Prenatal Detection of Aneuploidy and Imbalanced Chromosomal Arrangements by Massively Parallel Sequencing

Shan Dan,Jingrong Lin,Tze Kin Lau,Fang Chen,Weiyuan Zhang,Zhaoling Xuan,Kwong Wai Choy,Xiuqing Zhang,Fuman Jiang,Hui Jiang,Xuchao Li,Shengpei Chen,Tak Yeung Leung,Wei Wang,Yue Su,Reiner Albert Veitia

doi:10.1371/journal.pone.0027835

Abstract

Fetal chromosomal abnormalities are the most common reasons for invasive prenatal testing. Currently, G-band karyotyping and several molecular genetic methods have been established for diagnosis of chromosomal abnormalities. Although these testing methods are highly reliable, the major limitation remains restricted resolutions or can only achieve limited coverage on the human genome at one time. The massively parallel sequencing (MPS) technologies which can reach single base pair resolution allows detection of genome-wide intragenic deletions and duplication challenging karyotyping and microarrays as the tool for prenatal diagnosis. Here we reported a novel and robust MPS-based method to detect aneuploidy and imbalanced chromosomal arrangements in amniotic fluid (AF) samples. We sequenced 62 AF samples on Illumina GAIIx platform and with averagely 0.01× whole genome sequencing data we detected 13 samples with numerical chromosomal abnormalities by z-test. With up to 2× whole genome sequencing data we were able to detect microdeletion/microduplication (ranged from 1.4 Mb to 37.3 Mb of 5 samples from chorionic villus sampling (CVS) using SeqSeq algorithm. Our work demonstrated MPS is a robust and accurate approach to detect aneuploidy and imbalanced chromosomal arrangements in prenatal samples.

Highlights

Chromosomal abnormalities occur in 1 of 160 live births [1].The risk of giving birth to a child with chromosomal abnormalities, especially Down syndrome (OMIM# 190685), increases throughout a woman’s reproductive years [2,3]
In this study we have developed a new method based on massively parallel sequencing (MPS) platform to detect fetal chromosomal abnormalities, which is independent of particular genetic markers and cell culture in medical practice
Parallel sequencing has been reported only to apply in noninvasive prenatal diagnosis of trisomy 21, 18 and 13 based on cell-free fetal DNA, due to it is limited amount of fragmented fetal DNA [11]

Summary

Introduction

Chromosomal abnormalities occur in 1 of 160 live births [1].The risk of giving birth to a child with chromosomal abnormalities, especially Down syndrome (OMIM# 190685), increases throughout a woman’s reproductive years [2,3]. G-band karyotyping and several molecular genetic methods including multiplex ligationdependent probe amplification (MLPA), fluorescence in situ hybridization (FISH), quantitative fluorescent PCR (QF-PCR) and microarray-based comparative genomic hybridization (arrayCGH) have been well established for prenatal diagnosis of chromosomal abnormalities in clinical labs [7,8]. These testing methods have been proved to be highly reliable, the major limitation remains restricted resolution or can only achieve limited coverage on the human genome at one time [9,10]

Methods

Results

Conclusion