fluffy usage

[smruti241]

I want to know how we can use fluffy? It has wisecondorX, PREFACE and AMYCNE joined in it. How it can tell about fetal gender and fetal fraction?

[J35P312]

Hello!
Fluffy computes the fetal fraction using Preface and AMYCNE:
PREFACE computes FFX (based on X chromosome) and fetal fraction based on some machine learning model (PREFACE FF).
AMYCNE estimates the fetal fraction based on the Y chromosome (FFY).

Fluffy will therefore provide you three separate fetal fraction estimates FFY, FFX and PREFACE FF.

Note that you will need to construct a model for PREFACE. For a decent model, you will need at least 500-1000 samples.

You can determine the fetal gender based on these fetal fraction estimates:

if XY: FFY, FFX, and PREFACE FF are roughly the same
if XX: FFX and FFY will be roughly 0, and PREFACE FF > 1
if X0: FFY will be 0, FFX and PREFACE FF will be similar ( >1) .
if XXX: FFY will be 0, FFX negative, and PREFACE FF positive.

This will only work if the fetal fraction is high enough, and the limit will depend on the quality of your preface model and input data.

You will also get a crude guess from the WisecondorX gender model; however this model does not take sex chromosome abnormalities in account.

The fetal fraction estimates will be found in the summary file, and the wisecondorX gender estimate is found in the
sample.npz.gender.txt files

I recomend plotting the fetal fraction according to Figure 4 (PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction, Raman Et al); this will help you determine the fetal gender.

Good luck!

[smruti241]

But how preface can give fetal fraction with unknown samples? If I have samples with unknown gender, will it help me in identifying the gender and then calculate the fetal fraction?

[smruti241]

Please tell me the inputs included in the analysis. I got confused actually

[smruti241]

@J35P312 Hiii, I want to know what are the inputs you used for PREFACE? I have only z-scores after using wisecondorX. After that how can I make input file for PREFACE? I dont have fetal fractions, I need it. Please tell me how can I get it.

[J35P312]

Hello!
I recomend calculating FFX or FFY; then you can train PREFACE with those values.

I use AMYCNE for FFY estimation, you will however need to fine tune the mapping quality and coefficient.

Alternatively, you can get a rough FFX model by using the wisecondorX chromosome X ratio:

chromosomeXRatio*100

Before training the model, you also need to make sure that it correlates with the ratio of known trisomies. (for instance, you could plot FFX vs ratio21 in known trisomy 21 pregnancies).

[smruti241]

Can you give me your trained and test data? I can take reference from that.

[smruti241]

@J35P312 how can I generate reference file and how can i run the samples? please explain me that.