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. 2014 Oct 20;9(10):e110240.
doi: 10.1371/journal.pone.0110240. eCollection 2014.

The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform

Young Joo Jeon  1 , Yulin Zhou  2 , Yihan Li  3 , Qiwei Guo  2 , Jinchun Chen  3 , Shengmao Quan  4 , Ahong Zhang  4 , Hailing Zheng  4 , Xingqiang Zhu  4 , Jin Lin  4 , Huan Xu  4 , Ayang Wu  5 , Sin-Gi Park  1 , Byung Chul Kim  6 , Hee Jae Joo  1 , Hongliang Chen  4 , Jong Bhak  7
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The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform

Young Joo Jeon et al. PLoS One. .

Abstract

Objective: Recent non-invasive prenatal testing (NIPT) technologies are based on next-generation sequencing (NGS). NGS allows rapid and effective clinical diagnoses to be determined with two common sequencing systems: Illumina and Ion Torrent platforms. The majority of NIPT technology is associated with Illumina platform. We investigated whether fetal trisomy 18 and 21 were sensitively and specifically detectable by semiconductor sequencer: Ion Proton.

Methods: From March 2012 to October 2013, we enrolled 155 pregnant women with fetuses who were diagnosed as high risk of fetal defects at Xiamen Maternal & Child Health Care Hospital (Xiamen, Fujian, China). Adapter-ligated DNA libraries were analyzed by the Ion Proton™ System (Life Technologies, Grand Island, NY, USA) with an average 0.3× sequencing coverage per nucleotide. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%. The results of this study were derived from BWA mapping. Z-score was used for fetal trisomy 18 and 21 detection.

Results: Interactive dot diagrams showed the minimal z-score values to discriminate negative versus positive cases of fetal trisomy 18 and 21. For fetal trisomy 18, the minimal z-score value of 2.459 showed 100% positive predictive and negative predictive values. The minimal z-score of 2.566 was used to classify negative versus positive cases of fetal trisomy 21.

Conclusion: These results provide the evidence that fetal trisomy 18 and 21 detection can be performed with semiconductor sequencer. Our data also suggest that a prospective study should be performed with a larger cohort of clinically diverse obstetrics patients.

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Conflict of interest statement

Competing Interests: We have the following interests: co-authors Young Joo Jeon, Sin-Gi Park, Hee Jae Joo, and Jong Bhak are employed by TheragenEtex Bio Institute. Co-authors Young Joo Jeon, Sin-Gi Park, Hee Jae Joo, and Jong Bhak are employed by Genome Care. Co-authors Shengmao Quan, Ahong Zhang, Hailing Zheng, Xingqiang Zhu, Jin Lin, Huan Xu, and Hongliang Chen are employed by Xiamen Vangenes BioTech. Co-author Byung Chul Kim is employed by Clinomics. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Interactive dot diagrams of trisomy 18 and 21.
(A) Interactive dot diagram of trisomy 18. (B) Interactive dot diagram of trisomy 21.
See this image and copyright information in PMC

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