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We also found that the depth of sequencing strongly influenced the accuracy of aneuploidy detection.We isolated 150 plasma samples with euploid fetuses to inspect the relationship between the tags number (unique reads) and the standard deviation of relative reads coverage.In this study, we developed an advanced GC-correlation methodology for an MPS-based, noninvasive fetal trisomy (NIFTY) test.Our technique has higher sensitivity and specificity than all previously reported z-score approaches for the detection of autosomal and sex chromosomal aneuploidy.We constructed a comprehensive bioinformatics pipeline to scan for fetal chromosomal aneuploidies.The pipeline comprised short reads alignment, GC content correction, fetal DNA concentration estimation, t-test of a binary hypothesis, and fetal gender classification (Figure The flowchart of the whole bioinformatics pipeline.We applied the NIFTY test to 903 pregnancies and compared the diagnostic results with those of full karyotyping.

The Noninvasive Fetal Trisomy (NIFTY) test, combines an optimized Student’s t-test with a locally weighted polynomial regression and binary hypotheses.Turner’s syndrome (45, X), Klinefelter’s syndrome (47, XXY) and XYY syndrome are common sex chromosomal aneuploidies that are associated with reproductive loss, infertility and language development delays, among others [], and they highlighted its potential clinical utility as a biomarker because it can be detected from as early as four gestational weeks.Cell-free fetal DNA clears rapidly from the maternal circulation after delivery [].We enrolled 903 pregnant women with ages ranging from 20 to 45 years.

The gestational ages varied from 10 to 34 weeks, covering the first to the third trimesters.

Among the chromosomes with average GC content close to 41% the reads coverage was not correlated with GC content (Additional file : Figure S2).



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