Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms

PloS One
Angela BarrettMahesh Choolani

Abstract

Cell-free DNA from maternal plasma can be used for non-invasive prenatal testing for aneuploidies and single gene disorders, and also has applications as a biomarker for monitoring high-risk pregnancies, such as those at risk of pre-eclampsia. On average, the fractional cell-free fetal DNA concentration in plasma is approximately 15%, but can vary from less than 4% to greater than 30%. Although quantification of cell-free fetal DNA is straightforward in the case of a male fetus, there is no universal fetal marker; in a female fetus measurement is more challenging. We have developed a panel of multiplexed insertion/deletion polymorphisms that can measure fetal fraction in all pregnancies in a simple, targeted sequencing reaction. A multiplex panel of primers was designed for 35 indels plus a ZFX/ZFY amplicon. cfDNA was extracted from plasma from 157 pregnant women, and maternal genomic DNA was extracted for 20 of these samples for panel validation. Sixty-one samples from pregnancies with a male fetus were subjected to whole genome sequencing on the Ion Proton sequencing platform, and fetal fraction derived from Y chromosome counts was compared to fetal fraction measured using the indel panel. A total of 157 cell-free DNA samples...Continue Reading

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Citations

Dec 11, 2019·Prenatal Diagnosis·Lisa Hui, Diana W Bianchi
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Mar 22, 2019·Journal of Assisted Reproduction and Genetics·Denice BelandresNabil Arrach
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Methods Mentioned

BETA
blood-draw
PCR
blood draw
PCRs
chip
electrophoresis

Software Mentioned

GraphPad Prism
Picard
Python
SANEFALCON
fastq
R
NIPT
SEQFF
Multiple Primer Analyzer
FetalQuant SD

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