Format

Send to

Choose Destination
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14670-5. doi: 10.1073/pnas.1518151112. Epub 2015 Nov 9.

Noninvasive detection of fetal subchromosomal abnormalities by semiconductor sequencing of maternal plasma DNA.

Author information

1
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.
2
CapitalBio Genomics Co., Ltd., Dongguan 523808, China;
3
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;
4
Institute for Genomic Medicine and Shiley Eye Institute, University of California, San Diego, La Jolla, CA 92328;
5
Kangrui Biological Pharmaceutical Technology Co., Ltd., Guangzhou 510005, China;
6
Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital and Sichuan University, Chengdu 610041, China;
7
CapitalBio Genomics Co., Ltd., Dongguan 523808, China; yinaiwa@vip.126.com qfhuang@capitalgenomics.com mkarin@ucsd.edu kang.zhang@gmail.com.
8
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.
9
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.

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.

KEYWORDS:

NIPT; cell-free DNA; maternal plasma DNA; noninvasive prenatal testing; semiconductor sequencing

PMID:
26554006
PMCID:
PMC4664371
DOI:
10.1073/pnas.1518151112
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center