title: Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.
abstract: Semiconductor high-throughput sequencing, represented by Ion Torrent PGM/Proton, proves to be feasible in the noninvasive prenatal diagnosis of fetal aneuploidies. It is commendable that, with less data and relevant cost also, an accurate result can be achieved owing to the high sensitivity and specificity of such kind of technology. We conducted a comparative analysis of the performance of four different Ion chips in detecting fetal chromosomal aneuploidies. Eight maternal plasma DNA samples, including four pregnancies with normal fetuses and four with trisomy 21 fetuses, were sequenced on Ion Torrent 314/316/318/PI chips, respectively. Results such as read mapped ratio, correlation coefficient and phred quality score were calculated and parallelly compared. All samples were correctly classified even with low-throughput chip, and, among the four chips, the 316 chip had the highest read mapped ratio, correlation coefficient, mean read length and phred quality score. All chips were well consistent with each other. Our results showed that all Ion chips are applicable in noninvasive prenatal fetal aneuploidy diagnosis. We recommend researchers or clinicians to use the appropriate chip with barcoding technology on the basis of the sample number.
authors.affiliation: 1] Prenatal Diagnosis Center, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University, Shanghai, China [2] Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
authors.forename: Yanlin
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Zujia
authors.initials: Z
authors.lastname: Wen
authors.affiliation: Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Jiawei
authors.initials: J
authors.lastname: Shen
authors.affiliation: Prenatal Diagnosis Center, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Cheng
authors.affiliation: Department of General Surgery, Shanghai Changning Center Hospital, Shanghai, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Shanghai genomePilot Institutes of Genomics and Human Health, Shanghai, China.
authors.forename: Xiaolan
authors.initials: X
authors.lastname: Qin
authors.affiliation: 1] Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China [2] Shanghai Key Laboratory of Prevention and Intervention of Birth Defects, Shanghai, China.
authors.forename: Duan
authors.initials: D
authors.lastname: Ma
authors.affiliation: Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
authors.forename: Yongyong
authors.initials: Y
authors.lastname: Shi
mesh_terms: D005260:Female; D006801:Humans; D007621:Karyotyping; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods* / Q000592:standards; D015203:Reproducibility of Results; D014314:Trisomy / Q000175:diagnosis* / Q000235:genetics