Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma

Abstract

Chromosomal aneuploidy is the major reason why couples opt for prenatal diagnosis. Current methods for definitive diagnosis rely on invasive procedures, such as chorionic villus sampling and amniocentesis, and are associated with a risk of fetal miscarriage. Fetal DNA has been found in maternal plasma but exists as a minor fraction among a high background of maternal DNA. Hence, quantitative perturbations caused by an aneuploid chromosome in the fetal genome to the overall representation of sequences from that chromosome in maternal plasma would be small. Even with highly precise single molecule counting methods such as digital PCR, a large number of DNA molecules and hence maternal plasma volume would need to be analyzed to achieve the necessary analytical precision. Here we reasoned that instead of using approaches that target specific gene loci, the use of a locus-independent method would greatly increase the number of target molecules from the aneuploid chromosome that could be analyzed within the same fixed volume of plasma. Hence, we used massively parallel genomic sequencing to quantify maternal plasma DNA sequences for the noninvasive prenatal detection of fetal trisomy 21. Twenty-eight first and second trimester maternal plasma samples were tested. All 14 trisomy 21 fetuses and 14 euploid fetuses were correctly identified. Massively parallel plasma DNA sequencing represents a new approach that is potentially applicable to all pregnancies for the noninvasive prenatal diagnosis of fetal chromosomal aneuploidies.Down syndrome ͉ Solexa sequencing ͉ trisomy 21

Preferences for prenatal tests for Down syndrome: an international comparison of the views of pregnant women and health professionals

“…2,3 NIPT allows screening for these conditions with much greater specificity than traditional DS screening (DSS) 4 and thereby significantly reduces the need for invasive testing (chorionic villus sampling or amniocentesis) with the associated small miscarriage risk. 5 Following the first evidence in 2008 that NIPT for DS was feasible, 6,7 this test has moved swiftly into clinical practice with testing available in the private sector since 2011. Several USA and Hong Kong/China based companies now offer NIPT and have made their commercial tests widely available.…”

Review of massively parallel DNA sequencing technologies

“…• Multi-gene diagnostic panels (Morgan et al 2010) • Achieving a molecular diagnosis for rare genetic diseases (Lupski et al 2010;Ng et al 2010a, b;Worthey et al 2011;Vissers et al 2010) • Tissue matching and HLA-typing (Bentley et al 2009;Gabriel et al 2009;Lind et al 2010) • Non-invasive prenatal diagnosis (Chiu et al 2008;Fan et al 2008;Lo et al 2010) • Quantifying the burden of disease from solid tumours (Leary et al 2010;McBride et al 2010) and • Cancer genome profiling leading to stratified treatment regimens Diamandis et al 2010;Stratton et al 2009) RNA sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) sequencing can also be used to study gene expression and for detection of somatic mutations, gene fusions, and other non-mutational events, an understanding of which can have an impact on management of diseases such as cancer (Cowin et al 2010;Robison 2010). However, numerous barriers to clinical translation still exist, including: validation of the technology; standardisation of the analysis pipeline; integration of information from the numerous databases of genomic variation; building a robust evidence base to allow clinical interpretation of novel variants; developing a service delivery infrastructure that can capitalise upon the high-throughput advantages of new sequencing technologies; providing an appropriately skilled health care workforce to deal with genomic medicine; and addressing the numerous ethical, legal and social implications of sequencing, storing and accessing whole genomes.…”

The high incidence of STR D21S1446 homozygosity in Han and She populations living in South Eastern China

“…Multiple approaches are available to determine if a fetus has abnormal chromosomes including karyotyping [12][13][14], genomic sequencing [15][16][17]; micro-array analysis [18] and PCR based methods [8]. The non-microscope techniques have the advantage of being rapid and cost effective.…”