Biological Intrinsic Classification of Breast Cancer by Immunohistochemistry and qPCR Using Blocks from the NCIC MA.12 Trial
K Ung, SK Chia, M Cheang, CM Perou, PS Bernard, L Sheperd, TO Nielsen. University of British Columiba, Vancouver, BC, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; University of North Carolina at Chapel Hill, Chapel Hill, NC; University of Utah Health Science Center, Salt Lake City, UT; NCIC Clinical Trials Group, Kingston, ON, Canada
Background: Gene expression profiling classifies breast cancer into biological intrinsic subtypes luminal A, luminal B, HER2-enriched (HER2-E), basal-like and normal-like. qPCR is the gold standard for gene expression profiling from tissue blocks but requires additional sample handling and complex data analyses. Immunohistochemistry (IHC) is a readily available and cost effective morphologic alternative, although lacks accuracy for some subtypes. We used tissue materials from clinical trial NCIC MA.12 with primary breast cancer and subtyped them using IHC and qPCR.
Design: Tissue microarrays were constructed using formalin-fixed paraffin-embedded cores from 472 patients in the the MA.12 trial. IHC for ER, PR, HER2, CK5/6, EGFR and Ki67 was used to define intrinsic subytpes using established criteria. Total RNA from 399 patients was sufficient for gene profiling with a 50 gene predictor (PAM50) by qPCR. In 354 cases, intrinsic subtyping into luminal A, luminal B, HER2-E and basal-like was obtained using both methods.
Results: Of the 472 cases in the tissue microarray, using IHC, 39% (n=190) were luminal A, 30% (n=143) luminal B, 7% (n=33) HER2-E, 17% (n=80) basal-like and 6% (n=26) unclassifiable. Of 399 cases with PAM50 qPCR expression profiles, 35% (n=141) were luminal A, 21% (n=85) luminal B, 18% (n=72) HER2-E, 21% (n=85) basal-like and 4% (n=16) normal like.
|biologic intrinsic subtype by qPCR||definition by IHC||sensitivity||specificity|
|luminal A||(ER or PR)+, HER2-, Ki67 low||79%||85%|
|luminal B||(ER or PR)+, HER2+/-, Ki67 high||67%||76%|
|HER2-E||ER-, PR-, HER2+||35%||99%|
|basal-like||ER-, PR-, HER2-, (CK5/6 or EGFR)+||93%||99%|