PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction.

ABSTRACT:

Objective

During routine noninvasive prenatal testing (NIPT), cell-free fetal DNA fraction is ideally derived from shallow-depth whole-genome sequencing data, preventing the need for additional experimental assays. The fraction of aligned reads to chromosome Y enables proper quantification for male fetuses, unlike for females, where advanced predictive procedures are required. This study introduces PREdict FetAl ComponEnt (PREFACE), a novel bioinformatics pipeline to establish fetal fraction in a gender-independent manner.

Methods

PREFACE combines the strengths of principal component analysis and neural networks to model copy number profiles.

Results

For sets of roughly 1100 male NIPT samples, a cross-validated Pearson correlation of 0.9 between predictions and fetal

SUBMITTER: Raman L 

PROVIDER: S-EPMC6771918 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature