Segmental duplication as potential biomarkers for non-invasive prenatal testing of aneuploidies
Xinwen Chen,
Yifan Li,
Qiuying Huang,
Xingming Lin,
Xudong Wang,
Yafang Wang,
Ying Liu,
Qiushun He,
Yinghua Liu,
Ting Wang,
Zhi-Liang Ji,
Qingge Li
Affiliations
Xinwen Chen
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Yifan Li
National Institute for Data Science in Health and Medicine, School of Informatics, Xiamen University, Xiamen, Fujian 361102, China
Qiuying Huang
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Xingming Lin
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Xudong Wang
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Yafang Wang
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Ying Liu
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Qiushun He
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
Yinghua Liu
Centre for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu 215002, China
Ting Wang
Centre for Reproduction and Genetics, the Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, Jiangsu 215002, China; Corresponding authors.
Zhi-Liang Ji
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Corresponding authors.
Qingge Li
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, State Key Laboratory of Cellular Stress Biology, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Corresponding authors.
Background: Segmental duplication (SD) regions are distinct targets for aneuploidy detection owing to the virtual elimination of amplification bias. The difficulty of searching SD sequences for assay design has hampered their applications. Methods: We developed a computational program, ChAPDes, which integrates SD searching, refinement, and design of specific PCR primer/probe sets in a pipeline to remove most of the manual work. The generated primer/probe sets were first tested in a multiplex multicolour melting curve analysis for the detection of five common aneuploidies. The primer/probe sets were then tested in a digital PCR assay for the detection of trisomy 21. Finally, a digital PCR protocol was established to quantify maternal plasma DNA sequences for the non-invasive prenatal detection of fetal trisomy 21. Findings: ChAPDes could output 21,772 candidate primer/probe sets for trisomy 13, 18, 21 and sex chromosome aneuploidies within 2 working days. Clinical evaluation of the multiplex multicolour melting curve analysis involving 463 fetal genomic DNA samples revealed a sensitivity of 100% and specificity of 99.64% in comparison with the reference methods. Using the established digital PCR protocol, we correctly identified two trisomy 21 fetuses and thirteen euploid foetuses from the maternal plasma samples. Interpretation: The combination of ChAPDes with digital PCR detection could facilitate the use of SD as potential biomarkers for the non-invasive prenatal testing of fetal chromosomal aneuploidies.