1. Enabling biomarker validation in breast cancer molecular subtypes: sensitivity and specificity of array-based subtype classification in 983 patients Balázs Győrffy and András Lánczky Research Laboratory for Pediatrics and Nephrology, Hungarian Academy of Sciences - Semmelweis University 1st Dept. of Pediatrics, Budapest, Hungary
Abstract
Objective
Results
Summary
Background: The diverse breast cancer molecular subtypes have different clinicopathological characteristics and outcomes. Here, we assessed the correlation between microarray-defined and author-reported molecular subtypes using publicly available breast cancer datasets.
Methods: GEO was searched for datasets where the authors determined molecular subtypes. The molecular subtype was re-calculated for each patient using the StGallen guidelines by assessing the microarray-based expression of ER, HER2 and MKI67 (Basal: ER negative + HER2 negative, Luminal A: ER positive + HER2 negative + low MKI67, HER2 enriched: HER2 positive + ER negative, Luminal B: ER positive + HER2 positive and ER positive + HER2 negative + high MKI67). The thresholds used were 500 for ER (probe set _at), 4800 for HER2 (216836_s_at) and 470 for MKI67 (212021_s_at). Sensitivity and specificity were calculated for each subtype separately.
Results: Molecular subtype was published in all together six datasets (GSE1456, GSE21653, GSE25066, GSE20711, GSE31519 and GSE17907) for 983 patients. In these, 380, 306, 169 and 128 were Basal, Luminal A, Luminal B and HER2 enriched, respectively. The microarray-based molecular subtype determination resulted in a sensitivity of 0.70, 0.55, 0.63 and 0.38 and a specificity of 0.96, 0.87, 0.67 and 0.99 for Basal, Luminal A, Luminal B and HER2 enriched subtypes, respectively. Finally, the option to filter for molecular subtypes was implemented into our online biomarker validation platform at
Discussion: Microarray data provided highest sensitivity and specificity to independent subtype classification for Basal tumors, while the luminal B subtype displayed the highest discordance. Our registration-free online service enables the validation of gene expression based biomarkers in each subtype separately.
What is the correlation between author-reported (IHC-based) and microarray-based molecular subtype determination?
Microarray database
GEO datasets: GSE1456, GSE21653, GSE25066, GSE20711, GSE31519 and GSE17907
Clinical characteristics (n=983):
Relation of published subtype distributions:
author: as published in GEO by the authors of the datasets
computed: distribution for all arrays in the KM-plotter database
Statistics (array vs. IHC, n=983)
Highest sensitivity and specificity: Basal tumors
Highest discordance: Luminal B
Use the classification to validate survival- associated genes in each subtype separately at
Materials & Methods
RFS OS
LN+
EndocrineTh.
ChemoTh.
Basal
3.31
6.00
51%
8.8% (375)
87% (377)
Luminal A
4.61
6.67
95% (291)
73% (293)
Luminal B
4.35
6.73
58%
33% (147)
74% (147)
HER2
3.87
6.49
64%
35% (100)
95% (104)
GEO search for:
studies publishing molecular subtypes
raw Affymetrix HGU133A and HGU133plus2 arrays
at least 30 patients
Definition of molecular subtypes using the StGallen guidelines:
Microarray probe sets used for the classification:
Statistics:
sensitivity [=TP/(TP+FN)]
specificity [=TN/(TN+FP)]
Basal
Luminal A
Luminal B
HER2+ ER
Low
High
HER2
MKI67
N.R.
Background
Homepages
Breast cancer molecular subtypes:
different pathological characteristics
different outcomes
different treatment
Can be identified by:
IHC
RT-PCR
microarray
assess the effect of 22,277 genes on survival in 2,977 breast cancer patients
assess the effect of 22,277 genes on survival in 1,464 ovarian cancer patients
compute the ER & HER2 status and the recurrence score for free using microarrays
gyer1-6.sote.hu/gyorffy
personal homepage
Gene
Probe
Cutoff ER
205225_at
500
HER2
216836_s_at
4800
MKI67
212021_s_at
470
Annual hazard of recurrence and overall survival according to subtypes (Park et al, Breast, 2012): n
Sensitivity
Specificity
Basal
380
0,70
0,96
Luminal A
306
0,55
0,87
Luminal B
169
0,63
0,67
HER2
128
0,38
0,99
Supported by the OTKA PD grant.
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