Supplemental methods
We used the prcomp function from the R base package stats to plot samples mapped to
the first two principal components to assess clustering of BAC and mapped
oligonucleotide CGH data. We used KCsmart to compare 1000 times 50 paired BAC and
mapped oligonucleotide CGH profiles with 50 non-paired profiles at 200 permutations
with an FDR of 5%, kernel size of 1mb and sample density of 50kb. We averaged the
size of the genome called significantly different between both groups and plotted these.
Supplementary Figure legends
Supp 1a) . Bootstrapped hierarchical clustering of log ratios CGH profiles. Only ratios
present in the BRCA1 classifier are used. Red and green column colors represent BAC
and oligo-mapped oligonucleotide CGH profiles. Heatmap colors range from 0 (never
clustered in same cluster, blue) to 1 (always clustered in same cluster, yellow). The
blowout shows sample names to demonstrate clustering of biological pairs. Clustering
segmented data shows less clustering by platform, indicated by blocks of red and green in
the columns.
Supp 1b) . Bootstrapped hierarchical clustering of segmented log ratios CGH profiles.
Only ratios present in the BRCA2 classifier are used. Red and green column colors
represent BAC and oligo-mapped oligonucleotide CGH profiles. Heatmap colors range
from 0 (never clustered in same cluster, blue) to 1 (always clustered in same cluster,
yellow). The blowout shows sample names to demonstrate clustering of biological pairs.
Clustering segmented data shows less clustering by platform, indicated by blocks of red
and green in the columns.
Supp 1c) Principal component analysis of log ratios and BAC (red) and mapped (green)
profiles.
Supp 1d) Principal component analysis of segmented log ratios and BAC (red) and
mapped (green) profiles.
Supp 1e) Density plot of KCsmart analysis of 50 paired BAC-mapped and non-paired log
ratio samples sampled 1000 times. Size of genome called aberrantly was summed for
each sample.
Supp 1f) Density plot of KCsmart analysis of 50 paired BAC-mapped and non-paired
segmented log ratio samples sampled 1000 times. Size of genome called aberrantly was
summed for each sample.
Supp 2) A) BRCA1 probability scores of a classifier optimized on oligonucleotide data
plotted against the scores of the original BAC classifier. B) BRCA1 probability scores of
a classifier optimized on segmented oligonucleotide data plotted against the scores of the
original BAC classifier. C) BRCA1 probability scores of a classifier optimized on oligomapped data plotted against scores of the original BAC classifier. D) BRCA1 probability
scores of the oligo-mapped data classified by the BAC classifier plotted against the
original BAC classifier.
Supp 3) Quality scores of samples that were discordantly assigned to the non-BRCA or
BRCA class per classifier.
Supp 4) Quality scores assigned by the svm quality classifier plotted against BRCA1
probability scores. + are samples with BRCA1 methylation, x are samples with a
pathogenic BRCA1 mutation, . are samples without BRCA1 methylation or a known
pathogenic BRCA1 mutation.
Supp 5) Top panel: Averaged BAC profiles (red) of segmented log ratios employed in the
BRCA1 classifier for cases that switch from non-BRCA1 like to BRCA1 like. Averaged
mapped profiles (red) and difference of non-BRCA1 like and BRCA1 like centroids
(purple). Blue spots represent log ratios for which a switch to closest centroid occurs and
whether the BAC log ratio is closest or the mapped log ratio is closest to the BRCA1
centroid. Bottom panel: Averaged BAC profiles (red) of segmented log ratios employed
in the BRCA1 classifier for cases that switch from BRCA1 like to non-BRCA1 like.
Averaged mapped profiles (red) and difference of non-BRCA1 like and BRCA1 like
centroids (purple). Blue spots represent log ratios for which a switch to closest centroid
occurs and whether the BAC log ratio is closest or the mapped log ratio is closest to the
BRCA1 centroid.
Supp 6) Top panel: Averaged BAC profiles (red) of segmented log ratios employed in the
BRCA1 classifier for cases that switch from non-BRCA2 like to BRCA2 like. Averaged
mapped profiles (red) and difference of non-BRCA2 like and BRCA2 like centroids
(purple). Blue spots represent log ratios for which a switch to closest centroid occurs and
whether the BAC log ratio is closest or the mapped log ratio is closest to the BRCA2
centroid. Bottom panel: Averaged BAC profiles (red) of segmented log ratios employed
in the BRCA2 classifier for cases that switch from BRCA2 like to non-BRCA2 like.
Averaged mapped profiles (red) and difference of non-BRCA2 like and BRCA2 like
centroids (purple). Blue spots represent log ratios for which a switch to closest centroid
occurs and whether the BAC log ratio is closest or the mapped log ratio is closest to the
BRCA1 centroid.
Supp 7) For each patient the difference between the Euclidean distance of the BAC data
to BRCA centroid and the non-BRCA centroid. Discordant cases are marked in red.