The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analyses.
OBJECTIVE
Our aims in this pilot study were to determine whether fine needle aspirates (FNAs) provide a sufficient quantity of mRNA for cDNA microarray analysis, produce a set of quality control criteria to accept individual arrays, and determine whether gene expression profiles obtained from FNAs were representative of the source tumor.


METHODS
Twenty-seven women with breast cancer for treatment with primary surgery had a FNA before and at the time of surgery, and a portion of excised tumor was taken for array analysis. Control experiments were performed using two Ewing's sarcoma xenograft models. mRNA was extracted from the samples and hybridized with the reference (MCF7 cell line) on cDNA microarrays. Statistical methods were applied to identify acceptability criteria for the arrays.


RESULTS
Statistical analyses demonstrated that an adequate array could be identified by calculating the SD of the log of fluorescence intensities from the arrays. Using this criterion, only 4 of the 27 patients (15%) had FNA samples suitable for array analysis. Gene expression profiles from the FNAs closely resembled that of the corresponding source tumors and were clearly distinguished from FNAs derived from the xenografts.


CONCLUSIONS
SD is a useful quality index for the clinical application of cDNA microarrays. This "proof of principle" study demonstrates that FNAs from primary breast cancers can be used for microarray analysis, although without amplification, it is feasible in only a small proportion of patients. For this to be clinically useful, validated amplification techniques for FNA samples are probably required.
Assersohn
Laura
L
Royal Marsden Hospital, Surrey SM2 5PT, United Kingdom.
Gangi
Lisa
L
Zhao
Yingdong
Y
Dowsett
Mitch
M
Simon
Richard
R
Powles
Trevor J
TJ
Liu
Edison T
ET
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000818:Animals; D001707:Biopsy, Needle; D001943:Breast Neoplasms / Q000235:genetics*; D002285:Carcinoma, Intraductal, Noninfiltrating / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis*; D005240:Feasibility Studies; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D051379:Mice; D008819:Mice, Nude; D016513:Mice, SCID; D008875:Middle Aged; D009361:Neoplasm Invasiveness; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010865:Pilot Projects; D012333:RNA, Messenger / Q000032:analysis; D015203:Reproducibility of Results; D014407:Tumor Cells, Cultured / Q000378:metabolism
D004273:DNA, Neoplasm; D012333:RNA, Messenger