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
Objective
Abstract
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 205225_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
www.kmplot.com.
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.
Background
Results
What is the correlation between author-reported
(IHC-based) and microarray-based molecular
subtype determination?
GEO search for:
studies publishing molecular subtypes
raw Affymetrix HGU133A and HGU133plus2 arrays
at least 30 patients
ER
HER2
Luminal A
High
Low
MKI67
N.R.
Low
Luminal B
High
High
Low
High
High
1. Highest sensitivity and specificity: Basal tumors
 GEO datasets: GSE1456, GSE21653, GSE25066,
GSE20711, GSE31519 and GSE17907
2. Highest discordance: Luminal B
N.R.
RFS
OS
LN+
EndocrineTh.
ChemoTh.
Basal
3.31
6.00
51%
8.8% (375)
87% (377)
Luminal A
4.61
6.67
51%
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)
HER2+
Low
High
Homepages
N.R.
Breast cancer molecular subtypes:
 different pathological characteristics
 different outcomes
 different treatment
Can be identified by:
 IHC
 RT-PCR
 microarray
Supported by the OTKA PD 83154 grant.
Annual hazard of recurrence and overall
survival according to subtypes (Park et al,
Breast, 2012):
3. Use the classification to validate survivalassociated genes in each subtype separately at
www.kmplot.com/breast:
2. Relation of published subtype distributions:
2. Definition of molecular subtypes using the
StGallen guidelines:
Basal
Low
Low
1. Microarray database
 Clinical characteristics (n=983):
Materials & Methods
1.



Summary
www.kmplot.com/breast
3. Microarray probe sets used for the classification:
Gene
ER
HER2
Probe
205225_at
216836_s_at
Cutoff
500
4800
MKI67
212021_s_at
470
4. Statistics:
 sensitivity [=TP/(TP+FN)]
 specificity [=TN/(TN+FP)]
assess the effect of 22,277 genes on survival
in 2,977 breast cancer patients
author: as published in GEO by the authors of the datasets
computed: distribution for all arrays in the KM-plotter database
www.kmplot.com/ovar
assess the effect of 22,277 genes on survival
in 1,464 ovarian cancer patients
3. Statistics (array vs. IHC, n=983)
Basal
Luminal A
Luminal B
HER2
gyorffy@kmplot.com
n
380
306
169
128
Sensitivity
0,70
0,55
0,63
0,38
Specificity
0,96
0,87
0,67
0,99
www.recurrenceonline.com
compute the ER & HER2 status and the
recurrence score for free using microarrays
gyer1-6.sote.hu/gyorffy
personal homepage
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