In additional cases, copy number assessment afforded by WES revealed critical diagnostic information (tier 1); for example, in an otherwise poorly described CNS embryonal tumor, focal amplification of 19q13.42 was detected, which is entity-defining for “embryonal tumor with multilayered rosettes, C19MC-altered.” Additional critical CNAs included detection of SMARCB1 loss in a case of chordoma, leading to a diagnosis of poorly differentiated chordoma in a case with poor characterization of INI1 expression by immunohistochemistry (IHC), and CDKN2A/B loss in the case of PXA mentioned above. The gene discussed is CDKN2A; the disease is chordoma.