Simultaneous detection of fetal chromosome aneuploidy and monogenic diseases by a novel noninvasive prenatal testing method: Targeted And Genome-wide simultaneous sequencing (TAGs-seq)
Lin Yang1, Jia Zhao2, Haiping Zhang3, Zhu Zhu4, Yicong Wang5, Fang Chen6, Yanping Lu7, Ya Gao8
1BGI-Shenzhen, Shenzhen, China, ShenZhen,Guangdong province, China
2BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
3BGI-Shenzhen, Shenzhen, NA, China
4BGI-Shenzhen, Shenzhen, China
5BGI China, Shenzhen, China
6BGI Research, Shenzhen, China
7Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing 100853, China, Beijing, China
8BGI, Shenzhen, China
Objectives
Next generation sequencing (NGS)-based cell-free DNA (cfDNA) analysis has been widely adopted for non-invasive prenatal testing (NIPT) for fetal chromosomal aneuploidy and monogenic diseases. However, the detection of chromosome aneuploidy and monogenic diseases requires different experiment procedures due to distinct sequencing strategies, and thus cannot be carried out at the same time. We intended to develop a new sequencing method embracing both advantages of targeted and genome-wide sequencing, so that it can simultaneously screen for fetal chromosome aneuploidy and dominant monogenic diseases in a noninvasive manner.
Methods
The novel method, called Targeted And Genome-wide simultaneous sequencing (TAGs-seq), integrates a step of multiplex PCR into the genome-wide NIPS library construction of cfDNA. As a result, whole genome and target region can be simultaneously amplified in one tube (Figure 1). After NGS, the genome-wide region displays a low sequencing depth (0.1-0.5Χ) and the target regions an ultra-high depth (1000-10000Χ), which were sufficient for measuring chromosome aneuploidy and detecting singe base mutations, respectively.
Results
We validated in-blind the TAGs-seq NIPT in 66 plasma samples with previously confirmed outcomes. The NGS data of all samples for TAGs-seq with a 0.2-0.8Χ genome coverage and a >1000Χ targeted coverage , the percentage of on-target reads are 0.22-2.63%. The TAGs-seq NIPT identified 7 cases of common aneuploidy (T21, n=3; T18, n=2; T13, n=2), 6 cases of de novo single base mutations (FGFR3 c.1138G>A, n=5; c.1118A>G, n=1), and 53 cases of normal controls. All results were concordant to the invasive diagnostic results.
Conclusions
We developed a novel TAGs-seq NIPT, which exploited low-coverage whole-genome sequencing data to analyze chromosome aneuploidy, and high-depth targeted sequencing data to analyze single base mutations. Compared to conventional NIPT method, TAGs-seq NIPT provides a convenient, low-cost and expandable solution to detect fetal chromosome aneuploidy and de novo mutations in a single experiment.
