Correcting the LRR for aneuploidy improves CN determination. Data from three chromosome arms from a primitive neuroectodermal tumor assayed on the SNP array and analyzed by FISH. The top two rows of plots show BAF and LRR. The third row shows the LRR after correction for aneuploidy. Considering the corrected LRR values in conjunction with the BAF leads to the CN determinations plotted in the fourth row, which reflect the number of copies seen in the FISH images at the bottom. (A) The chromosome initially appears to be a CN loss (homozygous and negative LRR), but is present in two copies by FISH; this is consistent with the corrected LRR near 0. (B,C) Similarly, the corrected LRR reflects the correct CN of three and four copies, respectively.
