Table 4 Calculating the EASILUNG score with two examples from the TCGA.

Substitution classes	%CA^∆	%GT^◊	%CT	%GA	%AC	%TG	%AG^*	%TC^‡
EASILUNG signature =	+175	+62	−9*(%CT)	−6*(%GA)	−17*(%AC)	−17*(%TG)	−74	−73
Example 1^(a)
Relative frequency	27	19	8	12	0	0	3	5
EASILUNG score =	+175	+62	−72	−72	+0	+0	+0	+0	=93
Example 2^(b)
Relative frequency	2	2	27	37	4	1	6	5
EASILUNG score =	+0	+0	−243	−222	−68	−17	−74	+0	=−624

%CA = relative frequency of C > A substitutions (%); %GT = relative frequency of G > T substitutions (%); %CT = relative frequency of C > T substitutions (%); %GA = relative frequency of G > A substitutions (%); %AC = relative frequency of A > C substitutions (%); %TG = relative frequency of T > G substitutions (%); %AG = relative frequency of A > G substitutions (%); %TC = relative frequency of T > C substitutions (%).
^∆For samples with %CA > 12.
^◊For samples with %GT > 13.
*For samples with %AG > 5.
^‡For samples with %TC > 5.
^(a)Example 1/Tumor sample barcode = TCGA-75–7027–01A-11D-1945–08 (lung cancer) with 27% C > A substitutions (+175 since > 12), 19% G > T substitutions(+62 since > 13), 8% C > T substitutions (−9*8), 12% G > A substitutions (−6*12), 0% A > C substitutions (−17*0), 0% T > G substitutions (−17*0), 3% A > G substitutions (0 since ≤5), 5% T > C substitutions (0 since ≤5).
^(b)Example 2/Tumor sample barcode = TCGA-75–7027–01A-11D-1945–08 (non-lung cancer) with 2% C > A substitutions (+0 since ≤12), 2% G > T substitutions(+0 since ≤ 13), 27% C > T substitutions (−9*27), 37% G > A substitutions (−6*37), 4% A > C substitutions (−17*4), 1% T > G substitutions (−17*1), 6% A > G substitutions (−74 since>5), 5% T > C substitutions (0 since ≤5).

Quick links

Search