cffDNA Library and gDNA

[ionbioin]

What is the difference between cffDNA (Cell-free fetal DNA)and genome DNA?
Is there any difference in Library preparation? and its effect on sequence data analysis.



Thanks

[nucacidhunter]

A definition and characteristics of cffDNA can be found here: http://en.wikipedia.org/wiki/Cell-free_fetal_DNA In this context genomic DNA is from mother cells.

There are small differences in shotgun library prep method between two. For library prep cffDNA is not fragmented as they are short but genomic DNA need to be sheared to a suitable size. Other difference is input amount. One can use standard or low input kits or methods for genomic DNA library prep depending on availability of DNA. But for cffDNA a low input kit need to be used as the amount obtained is usually low.

Maybe someone with experience in data analysis can provide info on differences in sequence analysis approach.