Fig. 2

Array (OncoScan) analysis. a Results for the uncultured amniotic fluid cells. b Results for cultured amniotic fluid cells. The left parts of the figures depict a genome-wide overview of copy number (upper panel. X-axis: chromosomes ordered from 1 to 22, X and Y. Y-axis: copy number state as log2 ratio) and B allele frequency (lower panel. X-axis: chromosome orders from 1 to 22, X and Y. Y-axis: BAF). The right part shows a box plot of the BAF observed in the uncultured (a) and cultured (b) amniotic fluid cells for the autosomes and for the X chromosome. Only markers for which the parents were informative homozygous (mother BB, father AA or vice versa) were analyzed. The dataset is normalized to a BAF of 1 in the mother and 0 in the father for all analyzed markers. The expected BAF in the analyzed fetal sample is 0.5 for all markers (heterozygous calls). Instead, we observed a skewing of the BAF for the autosomes towards 1 in the uncultured amniotic cells indicating presence of more maternal than paternal alleles. For the X chromosome in the cultured amniotic cells, BAF is shifted towards 0 indicating the extra X chromosome is of paternal origin