Transcriptomics,Genomics

Dataset Information

45

Clinical validation of a customized multiple signature microarray for breast cancer


ABSTRACT: PURPOSE: Current histopathologic systems for classifying breast tumors require evaluation of multiple variables and are often associated with significant interobserver variability. Recent studies suggest that gene expression profiles may represent a promising alternative for clinical cancer classification. Here, we investigated the use of a customized microarray as a potential tool for clinical practice. EXPERIMENTAL DESIGN: We fabricated custom 188-gene microarrays containing expression signatures for three breast cancer molecular subtypes [luminal/estrogen receptor (ER) positive, human epidermal growth factor receptor 2 (HER2), and "basaloid"], the Nottingham prognostic index (NPI-ES), and low histologic grade (TuM1). The reliability of these multiple-signature arrays (MSA) was tested in a prospective cohort of 165 patients with primary breast cancer. RESULTS: The MSA-ER signature exhibited a high concordance of 90% with ER immunohistochemistry reported on diagnosis (P < 0.001). This remained unchanged at 89% (P < 0.001) when the immunohistochemistry was repeated using current laboratory standards. Expression of the HER2 signature showed a good correlation of 76% with HER2 fluorescence in situ hybridization (FISH; ratio > or =2.2; P < 0.001), which further improved to 89% when the ratio cutoff was raised to > or =5. A proportion of low-level FISH-amplified samples (ratio, 2.2-5) behaved comparably to FISH-negative samples by HER2 signature expression, HER2 quantitative reverse transcription-PCR, and HER2 immunohistochemistry. Luminal/ER+ tumors with high NPI-ES expression were associated with high NPI scores (P = 0.001), and luminal/ER+ TuM1-expressing tumors were significantly correlated with low histologic grade (P = 0.002) and improved survival outcome in an interim analysis (hazard ratio, 0.2; P = 0.019). CONCLUSION: The consistency of the MSA platform in an independent patient population suggests that custom microarrays could potentially function as an adjunct to standard immunohistochemistry and FISH in clinical practice. Overall design: In the operating theater, morphologically visible tumor were removed by surgery and examined by a surgical pathologist to confirm the presence of cancer cells by cryosections. The tissue samples were divided into discrete aliquots, flash frozen and subsequently stored in liquid nitrogen

INSTRUMENT(S): Customized multiple signature arrays for breast cancer

SUBMITTER: Kun Yu  

PROVIDER: GSE7422 | GEO | 2008-07-23

SECONDARY ACCESSION(S): PRJNA97855

REPOSITORIES: GEO

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Publications

Clinical validation of a customized multiple signature microarray for breast cancer.

Tan Benita K T BK   Tan Lay Keng LK   Yu Kun K   Tan Puay Hoon PH   Lee Ming M   Sii Lang Hiong LH   Wong Chow Yin CY   Ho Gay Hui GH   Yeo Allen W Y AW   Chow Pierce K H PK   Koong Heng Nung HN   Yong Wei Sean WS   Lim Dennis T H DT   Ooi London L P J LL   Soo Khee Chee KC   Tan Patrick P  

Clinical cancer research : an official journal of the American Association for Cancer Research 20080101 2


PURPOSE: Current histopathologic systems for classifying breast tumors require evaluation of multiple variables and are often associated with significant interobserver variability. Recent studies suggest that gene expression profiles may represent a promising alternative for clinical cancer classification. Here, we investigated the use of a customized microarray as a potential tool for clinical practice. EXPERIMENTAL DESIGN: We fabricated custom 188-gene microarrays containing expression signatu  ...[more]

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