PRESENTATION OF GENOMIC ANALYSIS RESULTS WITH CHIPDX

The ChipDX homepage lists the

available diagnostic tests,
account management features
and upload/download tools

Selecting a diagnostic module takes you to

page describing the development and
function of the test, a page to submit a
previously uploaded GeneChip profile for
analysis, or a result viewing section.
BEGIN (AND MONITOR) ANALYSIS BY SIMPLY UPLOADING AN AFFYMETRIX .CEL FILE TO YOUR ACCOUNT

One-click GeneChip CEL

file upload.

After the user selects the appropriate GeneChip CEL file (output from Affymetrix GeneChip
Scanner), preprocessing and quality control begins automatically.

The user can observe the progress of the analysis and is notified via email when complete. At
this point the processed data can be submitted to one or more of the other ChipDX analysis
modules.
COLOR-CODED QUALITY MODULE RESULTS – RAPID INTEPRETATION OF DATA QUALITY ASSESSMENTS

Results from the ChipDX Quality

Module are presented prior to
diagnostic analysis and then
again along-side the results.

Color-coding is used to enable rapid interpretation of each quality

metric. Graphs of the entire genomic profile are also available in a sub-
section of the quality report.
CONFIRMATION OF TISSUE TYPE, MALIGNANT STATUS – ENSURE PROFILE MATCHES CLINICAL RECORDS

The Tumor Origin Module

detects the tumor type
represented by the GeneChip.
This information can be used to
assist in diagnosis metastatic or
poorly differentiated tumors, or
as an additional quality
measurement; i.e. to ensure the
genomic profile matches the
known clinical profile of the
patient.

For each tissue-type present in the Tumor

Origin database, a separate 100-gene
algorithm trained to predict the malignant
status of a specimen (tumor or normal) is
included. This can ensure that the genomic
profile represents the tumor of interest,
not the surrounding normal tissue.
DISPLAY OF RAW AND NORMALIZED MRNA VALUES FOR COMMON IMMUNOHISTOCHEMISTRY MARKERS

Inspect a panel of gene

expression
measurements
corresponding to a panel
of IHC markers to
validate the genomic
profile matches the
pathology workup.

Individual IHC probe

measurements are shown in
normalized-intensity format
and also scaled to the upper
value of each gene, as
calculated in the complete
ChipDX Tumor Origin
database.
GENECHIP DASHBOARD – VIEW ALL UPLOADS, TESTS PERFORMED AND QC DATA OVER TIME IN ONE PLACE

Observe trends in Quality Module

metric data over time, compare to
global ChipDX ranges over the
same time period

View the result of each quality metric

(pass/warning/fail) in table format and
reconcile uploads vs analysis results
PROGNOSTIC SIGNATURE OUTPUT – PROGNOSTIC SCORE, CONFIDENCE INTERNVAL, RESULT CONTEXT

Results from ChipDX

prognostic modules (currently
available for breast, lung and
colon cancer) include a clear
display of the prognostic
index, 95% confidence
interval and display of the
index in relation to the
training series of patients
used to develop the test.

Depending on the clinical stage of the

patient in question, the user may customize
the Kaplan Meier display accordingly.
DYNAMIC GENE EXPRESSION ‘HEATMAPS’ : COMPARISON OF GENOMIC PROFILE TO TOTAL DATABASE

Understand the results of the

multi-gene assay by viewing
the color-coded expression
values in relation to
equivalent data from the
patients used to develop and
validate the test.

In-line help and information windows assist

in interpreting these features, highlighting
the most important aspects of the analysis.
ANNOTATED TABLE OF INDIVIDUAL GENE EXPRESSION MEASUREMENTS FOR EACH SIGNATURE

View or export the gene-by-

gene expression
measurements used to
compute the diagnostic result.
Sort by (relative) high/low
expression level and link to
gene function databases.

ABILITY TO DISPLAY MULTIPLE GENOMIC SIGNATURES OR TWO-GENE RATIOS

Additional genomic signatures, such as

two-gene ratios corresponding to
probability of specific gene mutations,
can be represented in easily-understood
formats