Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing

Sheng‐Pei Chen ,Xuebin Wang,Huijuan Ge,Wei Wang,Yingrui Li,Songgang Li,Fuman Jiang,Xiaotian Yao,Jian Wang,Lijian Zhao,Lei Zhang,Xiaoyu Pan,Xiuqing Zhang,Jun Wang,Hui Jiang,Hancheng Zheng,Fang Chen,Huanming Yang,Xuchao Li,Chunlei Zhang,Peipei Li

doi:10.1186/gm422

Abstract

BackgroundThe applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. However, most previous research based on maternal plasma sequencing has been restricted to fetal aneuploidies. To detect specific parentally inherited mutations, invasive approaches to obtain fetal DNA are the current standard in the clinic because of the experimental complexity and resource consumption of previously reported non-invasive approaches.MethodsHere, we present a simple and effective non-invasive method for accurate fetal genome recovery-assisted with parental haplotypes. The parental haplotype were firstly inferred using a combination strategy of trio and unrelated individuals. Assisted with the parental haplotype, we then employed a hidden Markov model to non-invasively recover the fetal genome through maternal plasma sequencing.ResultsUsing a sequence depth of approximately 44X against a an approximate 5.69% cff-DNA concentration, we non-invasively inferred fetal genotype and haplotype under different situations of parental heterozygosity. Our data show that 98.57%, 95.37%, and 98.45% of paternal autosome alleles, maternal autosome alleles, and maternal chromosome X in the fetal haplotypes, respectively, were recovered accurately. Additionally, we obtained efficient coverage or strong linkage of 96.65% of reported Mendelian-disorder genes and 98.90% of complex disease-associated markers.ConclusionsOur method provides a useful strategy for non-invasive whole fetal genome recovery.

Highlights

The applications of massively parallel sequencing technology to fetal cell-free DNA have brought new insight to non-invasive prenatal diagnosis
Accurate fetal genome recovery through maternal plasma To perform haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing (Figure 1), we recruited a Chinese woman with pregnancy of 13 weeks of gestation and her family, including three generations, as well as fetal blood after delivery
In this study, we introduced an accurate method for fetal genome recovery in one step using maternal plasma sequencing

Summary

Introduction

The applications of massively parallel sequencing technology to fetal cell-free DNA (cff-DNA) have brought new insight to non-invasive prenatal diagnosis. It should be possible to recover the fetal genome non-invasively through maternal plasma sequencing to enable the comprehensive prenatal diagnosis of Mendelian diseases and lessen the need for invasive procedures [14,15]. Recent studies from Kitzman et al [15] and Fan et al [16] introduced accurate non-invasive fetal genotype inference methods assisted by maternal haplotype, but their methods showed uncertain performance in detecting paternal transition in low cff-DNA concentrations. The concentration of cff-DNA is approximately 3% to 6% of the total cell-free DNA [17], which may lead to uneven recovery of the paternal allele in the whole genome. The fetal haplotype information is especially useful in detecting some haplotype-related diseases, such as systemic lupus erythematosus [18], as well as personal genomic analyses in the future [19,20]

Methods

Results

Discussion

Conclusion