title: Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles.
abstract: OBJECTIVE
  While large fetal copy number aberrations can generally be detected through sequencing of DNA in maternal blood, the reliability of tests depends on the fraction of DNA that originates from the fetus. Existing methods to determine this fetal fraction require additional work or are limited to male fetuses. We aimed to create a sex-independent approach without additional work.
  
  
  METHODS
  DNA fragments used for noninvasive prenatal testing are cut only by natural processes; thus, influences on cutting by the packaging of DNA in nucleosomes will be preserved in sequencing. As cuts are expected to be made preferentially in linker regions, the shorter fetal fragments should be enriched for reads starting in nucleosome covered positions.
  
  
  RESULTS
  We generated genome-wide nucleosome profiles based on single end sequencing of cell-free DNA. We found a difference between DNA digestion of fetal cell-free DNA and maternal cell-free DNA and used this to calculate the fraction of fetal DNA in maternal plasma for both male and female fetuses.
  
  
  CONCLUSIONS
  Our method facilitates cost-effective noninvasive prenatal testing, as the fetal DNA fraction can be estimated without the need for expensive paired-end sequencing or additional tests. The methodology is implemented as a tool, which we called SANEFALCON (Single reAds Nucleosome-basEd FetAL fraCtiON). It is available for academic and non-profit purposes under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License. github.com/rstraver/sanefalcon. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
authors.affiliation: Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.
authors.forename: Roy
authors.initials: R
authors.lastname: Straver
authors.affiliation: Department of Clinical Chemistry, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.
authors.forename: Cees B M
authors.initials: CB
authors.lastname: Oudejans
authors.affiliation: Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.
authors.forename: Erik A
authors.initials: EA
authors.lastname: Sistermans
authors.affiliation: Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.|Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.
authors.forename: Marcel J T
authors.initials: MJ
authors.lastname: Reinders
mesh_terms: D025063:Chromosome Disorders / Q000097:blood / Q000175:diagnosis*; D003362:Cost-Benefit Analysis; D004247:DNA / Q000097:blood / Q000378:metabolism*; D005260:Female; D005333:Fetus / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D011247:Pregnancy; D011296:Prenatal Diagnosis; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D009707:Nucleosomes; D004247:DNA