Hi there,
I am now working on a mutant with the phenotype quite unstable. I suspect that it is possibly due to low penetrance. So I wonder usually how people
do the scoring to prove low penetrance. Is there a reference method to use?
Many thanks
Emily
Hi,
just out of interest, is the penetrance of your mutant phenotype temperature sensitive? That would make scoring easier.
Steve
Could you clarify your question? Penetrance means the frequency with which a given genotype causes a given phenotype, and so your question seems somewhat tautological. Is your question about how to be certain your strain really is homozygous for the mutation? Or might there be modifier loci floating around in the strain? Are you having a problem with a highly variable penetrance, such that sometimes most or all progeny show the phenotype and sometimes few do?
Assuming some combination of the above, I’d recommend that you be especially careful about conditions (bleach the strain to clean it, control temperature carefully, etcetera) and clone out a number of individuals to see whether their progeny all show the phenotype at similar penetrance when grown in parallel under identical conditions. Mapping the mutation and outcrossing could also help if you’re uncertain about whether your mutation is homozygous or about modifier loci, and might make your phenotype more consistent.
hey emily,
exactly how you do it is going to depend on the particular genetic background and the phenotype you are scoring.
let’s assume that your phenotype (Phe) is not sterile or lethal. probably you are dealing with a situation like this:
you pick a worm that is Phe and it produces a brood where only a few of the F1 progeny are Phe.
you pick an F1 Phe animal and once again it produces a brood where only a few F2 progeny are Phe.
and so on with F3 etc.
if this is what you observe, then it is highly likely that you have a homozygous strain that has low penetrance (there are other formal possibilities).
next you would check different temperatures to see if high or low temp increases the penetrance and then use the best conditions for further work.
then you can map it using CB4856 (or visible markers). assuming it isn’t dominant (unlikely) you can identify homozygotes just by picking Phe animals. this will work even if
there is maternal rescue (but you will have to go to the F3 to identify homozygotes).
good luck!
eric
Hey everyone, thanks for your replies. FYI, it seems that the low penetrance phenotype is not temperature sensitive, after I tried different incubation conditations (15c, 20c and 23c). Among one single worm’s progeny, only a few show non-phenotype. Just to clarify my question, I want to know usually how many worms I need to score to ascertain that it is low penetrance or not, because I want to do some quantification analysis.
Thanks again 
Emily
? you mean nearly all show the mutant phenotype? in that case you are talking about high penetrance. so, if you usually see 270/300 animals have mutant phenotype (and assuming it is homozygous etc) the phenotype is 90%
penetrant.
if you are going to do some manipulation and then want to know if any increase or decrease in penetrance is statistically significant, then just try plugging example ratios and sample sizes into your signficance test to see what approx.
sample size you need to achieve p < 0.05