Table 1

OQL data types and functionality.

Data typeKeywordCodeDescriptionExample
Copy numberCNAAMPShow amplified cases.CCNE1: AMP; CCNE1: CNA > GAIN; CCNE1: GAIN AMP
HOMDELShow homozygously deleted cases.
GAINShow single copy gained cases.
HETLOSSShow heterozygously deleted cases.
MutationsMUTMUTShow mutated cases.CCNE1: MUT
MUT = xShow cases with specific mutations or mutation types.BRAF: MUT = V600E; TP53: MUT = MISSENSE; TP53: MUT = NONSENSE; TP53: MUT = NONSTART; TP53: MUT = NONSTOP; TP53: MUT = FRAMESHIFT; TP53: MUT = INFRAME; TP53: MUT = SPLICE; TP53: MUT = TRUNC
mRNA/miRNA expression z scoresEXPEXP < xShow all underexpressed cases, less than x standard-deviations from the mean.TP53: EXP > 1.5
EXP > xShow all overexpressed cases, greater than x standard-deviations from the mean.
Protein-level z scoresPROTPROT < xShow all protein-level underexpressed cases, less than x standard from the mean.ERBB2: PROT < –2
PROT > xShow all protein-level overexpressed cases, greater than x standard from the mean.