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Noninvasive Prenatal Testing for Fetal Chromosomal Abnormalities Using Massively Parallel Sequencing: Clinical Experience from 7910 Korean Pregnancies

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Open Journal of Genetics 2018年第3期8卷 42-53页

作者： Seon Young Yun Hyuk Jung Kwon Amit Goyal Katiyar P. Shashank heesu im Joungsu Joo Jin-Sik Bae Min Seob Lee Sunghoon Lee EONE-DIAGNOMICS Genome Center (EDGC) Incheon South Korea

Objective: The purpose of this study is to review the clinical experience and performance of noninvasive prenatal testing (NIPT) method, using cell-free DNAto detect chromosomes 21, 18, 13, X, and Y abnormalities in over 7910 clinical samples from South Korean population. Method: Pregnant women between 1st of November 2015 to 18th of February 2018, with obstetric clinical findings participated in the study. NIPT was performed based on masivelly parallel sequencing with 0.3× low coverage paired-end sequencing using cell-free DNA in maternal plasma. Further invasive prenatal testing was recommended for pregnant women with positive NIPT results. Results: Of the total 7910 participants, 7890 (99.75%) were tested for NIPT and the remaining 20 (0.25%) were below the Quality Control (QC) standards. T13, T18, XXX, XXY and XYY had 100% of sensitivity, specificity, positive predictive values (PPV) and accuracy. The overall sensitivity was 100% and specificity, PPV and accuracy of all chromosomal abnormalities with further validation were 99.92%, 94.25%, and, 99.92% respectively. Conclusion: Our NIPT results showed high positive predictive value for the detection of autosomal trisomies and sex chromosome aneuploidies in our sample cohort.

关键词： Cell-Free DNA Trisomy Clinical Performance Mosaicism CPM Fetal Abnormality Noninvasive Prenatal Testing NIPT

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Multiple z-Score Based Method for Noninvasive Prenatal Test Using Cell-Free DNA in Maternal Plasma

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Open Journal of Genetics 2017年第1期7卷 1-8页

作者： Hyuk Jung Kwon Amit Goyal heesu im Kichan Lee Seon Young Yun Yoon Hee Kim Sungjong Lee Mi-Gyeong Lee Hyuna Lee Reena Garg Boram Park Soyoung Choi Joungsu Joo Jin-Sik Bae Min-Jeong Kim Min Seob Lee Sunghoon Lee EONE-DIAGNOMICS Genome Center Co. Ltd. Inchon Korea

Objective: To improve the detecting accuracy of chromosomal aneuploidy of fetus by non-invasive prenatal testing (NIPT) using next generation sequencing data of pregnant women’s cell-free DNA. Methods: We proposed the multi-Z method which uses 21 z-scores for each autosomal chromosome to detect aneuploidy of the chromosome, while the conventional NIPT method uses only one z-score. To do this, mapped read numbers of a certain chromosome were normalized by those of the other 21 chromosomes. Average and standard deviation (SD), which are used for calculating z-score of each sample, were obtained with normalized values between all autosomal chromosomes of control samples. In this way, multiple z-scores can be calculated for 21 autosomal chromosomes except oneself. Results: Multi-Z method showed 100% sensitivity and specificity for 187 samples sequenced to 3 M reads while the conventional NIPT method showed 95.1% specificity. Similarly, for 216 samples sequenced to 1 M reads, Multi-Z method showed 100% sensitivity and 95.6% specificity and the conventional NIPT method showed a result of 75.1% specificity. Conclusion: Multi-Z method showed higher accuracy and robust results than the conventional method even at low coverage reads.

关键词： Cell-Free DNA z-Score Multiple Thresholds Coefficient of Variance Noninvasive Prenatal Testing NIPT

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