Chenming Xu1,2, Ting Wang3, Chao Liu4, Hong Li3, Xiaoyan Chen4, Huanhuan Zhu4, Songchang Chen1,2, Qiuhong Xin4, Jing Tao4, Liming Huang4, Zhengwen Jiang5. 1. Institute of Embryo-Fetal Original Adult Disease affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. 2. International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. 3. Suzhou Municipal Hospital affiliated to Nanjing Medical University, Suzhou, Jiangsu, China. 4. Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China. 5. Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China. zhengwenj@geneskies.com.
Abstract
BACKGROUND: Noninvasive prenatal screening (NIPS) using plasma cell-free DNA has gained tremendous popularity in the clinical assessment of fetal aneuploidy. Most, if not all, of these tests rely on complex and expensive massively parallel sequencing (MPS) techniques, hindering the use of NIPS as a common screening procedure. METHODS: We have developed and optimized an MPS-independent noninvasive genetic test that can rapidly detect fetal aneuploidy at considerably lower costs. We used the high-throughput ligation-dependent probe amplification (HLPA) assay with standard z score statistics to identify the minute copy number change of targeted chromosomal regions. HLPA was modified from multiplex ligation-dependent probe amplification to allow quantification of up to 200 genomic loci in a single multiplex PCR. As a proof of principle, we conducted Down syndrome screening in 1182 women with singleton pregnancies [maternal age (SD): 32.7 (4.6)] using whole-genome sequencing-based NIPS and our method. RESULTS: Nineteen fetuses with trisomy 21 were detected by both methods and confirmed by karyotyping of amniotic fluid. Overall, our method showed 100.0% sensitivity (19/19) and 99.7% specificity (1076/1079) in trisomy 21 screening, generating a positive predictive value of 86.4% (19/22) and a 7.1% (84/1182) no-call rate. CONCLUSIONS: Our technique potentially opens new avenues for the development of inexpensive, yet effective, prenatal aneuploidy tests. The simplicity and accuracy of this method make it a good candidate for clinical implementation as a standard screening procedure.
BACKGROUND: Noninvasive prenatal screening (NIPS) using plasma cell-free DNA has gained tremendous popularity in the clinical assessment of fetal aneuploidy. Most, if not all, of these tests rely on complex and expensive massively parallel sequencing (MPS) techniques, hindering the use of NIPS as a common screening procedure. METHODS: We have developed and optimized an MPS-independent noninvasive genetic test that can rapidly detect fetal aneuploidy at considerably lower costs. We used the high-throughput ligation-dependent probe amplification (HLPA) assay with standard z score statistics to identify the minute copy number change of targeted chromosomal regions. HLPA was modified from multiplex ligation-dependent probe amplification to allow quantification of up to 200 genomic loci in a single multiplex PCR. As a proof of principle, we conducted Down syndrome screening in 1182 women with singleton pregnancies [maternal age (SD): 32.7 (4.6)] using whole-genome sequencing-based NIPS and our method. RESULTS: Nineteen fetuses with trisomy 21 were detected by both methods and confirmed by karyotyping of amniotic fluid. Overall, our method showed 100.0% sensitivity (19/19) and 99.7% specificity (1076/1079) in trisomy 21 screening, generating a positive predictive value of 86.4% (19/22) and a 7.1% (84/1182) no-call rate. CONCLUSIONS: Our technique potentially opens new avenues for the development of inexpensive, yet effective, prenatal aneuploidy tests. The simplicity and accuracy of this method make it a good candidate for clinical implementation as a standard screening procedure.
Authors: Fredrik Dahl; Olle Ericsson; Olof Karlberg; Filip Karlsson; Mathias Howell; Fredrik Persson; Fredrik Roos; Johan Stenberg; Tarja Ahola; Ida Alftrén; Björn Andersson; Emelie Barkenäs; Birgit Brandner; Jenny Dahlberg; Sara Elfman; Magnus Eriksson; Per-Ola Forsgren; Niels Francois; Anna Gousseva; Faizan Hakamali; Åsa Janfalk-Carlsson; Henrik Johansson; Johanna Lundgren; Atefeh Mohsenchian; Linus Olausson; Simon Olofsson; Atif Qureshi; Björn Skarpås; Anna Sävneby; Eva Åström; Ove Öhman; Magnus Westgren; Helena Kopp-Kallner; Aino Fianu-Jonasson; Argyro Syngelaki; Kypros Nicolaides Journal: Sci Rep Date: 2018-03-14 Impact factor: 4.379