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BMC Med Genomics. 2016 Apr 30;9(1):22. doi: 10.1186/s12920-016-0182-9.

Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy.

Author information

1
GenomeCare, Suwon, Republic of Korea.
2
Mirae & Heemang OB/GYN Clinic, Seoul, Republic of Korea.
3
Seoul Clinical Laboratories (SCL), Yongin, Republic of Korea.
4
Namujungwon Maternity Hospital, Yangju, Republic of Korea.
5
GN Maternity Hospital, Pyeongtak, Republic of Korea.
6
Xiamen Vangenes BioTech, Xiamen, Fujian, China.
7
Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.
8
TheragenEtex, Suwon, Republic of Korea.
9
The Genomics Institute (TGI), BioMedical Engineering, UNIST, Ulsan, 687-798, Republic of Korea. bckim00@gmail.com.
10
GenomeCare, Suwon, Republic of Korea. jongbhak@genomics.org.
11
The Genomics Institute (TGI), BioMedical Engineering, UNIST, Ulsan, 687-798, Republic of Korea. jongbhak@genomics.org.
12
Geromics, Ulsan, 687-798, Republic of Korea. jongbhak@genomics.org.
13
Genome Research Foundation, Osong, Chungbuk, Republic of Korea. jongbhak@genomics.org.

Abstract

BACKGROUND:

Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA reads for NIPT. However, the approval criteria vary among platforms and countries. This can delay the introduction of such devices and systems to clinics. A comparison of the sensitivity and specificity of two different platforms using the same sequencing chemistry could be useful in NIPT for fetal chromosomal aneuploidies. This would improve healthcare authorities' confidence in decision-making on sequencing-based tests.

METHODS:

One hundred and one pregnant women who were predicted at high risk of fetal defects using conventional prenatal screening tests, and who underwent definitive diagnosis by full karyotyping, were enrolled from three hospitals in Korea. Most of the pregnant women (69.79 %) received NIPT during weeks 11-13 of gestation and 30.21 % during weeks 14-18. We used Ion Torrent PGM and Proton semi-conductor-based sequencers with 0.3× sequencing coverage depth. The average total reads of 101 samples were approximately 4.5 and 7.6 M for PGM and Proton, respectively. A Burrows-Wheeler Aligner (BWA) algorithm was used for the alignment, and a z-score was used to decide fetal trisomy 21. Interactive dot diagrams from the sequencing data showed minimal z-score values of 2.07 and 2.10 to discriminate negative versus positive cases of fetal trisomy 21 for the two different sequencing systems.

RESULTS:

Our z-score-based discrimination method resulted in 100 % positive and negative prediction values for both ion semiconductor PGM and Proton sequencers, regardless of their sequencing chip and chemistry differences. Both platforms performed well at an early stage (11-13 weeks of gestation) compared with previous studies.

CONCLUSIONS:

These results suggested that, using two different sequencers, NIPT to detect fetal trisomy 21 in early pregnancy is accurate and platform-independent. The data suggested that the amount of sequencing and the application of common, simple, and robust statistical analyses are more important than sequencing chemistry and platform types. This result has practical implications in countries where PGM is approved for NIPT but the Proton system is not.

KEYWORDS:

Circulating fetal DNA; Genome; Non-invasive prenatal testing; Sequencing; Trisomy

PMID:
27129388
PMCID:
PMC4851803
DOI:
10.1186/s12920-016-0182-9
[Indexed for MEDLINE]
Free PMC Article

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