Published in Lab Invest on February 12, 2007
Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One (2009) 2.21
Retracted Simultaneous recovery of DNA and RNA from formalin-fixed paraffin-embedded tissue and application in epidemiologic studies. Cancer Epidemiol Biomarkers Prev (2010) 2.16
RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol (2008) 2.13
3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One (2010) 1.91
Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue. J Histochem Cytochem (2008) 1.81
Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer (2008) 1.74
Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay. Biotechniques (2008) 1.72
Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients. Clin Cancer Res (2011) 1.59
Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue. PLoS One (2011) 1.56
Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas. BMC Med Genomics (2009) 1.47
CD200 is induced by ERK and is a potential therapeutic target in melanoma. J Clin Invest (2007) 1.45
RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies. BMC Mol Biol (2007) 1.45
Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays. J Mol Diagn (2010) 1.44
Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens. J Mol Diagn (2010) 1.27
Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. Br J Cancer (2012) 1.19
Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples. Br J Cancer (2011) 1.18
Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS One (2012) 1.16
Whole genome RNA expression profiling of endoscopic biliary brushings provides data suitable for biomarker discovery in cholangiocarcinoma. J Hepatol (2011) 1.00
A second-generation microRNA-based assay for diagnosing tumor tissue origin. Oncologist (2012) 0.97
Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. PLoS One (2013) 0.97
Terminal Continuation (TC) RNA amplification enables expression profiling using minute RNA input obtained from mouse brain. Int J Mol Sci (2008) 0.96
Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation. Breast Cancer Res Treat (2010) 0.95
Maximizing RNA yield from archival renal tumors and optimizing gene expression analysis. J Biomol Screen (2009) 0.94
Genome-wide gene expression profiling of formalin-fixed paraffin-embedded breast cancer core biopsies using microarrays. J Histochem Cytochem (2011) 0.93
Expectations, validity, and reality in gene expression profiling. J Clin Epidemiol (2010) 0.93
Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens. BMC Cancer (2011) 0.92
Vascular endothelial growth factor C mRNA expression is a prognostic factor in epithelial ovarian cancer as detected by kinetic RT-PCR in formalin-fixed paraffin-embedded tissue. Virchows Arch (2009) 0.92
Gene expression profiling in patients with carcinoma of unknown primary site: from translational research to standard of care. Virchows Arch (2014) 0.91
Effect of immunohistochemistry on molecular analysis of tissue samples: implications for microdissection technologies. J Histochem Cytochem (2011) 0.89
Metastasis in an orthotopic murine model of melanoma is independent of RAS/RAF mutation. Melanoma Res (2010) 0.87
Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT). Nucleic Acids Res (2007) 0.86
Prognostic stromal gene signatures in breast cancer. Breast Cancer Res (2015) 0.84
Development of a microarray platform for FFPET profiling: application to the classification of human tumors. J Transl Med (2009) 0.84
Tubulin α-6 chain is a stably expressed reference gene in archival samples of normal oral tissue and oral squamous cell carcinoma. Exp Ther Med (2010) 0.81
A methodology for utilization of predictive genomic signatures in FFPE samples. BMC Med Genomics (2011) 0.80
A gene expression profile test to resolve head & neck squamous versus lung squamous cancers. Diagn Pathol (2013) 0.80
Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing. Oncotarget (2016) 0.79
Reliable gene expression measurements from fine needle aspirates of pancreatic tumors: effect of amplicon length and quality assessment. J Mol Diagn (2010) 0.79
A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay. Int J Mol Sci (2016) 0.79
A gene expression profile test for the differential diagnosis of ovarian versus endometrial cancers. Oncotarget (2012) 0.79
Analysis of microRNA from archived formalin-fixed paraffin-embedded specimens of amyotrophic lateral sclerosis. Acta Neuropathol Commun (2014) 0.78
A multiplex endpoint RT-PCR assay for quality assessment of RNA extracted from formalin-fixed paraffin-embedded tissues. BMC Biotechnol (2010) 0.78
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. Nucleic Acids Res (2009) 0.78
A reliable method for the selection of exploitable melanoma archival paraffin embedded tissues for transcript biomarker profiling. PLoS One (2012) 0.78
Ultrasound-accelerated formalin fixation improves the preservation of nucleic acids extraction in histological sections. Int J Legal Med (2009) 0.78
Molecular characterisation of breast cancer patients at high and low recurrence risk. Virchows Arch (2008) 0.76
Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq. Front Oncol (2014) 0.76
A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts. Oncotarget (2016) 0.75
A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples. PLoS One (2017) 0.75
Molecular fixative enables expression microarray analysis of microdissected clinical cervical specimens. Exp Mol Pathol (2014) 0.75
Evaluation of BrightGen HR RT-qDx assay to detect nuclear receptors mRNA overexpression in FFPE breast cancer tissue samples for selection of tamoxifen therapy. Int J Clin Exp Pathol (2014) 0.75
[Genome-wide expression profiling as a clinical tool: are we there yet?]. Pathologe (2009) 0.75
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A (2003) 34.68
Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA (2006) 24.01
Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol (2009) 22.22
Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature (2010) 19.68
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res (2004) 16.51
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12
Cardiovascular events associated with rofecoxib in a colorectal adenoma chemoprevention trial. N Engl J Med (2005) 15.46
Concordance among gene-expression-based predictors for breast cancer. N Engl J Med (2006) 13.50
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A (2002) 12.68
The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics (2006) 12.45
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res (2007) 11.56
Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst (2009) 10.91
Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res (2010) 10.90
Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol (2007) 10.49
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res (2010) 9.80
Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res (2005) 9.70
A custom microarray platform for analysis of microRNA gene expression. Nat Methods (2004) 9.44
Stem-cell ageing modified by the cyclin-dependent kinase inhibitor p16INK4a. Nature (2006) 9.20
A randomized trial of aspirin to prevent colorectal adenomas. N Engl J Med (2003) 9.18
p16INK4a induces an age-dependent decline in islet regenerative potential. Nature (2006) 9.09
The regulation of INK4/ARF in cancer and aging. Cell (2006) 8.75
Ink4a/Arf expression is a biomarker of aging. J Clin Invest (2004) 8.30
Increasing p16INK4a expression decreases forebrain progenitors and neurogenesis during ageing. Nature (2006) 8.06
Residual breast cancers after conventional therapy display mesenchymal as well as tumor-initiating features. Proc Natl Acad Sci U S A (2009) 7.95
Folic acid for the prevention of colorectal adenomas: a randomized clinical trial. JAMA (2007) 7.93
LKB1 modulates lung cancer differentiation and metastasis. Nature (2007) 7.80
Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A (2010) 7.70
Intestinal inflammation targets cancer-inducing activity of the microbiota. Science (2012) 7.54
Basal-like breast cancer defined by five biomarkers has superior prognostic value than triple-negative phenotype. Clin Cancer Res (2008) 7.39
Burden of gastrointestinal disease in the United States: 2012 update. Gastroenterology (2012) 7.15
Epidemiology of basal-like breast cancer. Breast Cancer Res Treat (2007) 7.08
Understanding cancer treatment and outcomes: the Cancer Care Outcomes Research and Surveillance Consortium. J Clin Oncol (2004) 7.02
Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol (2006) 6.86
Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods (2005) 6.23
Loss of the Lkb1 tumour suppressor provokes intestinal polyposis but resistance to transformation. Nature (2002) 6.10
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics. Cancer Res (2009) 5.68
Deconstructing the molecular portraits of breast cancer. Mol Oncol (2010) 5.37
The impact of human EGFR kinase domain mutations on lung tumorigenesis and in vivo sensitivity to EGFR-targeted therapies. Cancer Cell (2006) 5.34
Adjustment of systematic microarray data biases. Bioinformatics (2004) 5.22
Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol (2002) 5.20
Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA (2012) 5.16
Epidermal growth factor receptor and Ink4a/Arf: convergent mechanisms governing terminal differentiation and transformation along the neural stem cell to astrocyte axis. Cancer Cell (2002) 5.11
Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers. J Clin Oncol (2006) 4.84
Breast cancer subtypes and response to docetaxel in node-positive breast cancer: use of an immunohistochemical definition in the BCIRG 001 trial. J Clin Oncol (2009) 4.66
A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res (2010) 4.61
Colorectal cancer in patients under close colonoscopic surveillance. Gastroenterology (2005) 4.31
Prognostic significance of progesterone receptor-positive tumor cells within immunohistochemically defined luminal A breast cancer. J Clin Oncol (2012) 4.14
Mutation of GATA3 in human breast tumors. Oncogene (2004) 3.92
Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell (2004) 3.91
Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet (2010) 3.89
Common markers of proliferation. Nat Rev Cancer (2006) 3.85
Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts. Cell Rep (2013) 3.85
Ductal carcinoma in situ and the emergence of diversity during breast cancer evolution. Clin Cancer Res (2008) 3.83
The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas. Breast Cancer Res (2008) 3.80
Direct health care costs of Crohn's disease and ulcerative colitis in US children and adults. Gastroenterology (2008) 3.79
Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer. Cell (2012) 3.77
Esophageal dilation in eosinophilic esophagitis: safety and predictors of clinical response and complications. Gastrointest Endosc (2010) 3.74
Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest (2012) 3.64
Vitamin D, calcium supplementation, and colorectal adenomas: results of a randomized trial. J Natl Cancer Inst (2003) 3.44
Clinical practice. Screening for colorectal cancer. N Engl J Med (2002) 3.43
Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell (2010) 3.40
A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer. Nat Genet (2011) 3.37
Expression of autotaxin and lysophosphatidic acid receptors increases mammary tumorigenesis, invasion, and metastases. Cancer Cell (2009) 3.36
EGFR associated expression profiles vary with breast tumor subtype. BMC Genomics (2007) 3.35
A randomized trial of rofecoxib for the chemoprevention of colorectal adenomas. Gastroenterology (2006) 3.35
Constipation and a low-fiber diet are not associated with diverticulosis. Clin Gastroenterol Hepatol (2013) 3.31
Molecular portraits and the family tree of cancer. Nat Genet (2002) 3.28
Triple-negative breast cancer: risk factors to potential targets. Clin Cancer Res (2008) 3.25
A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response. Nature (2012) 3.24
Evaluating the comparability of gene expression in blood and brain. Am J Med Genet B Neuropsychiatr Genet (2006) 3.19
Aspirin for the chemoprevention of colorectal adenomas: meta-analysis of the randomized trials. J Natl Cancer Inst (2009) 3.15
Survival differences between patients with scalp or neck melanoma and those with melanoma of other sites in the Surveillance, Epidemiology, and End Results (SEER) program. Arch Dermatol (2008) 3.11
Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res (2009) 3.09
Monitoring tumorigenesis and senescence in vivo with a p16(INK4a)-luciferase model. Cell (2013) 3.04