I have MYOS_00111 (in vitro -1.2) and MYOS_00128 (in vitro -3.2), is it correct to say 00128 has a better in vitro result than 00111, or is correct to say the both have equally good in vitro results (=0 growth)?

[mattodd]

My first guess would be that those numbers are within the experiment's margin of error.

On Thu, 8 Jul 2021, 01:42 Hung Phat Duong, @.***> wrote:

@wwjvdsande https://github.com/wwjvdsande I think this question has been asked before in a meeting but I can't trace back the answer. Making a new GHI for this for future reference.

The quoted in vitro results are growth of mycetoma at 100 uM of a compound. If the growth is negative, how should I interpret this result? Is a more negative result better or is a negative growth considered "zero"? For instance, if I have MYOS_00111 (in vitro -1.2) and MYOS_00128 (in vitro -3.2), is it correct to say 00128 has a better in vitro result than 00111, or is correct to say the both has equally good in vitro results (=0 growth)?

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[wwjvdsande]

Due to the nature of the assay, a number below zero means that it is completely inhibited. Since we use a hyphal inoculum and madurella forms a pigment which might interfere with the viability dye used there is always a bit of variation between the wells. That is also why we use the treshold of 20%. Biologically seen we say that everything below 20% growth is completely inhibited. It does not matter if we see -5% growth or 15% growth. Those are in ther margin of error so we classify them all the same as no growth.

[fantasy121]

Due to the nature of the assay, a number below zero means that it is completely inhibited. Since we use a hyphal inoculum and madurella forms a pigment which might interfere with the viability dye used there is always a bit of variation between the wells. That is also why we use the treshold of 20%. Biologically seen we say that everything below 20% growth is completely inhibited. It does not matter if we see -5% growth or 15% growth. Those are in ther margin of error so we classify them all the same as no growth.

Thanks for the clarification. This will help with my SAR exploration a great deal.

For the growth between 20% and 100+%, how sensitive are the in vitro values? Is it going to be down to every 1%, every 5%, every 10%, every 20% or something else? Is the sensitivity going to be less accurate towards the 20% range, compared to towards to 100% range, or is the sensitivity similar for everything in the 20% to 100+% range? @wwjvdsande