Non-invasive aneuploidy detection using free fetal DNA and RNA in maternal plasma: recent progress and future possibilities

BACKGROUND: Cell-free fetal DNA (cff DNA) and RNA can be detected in maternal plasma and used for non-invasive prenatal diagnostics. Recent technical advances have led to a drastic change in the clinical applicability and potential uses of free fetal DNA and RNA. This review summarizes the latest clinical developments in non-invasive prenatal diagnosis in the context of the latest technical developments. METHODS: We searched PubMed with the search terms 'prenatal', 'non-invasive', 'fetalDNA', 'mRNA' and cross-referenced them with 'diagnostics', 'microRNA', 'aneuploidy', 'trisomy' and 'placenta'. We also searched the reference list of the articles identified by this search strategy. RESULTS: Genome-wide methods have been, or can be, successfully applied on total DNA(DNA-seq), methylated DNA immunoprecipitation (with tiling array), microRNA (Megaplex) and total RNA (RNA-seq). Chromosome-or gene-specific assays have been successively applied on placenta RNA (allele ratio) or DNA multiplex ligation-dependent probe amplification (MLPA). These methods are reviewed for their merits and pitfalls with consideration of the placental biology. For the purpose of clarity, the technical and clinical characteristics are limited to non-invasive prenatal detection of chromosomal aneuploidies, with emphasis on trisomy 21. CONCLUSIONS: The technical advances for non-invasive aneuploidy tests based on cff DNA and placental mRNA in maternal plasma have been enormous. Multimarker assays including genome-wide approaches with the option of qualitative information on variation (polymorphism or mutation) besides quantitative information are the preferred methods of choice. The time for population-based, double blind, large-scale clinical cohort trials has come.