Evaluation of MetriGenix custom 4D arrays applied for detection of breast cancer subtypes.
BACKGROUND
Previously, a total of five breast cancer subtypes have been identified based on variation in gene expression patterns. These expression profiles were also shown to be associated with different prognostic value. In this study tumour samples from 27 breast cancer patients, previously subtyped by expression analysis using DNA microarrays, and four controls from normal breast tissue were included. A new MetriGenix 4D array proposed for diagnostic use was evaluated.


METHODS
We applied MetriGenix custom 4D arrays for the detection of previously defined molecular subtypes of breast cancer. MetriGenix 4D arrays have special features including probe immobilization in microchannels with chemiluminescence detection that enable shorter hybridization time.


RESULTS
The MetriGenix 4D array platform was evaluated with respect to both the accuracy in classifying the samples as well as the performance of the system itself. In a cross validation analysis using "Nearest Shrunken Centroid classifier" and the PAM software, 77% of the samples were classified correctly according to earlier classification results.


CONCLUSIONS
The system shows potential for fast screening; however, improvements are needed.
Department of Genetics, Faculty division, The Norwegian Radium Hospital, University of Oslo, N-0310 Oslo, Norway. aslauam@ulrik.uio.no
Aslaug Aamodt
AA
Muggerud
Hilde
H
Johnsen
Debra A
DA
Barnes
Adam
A
Steel
Per Eystein
PE
Lønning
Bjørn
B
Naume
Therese
T
Sørlie
Anne-Lise
AL
Børresen-Dale
D001943:Breast Neoplasms / Q000145:classification* / Q000175:diagnosis; D002277:Carcinoma / Q000145:classification* / Q000175:diagnosis; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010865:Pilot Projects; D025341:Principal Component Analysis