Microarray-Based Cell-Free DNA Analysis Improves Noninvasive Prenatal Testing

Objective: To develop a microarray-based method for noninvasive prenatal testing (NIPT) and compare it with next-generation sequencing. Methods: Maternal plasma from 878 pregnant women, including 187 trisomy cases (18 trisomy 13, 37 trisomy 18, 132 trisomy 21), was evaluated for trisomy risk. Targeted chromosomes were analyzed using Digital Analysis of Selected Regions (DANSR™) assays. DANSR products were subsequently divided between two DNA quantification methods: microarrays and next-generation sequencing. For both microarray and sequencing methodologies, the Fetal-Fraction Optimized Risk of Trisomy Evaluation (FORTE™) algorithm was used to determine trisomy risk, assay variability across samples, and compute fetal fraction variability within samples. Results: NIPT using microarrays provided faster and more accurate cell-free DNA (cfDNA) measurements than sequencing. The assay variability, a measure of variance of chromosomal cfDNA counts, was lower for microarrays than for sequencing, 0.051 versus 0.099 (p < 0.0001). Analysis time using microarrays was faster, 7.5 versus 56 h for sequencing. Additionally, fetal fraction precision was improved 1.6-fold by assaying more polymorphic sites with microarrays (p < 0.0001). Microarrays correctly classified all trisomy and nontrisomy cases. Conclusions: NIPT using microarrays delivers more accurate cfDNA analysis than next-generation sequencing and can be performed in less time.

[1]  Hanmin Lee,et al.  Non-Invasive Chromosomal Evaluation (NICE) Study: results of a multicenter prospective cohort study for detection of fetal trisomy 21 and trisomy 18. , 2012, American journal of obstetrics and gynecology.

[2]  D. Ledbetter,et al.  Chromosomal microarray versus karyotyping for prenatal diagnosis. , 2012, The New England journal of medicine.

[3]  Arnold Oliphant,et al.  Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. , 2012, American journal of obstetrics and gynecology.

[4]  J. Canick,et al.  High-Throughput Massively Parallel Sequencing for Fetal Aneuploidy Detection from Maternal Plasma , 2013, PLoS ONE.

[5]  A. Oliphant,et al.  Gestational age and maternal weight effects on fetal cell‐free DNA in maternal plasma , 2013, Prenatal diagnosis.

[6]  L. Gianaroli,et al.  Multiple meiotic errors caused by predivision of chromatids in women of advanced maternal age undergoing in vitro fertilisation , 2012, European Journal of Human Genetics.

[7]  L. Rienzi,et al.  Sequential comprehensive chromosome analysis on polar bodies, blastomeres and trophoblast: insights into female meiotic errors and chromosomal segregation in the preimplantation window of embryo development. , 2013, Human reproduction.

[8]  Wade A. Barrett,et al.  Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy , 2012, Prenatal diagnosis.

[9]  K. Nicolaides,et al.  Analysis of Cell-Free DNA in Maternal Blood in Screening for Aneuploidies: Meta-Analysis , 2014, Fetal Diagnosis and Therapy.

[10]  K. Nicolaides,et al.  Noninvasive prenatal testing for fetal trisomies in a routinely screened first-trimester population. , 2012, American journal of obstetrics and gynecology.

[11]  K. Nicolaides,et al.  Cell-Free DNA Analysis for Trisomy Risk Assessment in First-Trimester Twin Pregnancies , 2013, Fetal Diagnosis and Therapy.

[12]  K. Nicolaides,et al.  Fetal Fraction in Maternal Plasma Cell-Free DNA at 11–13 Weeks’ Gestation: Effect of Maternal and Fetal Factors , 2012, Fetal Diagnosis and Therapy.

[13]  R. Stokowski,et al.  Influence of Temperature during Transportation on Cell-Free DNA Analysis , 2012, Fetal Diagnosis and Therapy.

[14]  J. Grifo,et al.  Validation of array comparative genome hybridization for diagnosis of translocations in preimplantation human embryos. , 2012, Reproductive biomedicine online.

[15]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.