KF09-LEU-1207R: Kohlmann et al.
Figure legends for Supplementary Figures
Figure S1
Reproducibility between centers and operator proficiency. In
total, 80 distinct gene expression profiles were included. The data was
generated by 10 laboratory operators using 4 different sample types from
commercially available total RNA sources (BRAIN, UHR, MCF-7, and
HEPG2). The data was partly generated in a recently published study called
DACH, i.e. contributed by the centers Basel, Geneva, and Linz.3 (a) In an
unsupervised hierarchical clustering using the top-10,000 variant genes clear
signatures can be observed. Importantly, the top dendrogram accurately
groups the 4 total RNA sources. The similarity was computed by Euclidean
distance, and then Ward’s method was used to cluster the gene expression
profiles based on these measures. The normalized expression value for each
gene is coded by color (standard deviation from mean). Red cells indicate
high expression and green cells indicate low expression. (b) In the
unsupervised principal component analysis based on the top-30,000 probe
sets in the dataset all samples were clearly clustered according to the sample
type. In the upper plot colors are representing the 6 laboratories. In the lower
plot colors are identifying the distinct total RNA sources. Each of the 80 gene
expression datasets is represented by a single sphere.
Figure S2
Comparison to Alcalay et al., Blood 2005. The panel on the right
is a representation of a 20-gene signature to identify cases with NPM1
mutations (NPM c+) as described in Figure 1C in the original publication by
Alcalay et al. in 2005.7 The panel on the left highlights the confirmation of 16
(80%) of 20 probes as common in both datasets, i.e. demonstrating a
differential gene expression between NPM1-mutated and wild type cases.
Gene symbols with asterisks were identified by multiple probe sets.
Figure S3 Comparison to Verhaak et al., Blood 2005. The panel on the right
is a representation of the 18-gene signature, represented by 22 probe sets to
identify cases with NPM1 mutations (NPM1 mutant) as described in Figure 2
in the original publication by Verhaak et al. in 2005. 8 The panel on the left
highlights in yellow the confirmation of 17 (94%) of 18 candidate genes as
common in both datasets. Note: Approved HGNC gene symbols are given for
SMC4 (previously SMC4L1) and DMXL2 (previously RC3).
Figure S4
Gene expression signature of CEBPA mutations in AML. In
the hierarchical clustering heatmap 234 cases are displayed, visualizing a
multicenter signature for CEBPA mutated AML. The top-500 differentially
expressed genes were calculated from a pairwise comparison according to
CEBPA mutation status. The similarity was computed by Euclidean distance,
and then Ward’s method was used to cluster the gene expression profiles
based on these measures. The normalized expression value for each gene is
coded by color (standard deviation from mean). Red cells indicate high
expression and green cells indicate low expression.
Figure S5
HOX genes expression signature of CEBPA-mutated AML. In
the hierarchical clustering heatmap 234 cases are displayed, visualizing a
signature for selected HOXA and HOXB cluster candidates. The normalized
expression value for each gene is coded by color (standard deviation from
mean). Red cells indicate high expression and green cells indicate low
expression.
Figure S6
AML-NK with a silenced CEBPA phenotype. The panel on the
left is a representation of a gene expression signature to identify cases with a
silenced CEBPA phenotype as described in Figure 5 in the original publication
by Wouters et al. in 2007.13 The panel on the right highlights an identical
signature of one case in our cohort with confirmed CEBPA wild type status.
Figure S7
Gene expression signature of FLT3-ITD mutations in AML. In
the hierarchical clustering heatmap 251 cases are displayed, visualizing a
multicenter signature for FLT3-ITD mutated AML. The top-500 differentially
expressed genes were calculated from a pairwise comparison according to
FLT3-ITD mutation status. The normalized expression value for each gene is
coded by color (standard deviation from mean). Red cells indicate high
expression and green cells indicate low expression.
Figure S8
Comparison to Bullinger et al., Blood 2008. The panel on the left
is a representation of a 20-gene signature to identify cases with FLT3-ITD
mutations as described in Figure 1A in the original publication by Bullinger et
al. in 2008.14 The panel on the right highlights the confirmation of 12 (60%) of
20 genes as common in both datasets. Additional genes marked with
asterisks were significantly differentially expressed, but not contained in the
top-500 probe sets list (DPPA4, HOXB2, PDE4B).