title: Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA.
abstract: Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China; Guangdong Thalassemia Diagnostic Centre, Guangzhou 510010, China; yinaiwa@vip.126.com qfhuang@capitalgenomics.com mkarin@ucsd.edu kang.zhang@gmail.com.
authors.forename: Ai-hua
authors.initials: AH
authors.lastname: Yin
authors.affiliation: CapitalBio Genomics Co., Ltd., Dongguan 523808, China;
authors.forename: Chun-fang
authors.initials: CF
authors.lastname: Peng
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
authors.forename: Bennett A
authors.initials: BA
authors.lastname: Caughey
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Jie-xia
authors.initials: JX
authors.lastname: Yang
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Jian
authors.initials: J
authors.lastname: Liu
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Wei-wei
authors.initials: WW
authors.lastname: Huang
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: CapitalBio Genomics Co., Ltd., Dongguan 523808, China;
authors.forename: Dong-hong
authors.initials: DH
authors.lastname: Luo
authors.affiliation: CapitalBio Genomics Co., Ltd., Dongguan 523808, China;
authors.forename: Hai-liang
authors.initials: HL
authors.lastname: Liu
authors.affiliation: CapitalBio Genomics Co., Ltd., Dongguan 523808, China;
authors.forename: Yang-yi
authors.initials: YY
authors.lastname: Chen
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Jing
authors.initials: J
authors.lastname: Wu
authors.affiliation: Kangrui Biological Pharmaceutical Technology Co., Ltd., Guangzhou 510005, China;
authors.forename: Rui
authors.initials: R
authors.lastname: Hou
authors.affiliation: Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital and Sichuan University, Chengdu 610041, China;
authors.forename: Mindy
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
authors.forename: Michael
authors.initials: M
authors.lastname: Ai
authors.affiliation: Kangrui Biological Pharmaceutical Technology Co., Ltd., Guangzhou 510005, China;
authors.forename: Lianghong
authors.initials: L
authors.lastname: Zheng
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
authors.forename: Rachel Q
authors.initials: RQ
authors.lastname: Xue
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Ming-qin
authors.initials: MQ
authors.lastname: Mai
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Fang-fang
authors.initials: FF
authors.lastname: Guo
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Yi-ming
authors.initials: YM
authors.lastname: Qi
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Dong-mei
authors.initials: DM
authors.lastname: Wang
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
authors.forename: Michal
authors.initials: M
authors.lastname: Krawczyk
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
authors.forename: Daniel
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou 510010, China;
authors.forename: Yu-nan
authors.initials: YN
authors.lastname: Wang
authors.affiliation: CapitalBio Genomics Co., Ltd., Dongguan 523808, China; yinaiwa@vip.126.com qfhuang@capitalgenomics.com mkarin@ucsd.edu kang.zhang@gmail.com.
authors.forename: Quan-fei
authors.initials: QF
authors.lastname: Huang
authors.affiliation: Department of Pharmacology, University of California, San Diego, La Jolla, CA 92328; yinaiwa@vip.126.com qfhuang@capitalgenomics.com mkarin@ucsd.edu kang.zhang@gmail.com.
authors.forename: Michael
authors.initials: M
authors.lastname: Karin
authors.affiliation: Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328; Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital and Sichuan University, Chengdu 610041, China; Veterans Administration Healthcare System, San Diego, CA 92161 yinaiwa@vip.126.com qfhuang@capitalgenomics.com mkarin@ucsd.edu kang.zhang@gmail.com.
authors.forename: Kang
authors.initials: K
authors.lastname: Zhang
mesh_terms: D002474:Cell-Free System; D002869:Chromosome Aberrations / Q000196:embryology*; D002872:Chromosome Deletion; D058674:Chromosome Duplication; D055028:Comparative Genomic Hybridization; D004247:DNA / Q000097:blood*; D005260:Female; D005333:Fetus / Q000002:abnormalities*; D006801:Humans; D008970:Molecular Weight; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*; D012666:Semiconductors; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA
keywords: NIPT; cell-free DNA; maternal plasma DNA; noninvasive prenatal testing; semiconductor sequencing