Accuracy and reproducibility of fetal-fraction measurement using relative quantitation at polymorphic loci with microarray

Ultrasound Obstet Gynecol. 2018 Jun;51(6):813-817. doi: 10.1002/uog.19036. Epub 2018 May 3.


Objectives: Various methods of fetal-fraction measurement have been employed in conjunction with different approaches to cell-free DNA testing for fetal aneuploidy. In this study, we determined the accuracy and reproducibility of fetal-fraction measurement using polymorphic assays that are incorporated into the test design as part of the Harmony® prenatal test and evaluated whether the single nucleotide polymorphisms selected for and used in these assays can be applied broadly to all patient populations.

Methods: Clinical maternal plasma samples were assayed using a custom microarray with Digital ANalysis of Selected Regions (DANSR) assays designed to cover non-polymorphic targets on chromosomes of interest for aneuploidy assessment (13, 18, 21, X and Y) and polymorphic targets for fetal-fraction assessment. In a consecutive series of 47 512 maternal plasma samples, fetal-fraction measurements based on polymorphic assays were compared with those from Y-sequence quantitation. Reproducibility was examined between first- and second-tube measurements for the same patient sample in 734 cases. The fraction of informative loci was calculated for 13 988 samples.

Results: There was a strong correlation between fetal fractions determined using the polymorphic assays and using Y-chromosome sequence quantitation (r = 0.97). Fetal-fraction measurement between the first and second tubes was highly reproducible (r = 0.98). The fraction of informative loci observed in a clinical series was consistent with predictions based on assay design.

Conclusions: The method based on relative quantitation at polymorphic loci on a microarray is accurate and reproducible for fetal-fraction estimation and is equally informative across global populations. This study provides a useful benchmark for ensuring the reliability and accuracy of fetal-fraction measurement. © 2018 Roche Sequencing Solutions. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Keywords: NIPT; cell-free DNA; fetal fraction; prenatal screening; quality.

Publication types

  • Evaluation Study

MeSH terms

  • Chromosome Disorders / blood
  • Chromosome Disorders / diagnosis*
  • Chromosomes, Human, Pair 13
  • Chromosomes, Human, Pair 18
  • Chromosomes, Human, Pair 21
  • Chromosomes, Human, X
  • Chromosomes, Human, Y
  • Female
  • Fetus / metabolism
  • Genetic Testing
  • Humans
  • Predictive Value of Tests
  • Pregnancy
  • Prenatal Diagnosis*
  • Reproducibility of Results
  • Sensitivity and Specificity