ORIGINAL RESEARCH

Quantification of fetal DNA in the plasma of pregnant women using next generation sequencing of frequent single nucleotide polymorphisms

Shubina J1,2, Jankevic T2, Goltsov AYu2, Mukosey IS, Kochetkova TO, Bystritsky AA, Barkov IYu, Tetruashvili NK, Kim LV, Trofimov DYu2
About authors

1 Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia

2 DNA-Technology LLC, Moscow, Russia

Correspondence should be addressed: Jekaterina Shubina
Akademika Oparina 4, Moscow, 117997; moc.liamg@anibuhs.aniretakej

About paper

Funding: this work was supported by the Ministry of Education and Science of the Russian Federation (Agreement 14.607.21.0136, Project ID RFMEFI60715X0136).

Received: 2018-04-15 Accepted: 2018-04-18 Published online: 2018-08-11
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Introduced into clinical practice in 2011, non-invasive prenatal testing (NIPT) allows detection of chromosomal aneuploidies in the fetus using maternal blood samples. Multiple studies have shown that one of the key factors affecting the result of this test is the fetal DNA fraction. The aim of this work was to develop a method capable of measuring the fetal DNA fraction based on targeted SNP sequencing. We selected polymorphisms with high frequency of heterozygous genotype from the international HapMap database. To estimate the frequency of these polymorphisms in the Russian population, we used 827 DNA donor samples. Fetal DNA fraction was measured in 87 plasma samples of pregnant women. Sequencing was performed on Ion Proton and Ion S5. We determined the frequencies of the studied polymorphisms in the pooled samples and compared the data on 53 SNPs in the pooled and 87 individual samples. The median difference was 3.4%. The correlation between the results obtained by targeted SNP sequencing and Y chromosome read count was 0.7. Thus, the proposed method can be used to estimate the fetal DNA fraction using SNP genotyping regardless of the fetus’s sex.

Keywords: non-invasive prenatal testing, fetal DNA fraction, single nucleotide polymorphisms, chromosome aneuploidy

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