A Method to Quantify Cell-Free Fetal DNA Fraction in Maternal Plasma Using Next Generation Sequencing: Its Application in Non-Invasive Prenatal Chromosomal Aneuploidy Detection

PloS One
Xu-Ping XuYing-Song Wu

Abstract

The fraction of circulating cell-free fetal (cff) DNA in maternal plasma is a critical parameter for aneuploidy screening with non-invasive prenatal testing, especially for those samples located in equivocal zones. We developed an approach to quantify cff DNA fractions directly with sequencing data, and increased cff DNAs by optimizing library construction procedure. Artificial DNA mixture samples (360), with known cff DNA fractions, were used to develop a method to determine cff DNA fraction through calculating the proportion of Y chromosomal unique reads, with sequencing data generated by Ion Proton. To validate our method, we investigated cff DNA fractions of 2,063 pregnant women with fetuses who were diagnosed as high risk of fetal defects. The z-score was calculated to determine aneuploidies for chromosomes 21, 18 and 13. The relationships between z-score and parameters of pregnancies were also analyzed. To improve cff DNA fractions in our samples, two groups were established as follows: in group A, the large-size DNA fragments were removed, and in group B these were retained, during library construction. A method to determine cff DNA fractions was successfully developed using 360 artificial mixture samples in which cff DN...Continue Reading

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Feb 14, 2018·Molecular Reproduction and Development·Monica A StoopsTerri L Roth
Jul 26, 2018·Genetics and Molecular Biology·Carolina MalcherMaria Rita Passos-Bueno
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May 11, 2018·PloS One·Valeriy KuznyetsovClifford Librach

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Methods Mentioned

BETA
PCR
Chip

Software Mentioned

SPSS Statistics

Related Concepts

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