Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing

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.

Figure 1. UR-X% and UR-Y% of 62 amniotic fluid samples.

Figure 2. z-scores of 62 AF samples for chromosome 21,18 and X determined by MPS.

Broken lines indicate the z score cut-off value of ±3 for trisomy 21 and trisomy 18. All 11 trisomy cases have a z-score value greater than 3 and the 2 cases of Tuner syndrome have a z-score value less than minus 3.

Figure 3. The normalized UR% value per chromosome between different samples.

11 trisomy samples have a normalized UR% value of 1.5 and 2 cases of 45 XO have a normalized UR% value of 0.5.