title: Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: GenomeCare, Suwon, Republic of Korea.
authors.forename: Sunshin
authors.initials: S
authors.lastname: Kim
authors.affiliation: Mirae & Heemang OB/GYN Clinic, Seoul, Republic of Korea.
authors.forename: HeeJung
authors.initials: H
authors.lastname: Jung
authors.affiliation: Seoul Clinical Laboratories (SCL), Yongin, Republic of Korea.
authors.forename: Sung Hee
authors.initials: SH
authors.lastname: Han
authors.affiliation: Mirae & Heemang OB/GYN Clinic, Seoul, Republic of Korea.
authors.forename: SeungJae
authors.initials: S
authors.lastname: Lee
authors.affiliation: Mirae & Heemang OB/GYN Clinic, Seoul, Republic of Korea.
authors.forename: JeongSub
authors.initials: J
authors.lastname: Kwon
authors.affiliation: Namujungwon Maternity Hospital, Yangju, Republic of Korea.
authors.forename: Min Gyun
authors.initials: MG
authors.lastname: Kim
authors.affiliation: GN Maternity Hospital, Pyeongtak, Republic of Korea.
authors.forename: Hyungsik
authors.initials: H
authors.lastname: Chu
authors.affiliation: Xiamen Vangenes BioTech, Xiamen, Fujian, China.
authors.forename: Hongliang
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Nanobiomedical Science, BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea.
authors.forename: Kyudong
authors.initials: K
authors.lastname: Han
authors.affiliation: TheragenEtex, Suwon, Republic of Korea.
authors.forename: Hwanjong
authors.initials: H
authors.lastname: Kwak
authors.affiliation: TheragenEtex, Suwon, Republic of Korea.
authors.forename: Sunghoon
authors.initials: S
authors.lastname: Park
authors.affiliation: TheragenEtex, Suwon, Republic of Korea.
authors.forename: Hee Jae
authors.initials: HJ
authors.lastname: Joo
authors.affiliation: The Genomics Institute (TGI), BioMedical Engineering, UNIST, Ulsan, 687-798, Republic of Korea. bckim00@gmail.com.
authors.forename: Byung Chul
authors.initials: BC
authors.lastname: Kim
authors.affiliation: GenomeCare, Suwon, Republic of Korea. jongbhak@genomics.org.|The Genomics Institute (TGI), BioMedical Engineering, UNIST, Ulsan, 687-798, Republic of Korea. jongbhak@genomics.org.|Geromics, Ulsan, 687-798, Republic of Korea. jongbhak@genomics.org.|Genome Research Foundation, Osong, Chungbuk, Republic of Korea. jongbhak@genomics.org.
authors.forename: Jong
authors.initials: J
authors.lastname: Bhak
mesh_terms: D000328:Adult; D004314:Down Syndrome / Q000175:diagnosis* / Q000235:genetics*; D042241:Early Diagnosis; D005260:Female; D059014:High-Throughput Nucleotide Sequencing / Q000295:instrumentation*; D006801:Humans; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000295:instrumentation*; D012666:Semiconductors
keywords: Circulating fetal DNA; Genome; Non-invasive prenatal testing; Sequencing; Trisomy