How to calculate Z-score for aneuploidy?

[sachin]

Hello everyone,

I am working on down syndrome. I have referred some papers for NIPT (Noninvasive Prenatal Testing) in which they have detect trisomy using the z-score method.

So is any easy method to calculate Z score and GC correction for aneuploidy and how ??

Do anyone have suggestions for me to do this?

Thanks in advance.
Sachin

[Kashliks]

Hello,
It seems there is no easy way. I am trying to find reasonable method to do it and havent found yet.
As I understand this should be done this way:
1. QC data leaving only small, quality reads (somewhere it was written <50bp) (easy)
2. Align (easy, bowtie2)
3. Remove duplicates, ones that align in multiple places (picard)
4. GC bias correction to obtain correct coverage (split alignment into bins, get GC corrected coverage, plot it) (dont know how to do it )

If someone can help with DETAILED explanation how to do 4th step, it would be greatly appreciated.

[amitgsir]

Hello everyone,

I am working on down syndrome. I have referred some papers for NIPT (Noninvasive Prenatal Testing) in which they have detect trisomy using the z-score method.

So is any easy method to calculate Z score and GC correction for aneuploidy and how ??

Do anyone have suggestions for me to do this?

Thanks in advance.
Sachin

Hi Sachin,

Could you find any proper method? I am a starter and dealing with siimilar problem.
Thanks

[sachin]

Hi Sachin,

Could you find any proper method? I am a starter and dealing with siimilar problem.
Thanks

Hi Amit,
For the NIPT projects, you can use trial version ofSoftgenetic's Sensitive Aneuploidy Detection Tool (SAD) for the analysis (NCVs based), but for this tool you will require minimum 32 control samples.

Sachin

[amitgsir]

Thank you Sachin. I will try SAD.