The molecular mechanisms underlying chordoma pathogenesis are unknown. We 
therefore sought to identify novel mutations to better understand chordoma 
biology and to potentially identify therapeutic targets. Given the relatively 
high costs of whole genome sequencing, we performed a focused genetic analysis 
using matrix-assisted laser desorption/ionization-time of flight mass 
spectrometer (Sequenom iPLEX genotyping). We tested 865 hotspot mutations in 111 
oncogenes and selected tumor suppressor genes (OncoMap v. 3.0) of 45 human 
chordoma tumor samples. Of the analyzed samples, seven were identified with at 
least one mutation. Six of these were from fresh frozen samples, and one was 
from a paraffin embedded sample. These observations were validated using an 
independent platform using homogeneous mass extend MALDI-TOF (Sequenom hME 
Genotyping). These genetic alterations include: ALK (A877S), CTNNB1 (T41A), NRAS 
(Q61R), PIK3CA (E545K), PTEN (R130), CDKN2A (R58*), and SMARCB1 (R40*). This 
study reports on the largest comprehensive mutational analysis of chordomas 
performed to date. To focus on mutations that have the greatest chance of 
clinical relevance, we tested only oncogenes and tumor suppressor genes that 
have been previously implicated in the tumorigenesis of more common 
malignancies. We identified rare genetic changes that may have functional 
significance to the underlying biology and potential therapeutics for chordomas. 
Mutations in CDKN2A and PTEN occurred in areas of chromosomal copy loss. When 
this data is paired with the studies showing 18 of 21 chordoma samples 
displaying copy loss at the locus for CDKN2A, 17 of 21 chordoma samples 
displaying copy loss at PTEN, and 3 of 4 chordoma samples displaying deletion at 
the SMARCB1 locus, we can infer that a loss of heterozygosity at these three 
loci may play a significant role in chordoma pathogenesis.