Journal Article
. 2003 Dec;164(1).
doi: 10.1016/S0002-9440(10)63093-3.

Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay

Maureen Cronin 1 Mylan Pho  Debjani Dutta  James C Stephans  Steven Shak  Michael C Kiefer  Jose M Esteban  Joffre B Baker  
Affiliations
  • PMID: 14695316
  •     35 References
  •     179 citations

Abstract

Throughout the last decade many laboratories have shown that mRNA levels in formalin-fixed and paraffin-embedded (FPE) tissue specimens can be quantified by reverse transcriptase-polymerase chain reaction (RT-PCR) techniques despite the extensive RNA fragmentation that occurs in tissues so preserved. We have developed RT-PCR methods that are sensitive, precise, and that have multianalyte capability for potential wide use in clinical research and diagnostic assays. Here it is shown that the extent of fragmentation of extracted FPE tissue RNA significantly increases with archive storage time. Probe and primer sets for RT-PCR assays based on amplicons that are both short and homogeneous in length enable effective reference gene-based data normalization for cross comparison of specimens that differ substantially in age. A 48-gene assay used to compare gene expression profiles from the same breast cancer tissue that had been either frozen or FPE showed very similar profiles after reference gene-based normalization. A 92-gene assay, using RNA extracted from three 10- micro m FPE sections of archival breast cancer specimens (dating from 1985 to 2001) yielded analyzable data for these genes in all 62 tested specimens. The results were substantially concordant when estrogen receptor, progesterone receptor, and HER2 receptor status determined by RT-PCR was compared with immunohistochemistry assays for these receptors. Furthermore, the results highlight the advantages of RT-PCR over immunohistochemistry with respect to quantitation and dynamic range. These findings support the development of RT-PCR analysis of FPE tissue RNA as a platform for multianalyte clinical diagnostic tests.

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Kim M Clark-Langone, Chithra Sangli, Jayadevi Krishnakumar, Drew Watson.
BMC Cancer, 2010 Dec 24; 10. PMID: 21176237    Free PMC article.
Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens.
Raji Pillai, Rebecca Deeter, +4 authors, W David Henner.
J Mol Diagn, 2011 Jan 14; 13(1). PMID: 21227394    Free PMC article.
MicroRNA isolation from formalin-fixed, paraffin-embedded tissues.
Aihua Liu, Xiaowei Xu.
Methods Mol Biol, 2011 Mar 04; 724. PMID: 21370018    Free PMC article.
Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections.
Ran Xie, Joon-Yong Chung, +5 authors, Stephen M Hewitt.
J Histochem Cytochem, 2011 Mar 18; 59(4). PMID: 21411807    Free PMC article.
Immunohistochemical and molecular analyses of HER2 status in breast cancers are highly concordant and complementary approaches.
J Lehmann-Che, F Amira-Bouhidel, +17 authors, P Bertheau.
Br J Cancer, 2011 May 05; 104(11). PMID: 21540864    Free PMC article.
mRNA transcript quantification in archival samples using multiplexed, color-coded probes.
Patricia P Reis, Levi Waldron, +7 authors, Suzanne Kamel-Reid.
BMC Biotechnol, 2011 May 10; 11. PMID: 21549012    Free PMC article.
Highly Cited.
Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens.
Al Muktafi Sadi, Dong-Yu Wang, +4 authors, Wey L Leong.
BMC Cancer, 2011 Jun 18; 11. PMID: 21679412    Free PMC article.
Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients.
Yang Xie, Guanghua Xiao, +11 authors, Ignacio I Wistuba.
Clin Cancer Res, 2011 Jul 12; 17(17). PMID: 21742808    Free PMC article.
Update on the diagnosis of cancer of unknown primary (CUP) origin.
Aurelio Ariza, Carmen Balañá, +4 authors, Emilio Alba.
Clin Transl Oncol, 2011 Jul 22; 13(7). PMID: 21775269
Relationship between quantitative GRB7 RNA expression and recurrence after adjuvant anthracycline chemotherapy in triple-negative breast cancer.
Joseph A Sparano, Lori J Goldstein, +13 authors, Robert Gray.
Clin Cancer Res, 2011 Sep 22; 17(22). PMID: 21933890    Free PMC article.
Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform.
M Abramovitz, B G Barwick, +8 authors, B Leyland-Jones.
Br J Cancer, 2011 Nov 10; 105(10). PMID: 22067903    Free PMC article.
Micro-RNAs as diagnostic or prognostic markers in human epithelial malignancies.
Angela Hui, Christine How, Emma Ito, Fei-Fei Liu.
BMC Cancer, 2011 Dec 02; 11. PMID: 22128797    Free PMC article.
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Whole genome RNA expression profiling of endoscopic biliary brushings provides data suitable for biomarker discovery in cholangiocarcinoma.
Michael H Chapman, Robert Tidswell, +7 authors, Stephen P Pereira.
J Hepatol, 2011 Dec 17; 56(4). PMID: 22173169    Free PMC article.
Early developments in gene-expression profiling of breast tumors: potential for increasing black-white patient disparities in breast cancer outcomes?
Donna H Odierna, Aimee Afable-Munsuz, +5 authors, Ninez A Ponce.
Per Med, 2011 Dec 23; 8(6). PMID: 22190978    Free PMC article.
Determination of SGK1 mRNA in non-small cell lung cancer samples underlines high expression in squamous cell carcinomas.
Claudia Abbruzzese, Stefano Mattarocci, +11 authors, Marco G Paggi.
J Exp Clin Cancer Res, 2012 Jan 14; 31. PMID: 22240294    Free PMC article.
Gene expression profiling: changing face of breast cancer classification and management.
Robert Wesolowski, Bhuvaneswari Ramaswamy.
Gene Expr, 2012 Jan 25; 15(3). PMID: 22268293    Free PMC article.
Review.
A reliable method for the selection of exploitable melanoma archival paraffin embedded tissues for transcript biomarker profiling.
Celeste Lebbe, Mickael Guedj, +4 authors, Samia Mourah.
PLoS One, 2012 Jan 25; 7(1). PMID: 22272228    Free PMC article.
The epigenetic silencing of the estrogen receptor (ER) by hypermethylation of the ESR1 promoter is seen predominantly in triple-negative breast cancers in Indian women.
Jyothi S Prabhu, Kanu Wahi, +5 authors, T S Sridhar.
Tumour Biol, 2012 Mar 01; 33(2). PMID: 22362381
Impact of preanalytic factors on the design and application of integral biomarkers for directing patient therapy.
Stephen M Hewitt, Sunil S Badve, Lawrence D True.
Clin Cancer Res, 2012 Mar 17; 18(6). PMID: 22422404    Free PMC article.
Transcriptional profiling of formalin fixed paraffin embedded tissue: pitfalls and recommendations for identifying biologically relevant changes.
Matilda Rentoft, Philip John Coates, Göran Laurell, Karin Nylander.
PLoS One, 2012 Apr 25; 7(4). PMID: 22530001    Free PMC article.
Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation.
J S Hall, J Taylor, +5 authors, C M L West.
Br J Cancer, 2012 Jul 19; 107(4). PMID: 22805332    Free PMC article.
Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue.
Dominick Sinicropi, Kunbin Qu, +14 authors, Joffre Baker.
PLoS One, 2012 Jul 19; 7(7). PMID: 22808097    Free PMC article.
Ribonucleic acid extraction from archival formalin fixed paraffin embedded myocardial tissues for gene expression and pathogen detection.
Mirnalini Sharma, Baijayantimala Mishra, +4 authors, Kewal K Talwar.
J Clin Lab Anal, 2012 Jul 20; 26(4). PMID: 22811362    Free PMC article.
Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications.
Katey S S Enfield, Larissa A Pikor, Victor D Martinez, Wan L Lam.
Genet Res Int, 2012 Aug 02; 2012. PMID: 22852089    Free PMC article.
The non-crosslinking fixative RCL2®-CS100 is compatible with both pathology diagnosis and molecular analyses.
Florence Boissière-Michot, Amélie Denouël, +5 authors, Frédéric Bibeau.
Pathol Oncol Res, 2012 Aug 16; 19(1). PMID: 22893391
Gene expression profiling for guiding adjuvant chemotherapy decisions in women with early breast cancer: an evidence-based and economic analysis.
Medical Advisory Secretariat.
Ont Health Technol Assess Ser, 2010 Jan 01; 10(23). PMID: 23074401    Free PMC article.
Circulating tumor cells, disease recurrence and survival in newly diagnosed breast cancer.
Bas Franken, Marco R de Groot, +4 authors, Leon W M M Terstappen.
Breast Cancer Res, 2012 Oct 24; 14(5). PMID: 23088337    Free PMC article.
Personalized medicine in breast cancer: a systematic review.
Sang-Hoon Cho, Jongsu Jeon, Seung Il Kim.
J Breast Cancer, 2012 Oct 24; 15(3). PMID: 23091538    Free PMC article.
Non-invasive proteomics-thinking about personalized breast cancer screening and treatment.
Manuel Debald, Matthias Wolfgarten, +2 authors, Michael Braun.
EPMA J, 2010 Sep 01; 1(3). PMID: 23199085    Free PMC article.
The miR-221/222 cluster, miR-10b and miR-92a are highly upregulated in metastatic minimally invasive follicular thyroid carcinoma.
Tomoo Jikuzono, Masashi Kawamoto, +8 authors, Toshihiro Takizawa.
Int J Oncol, 2013 Apr 09; 42(6). PMID: 23563786    Free PMC article.
Development of a miR-26 companion diagnostic test for adjuvant interferon-alpha therapy in hepatocellular carcinoma.
Junfang Ji, Lei Yu, +12 authors, Xin Wei Wang.
Int J Biol Sci, 2013 Apr 10; 9(3). PMID: 23569435    Free PMC article.
A multigene expression assay to predict local recurrence risk for ductal carcinoma in situ of the breast.
Lawrence J Solin, Robert Gray, +13 authors, Sunil Badve.
J Natl Cancer Inst, 2013 May 04; 105(10). PMID: 23641039    Free PMC article.
Highly Cited.
Semi-nested real-time reverse transcription polymerase chain reaction methods for the successful quantitation of cytokeratin mRNA expression levels for the subtyping of non-small-cell lung carcinoma using paraffin-embedded and microdissected lung biopsy specimens.
Yoko Nakanishi, Tetsuo Shimizu, +10 authors, Norimichi Nemoto.
Acta Histochem Cytochem, 2013 May 31; 46(2). PMID: 23720607    Free PMC article.
Detection of cancer before distant metastasis.
Frank A W Coumans, Sabine Siesling, Leon W M M Terstappen.
BMC Cancer, 2013 Jun 15; 13. PMID: 23763955    Free PMC article.
Evaluation of a high-throughput, microfluidics platform for performing TaqMan™ qPCR using formalin-fixed paraffin-embedded tumors.
Ping Li, Elena Grigorenko, +3 authors, Hyung L Kim.
Bioanalysis, 2013 Jul 05; 5(13). PMID: 23822126    Free PMC article.
Epidermal growth factor receptor mutation subtypes and geographical distribution among Indian non-small cell lung cancer patients.
A Choughule, V Noronha, +6 authors, A Dutt.
Indian J Cancer, 2013 Aug 28; 50(2). PMID: 23979200    Free PMC article.
Reliable PCR quantitation of estrogen, progesterone and ERBB2 receptor mRNA from formalin-fixed, paraffin-embedded tissue is independent of prior macro-dissection.
Trine Tramm, Guido Hennig, +5 authors, Jens Overgaard.
Virchows Arch, 2013 Oct 09; 463(6). PMID: 24100522
Frequency of EGFR mutations in 907 lung adenocarcioma patients of Indian ethnicity.
Anuradha Chougule, Kumar Prabhash, +8 authors, Amit Dutt.
PLoS One, 2013 Oct 15; 8(10). PMID: 24124538    Free PMC article.
High stability of microRNAs in tissue samples of compromised quality.
Lorena Peiró-Chova, María Peña-Chilet, +6 authors, Gloria Ribas.
Virchows Arch, 2013 Nov 08; 463(6). PMID: 24197449
Expression of estrogen-related gene markers in breast cancer tissue predicts aromatase inhibitor responsiveness.
Irene Moy, Zhihong Lin, +3 authors, Serdar E Bulun.
PLoS One, 2013 Nov 14; 8(11). PMID: 24223121    Free PMC article.
MicroRNAs and long non-coding RNAs: prospects in diagnostics and therapy of cancer.
Nina Hauptman, Damjan Glavac.
Radiol Oncol, 2013 Dec 03; 47(4). PMID: 24294175    Free PMC article.
Review.
Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues.
Carine Steiner, Axel Ducret, +6 authors, Paul Cutler.
Proteomics, 2013 Dec 18; 14(4-5). PMID: 24339433    Free PMC article.
Review.
Micro-RNAs as potential new molecular biomarkers in oncology: have they reached relevance for the clinical imaging sciences?
Frank Berger, Maximilian F Reiser.
Theranostics, 2014 Jan 08; 3(12). PMID: 24396505    Free PMC article.
Review.
Accelerated neurodegeneration and neuroinflammation in transgenic mice expressing P301L tau mutant and tau-tubulin kinase 1.
Hirohide Asai, Seiko Ikezu, +3 authors, Tsuneya Ikezu.
Am J Pathol, 2014 Jan 15; 184(3). PMID: 24418258    Free PMC article.
Tissue fixation and the effect of molecular fixatives on downstream staining procedures.
William J Howat, Beverley A Wilson.
Methods, 2014 Feb 25; 70(1). PMID: 24561827    Free PMC article.
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A multiplex two-color real-time PCR method for quality-controlled molecular diagnostic testing of FFPE samples.
Jiyoun Yeo, Erin L Crawford, +6 authors, James C Willey.
PLoS One, 2014 Mar 04; 9(2). PMID: 24586747    Free PMC article.
Fusion transcript discovery in formalin-fixed paraffin-embedded human breast cancer tissues reveals a link to tumor progression.
Yan Ma, Ranjana Ambannavar, +10 authors, Kunbin Qu.
PLoS One, 2014 Apr 15; 9(4). PMID: 24727804    Free PMC article.
Study assessing the quality of quantification of estrogen receptor protein expression by immunohistochemistry and gene expression in breast cancer.
Sas Leen, Van Laere Steven, +7 authors, Lardon Filip.
Patholog Res Int, 2014 Apr 16; 2014. PMID: 24734208    Free PMC article.
Multiplex quantitative measurement of mRNAs from fixed tissue microarray sections.
Michael Armani, Michael Tangrea, +9 authors, Stephen M Hewitt.
Appl Immunohistochem Mol Morphol, 2014 May 09; 22(5). PMID: 24809843    Free PMC article.
Review.
In situ quantitative measurement of HER2mRNA predicts benefit from trastuzumab-containing chemotherapy in a cohort of metastatic breast cancer patients.
Maria Vassilakopoulou, Taiwo Togun, +11 authors, Amanda Psyrri.
PLoS One, 2014 Jun 27; 9(6). PMID: 24968015    Free PMC article.
Molecular analysis of different classes of RNA molecules from formalin-fixed paraffin-embedded autoptic tissues: a pilot study.
Barbara Muciaccia, Carmen Vico, +2 authors, Rossana Cecchi.
Int J Legal Med, 2014 Aug 20; 129(1). PMID: 25135750
Preanalytical variables and performance of diagnostic RNA-based gene expression analysis in breast cancer.
Christopher Poremba, Jennifer Uhlendorff, +10 authors, Carsten Denkert.
Virchows Arch, 2014 Sep 15; 465(4). PMID: 25218890    Free PMC article.
The impact of Oncotype DX testing on breast cancer management and chemotherapy prescribing patterns in a tertiary referral centre.
Terri Patricia McVeigh, Lauren M Hughes, +4 authors, Michael J Kerin.
Eur J Cancer, 2014 Sep 23; 50(16). PMID: 25240289    Free PMC article.
CD8+ T-cell immunosurveillance constrains lymphoid premetastatic myeloid cell accumulation.
Wang Zhang, Chunyan Zhang, +8 authors, Hua Yu.
Eur J Immunol, 2014 Oct 15; 45(1). PMID: 25310972    Free PMC article.
Estrogen receptor expression is high but is of lower intensity in tubular carcinoma than in well-differentiated invasive ductal carcinoma.
Julie M Jorns, Dafydd G Thomas, +7 authors, Daniel W Visscher.
Arch Pathol Lab Med, 2014 Oct 31; 138(11). PMID: 25357113    Free PMC article.
MicroRNA expression in human endometrial adenocarcinoma.
Sanja Jurcevic, Björn Olsson, Karin Klinga-Levan.
Cancer Cell Int, 2014 Nov 25; 14(1). PMID: 25419182    Free PMC article.
Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients.
Valeria Musella, Maurizio Callari, +8 authors, Vera Cappelletti.
PLoS One, 2015 Apr 07; 10(4). PMID: 25844937    Free PMC article.
Prospective Clinical Utility Study of the Use of the 21-Gene Assay in Adjuvant Clinical Decision Making in Women With Estrogen Receptor-Positive Early Invasive Breast Cancer: Results From the SWITCH Study.
Joseph Gligorov, Xavier B Pivot, +11 authors, Francilian Breast Intergroup.
Oncologist, 2015 Jun 27; 20(8). PMID: 26112003    Free PMC article.
A population-based validation study of the DCIS Score predicting recurrence risk in individuals treated by breast-conserving surgery alone.
Eileen Rakovitch, Sharon Nofech-Mozes, +18 authors, Lawrence Paszat.
Breast Cancer Res Treat, 2015 Jun 30; 152(2). PMID: 26119102    Free PMC article.
The relationship between quantitative human epidermal growth factor receptor 2 gene expression by the 21-gene reverse transcriptase polymerase chain reaction assay and adjuvant trastuzumab benefit in Alliance N9831.
Edith A Perez, Frederick L Baehner, +11 authors, Karla V Ballman.
Breast Cancer Res, 2015 Oct 03; 17(1). PMID: 26429296    Free PMC article.
Rates of MAGE-A3 and PRAME expressing tumors in FFPE tissue specimens from bladder cancer patients: potential targets for antigen-specific cancer immunotherapeutics.
Evelyne Lerut, Hendrik Van Poppel, +3 authors, Patrick Therasse.
Int J Clin Exp Pathol, 2015 Oct 16; 8(8). PMID: 26464715    Free PMC article.
miRNA Isolation from FFPET Specimen: A Technical Comparison of miRNA and Total RNA Isolation Methods.
Zsófia Brigitta Nagy, Barnabás Wichmann, +3 authors, Béla Molnár.
Pathol Oncol Res, 2015 Dec 19; 22(3). PMID: 26678076
Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples.
Fjoralba Zeka, Katrien Vanderheyden, +3 authors, Jo Vandesompele.
Sci Rep, 2016 Feb 24; 6. PMID: 26898768    Free PMC article.
Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids.
Jianguo Xu, Hongling Li, +3 authors, Lee Jia.
Theranostics, 2016 Feb 26; 6(3). PMID: 26909108    Free PMC article.
Signatures of breast cancer metastasis at a glance.
George S Karagiannis, Sumanta Goswami, +2 authors, John S Condeelis.
J Cell Sci, 2016 Apr 17; 129(9). PMID: 27084578    Free PMC article.
Review.
A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay.
Florenza Lüder Ripoli, Annika Mohr, +5 authors, Ingo Nolte.
Int J Mol Sci, 2016 May 18; 17(5). PMID: 27187374    Free PMC article.
Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay.
Mahesh Iddawela, Oscar M Rueda, +3 authors, Carlos Caldas.
BMC Med Genomics, 2016 Aug 21; 9(1). PMID: 27542606    Free PMC article.
Can Archival Tissue Reveal Answers to Modern Research Questions?: Computer-Aided Histological Assessment of Neuroblastoma Tumours Collected over 60 Years.
Albert Chetcuti, Nicole Mackie, +4 authors, Daniel Catchpoole.
Microarrays (Basel), 2014 Jan 01; 3(1). PMID: 27605031    Free PMC article.
The analytical validation of the Oncotype DX Recurrence Score assay.
Frederick L Baehner.
Ecancermedicalscience, 2016 Oct 13; 10. PMID: 27729940    Free PMC article.
Comparison of the QuantiGene 2.0 Assay and Real-Time RT-PCR in the Detection of p53 Isoform mRNA Expression in Formalin-Fixed Paraffin-Embedded Tissues- A Preliminary Study.
Brianna C Morten, Rodney J Scott, Kelly A Avery-Kiejda.
PLoS One, 2016 Nov 11; 11(11). PMID: 27832134    Free PMC article.
Differential long-term stability of microRNAs and RNU6B snRNA in 12-20 year old archived formalin-fixed paraffin-embedded specimens.
Sarah B Peskoe, John R Barber, +4 authors, Shawn E Lupold.
BMC Cancer, 2017 Jan 08; 17(1). PMID: 28061773    Free PMC article.
Proteomic Workflows for Biomarker Identification Using Mass Spectrometry - Technical and Statistical Considerations during Initial Discovery.
Dennis J Orton, Alan A Doucette.
Proteomes, 2013 Aug 27; 1(2). PMID: 28250400    Free PMC article.
Review.
Her2 assessment using quantitative reverse transcriptase polymerase chain reaction reliably identifies Her2 overexpression without amplification in breast cancer cases.
Gabriele Zoppoli, Anna Garuti, +14 authors, Alberto Ballestrero.
J Transl Med, 2017 May 04; 15(1). PMID: 28460632    Free PMC article.
A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology.
Jing Wang, Xue Yang, +5 authors, Jidong Gao.
Oncotarget, 2017 May 26; 8(28). PMID: 28545022    Free PMC article.
Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.
Mahesh Iddawela, Oscar Rueda, +4 authors, Carlos Caldas.
BMC Genomics, 2017 Jul 13; 18(1). PMID: 28697743    Free PMC article.
USP6 activation in nodular fasciitis by promoter-swapping gene fusions.
Nimesh R Patel, John S A Chrisinger, +10 authors, Wei-Lien Wang.
Mod Pathol, 2017 Jul 29; 30(11). PMID: 28752842
Multiplexed analysis of fixed tissue RNA using Ligation in situ Hybridization.
Joel J Credle, Christopher Y Itoh, +11 authors, H Benjamin Larman.
Nucleic Acids Res, 2017 Sep 01; 45(14). PMID: 28854731    Free PMC article.
Rapid Loss of RNA Detection by In Situ Hybridization in Stored Tissue Blocks and Preservation by Cold Storage of Unstained Slides.
Javier A Baena-Del Valle, Qizhi Zheng, +7 authors, Angelo M De Marzo.
Am J Clin Pathol, 2017 Nov 07; 148(5). PMID: 29106457    Free PMC article.
Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy.
Lokesh Agrawal, Kelly B Engel, Sarah R Greytak, Helen M Moore.
Semin Cancer Biol, 2017 Dec 21; 52(Pt 2). PMID: 29258857    Free PMC article.
Review.
The role of the pathology department in the preanalytical phase of molecular analyses.
Sergiu Susman, Ioana Berindan-Neagoe, +7 authors, Ciprian Tomuleasa.
Cancer Manag Res, 2018 Apr 27; 10. PMID: 29695931    Free PMC article.
RNA analysis of cancer predisposing genes in formalin-fixed paraffin-embedded tissue determines aberrant splicing.
Anne Ml Jansen, Heleen M van der Klift, +6 authors, Tom van Wezel.
Eur J Hum Genet, 2018 May 01; 26(8). PMID: 29706640    Free PMC article.
Selective insulin resistance with differential expressions of IRS-1 and IRS-2 in human NAFLD livers.
Midori Honma, Shojiro Sawada, +15 authors, Hideki Katagiri.
Int J Obes (Lond), 2018 May 03; 42(9). PMID: 29717275    Free PMC article.
The 21-gene Recurrence Score® assay predicts distant recurrence in lymph node-positive, hormone receptor-positive, breast cancer patients treated with adjuvant sequential epirubicin- and docetaxel-based or epirubicin-based chemotherapy (PACS-01 trial).
Frédérique Penault-Llorca, Thomas Filleron, +12 authors, Henri Roché.
BMC Cancer, 2018 May 08; 18(1). PMID: 29728098    Free PMC article.
Basal-like Breast Cancers: From Pathology to Biology and Back Again.
Barry Gusterson, Connie J Eaves.
Stem Cell Reports, 2018 Jun 07; 10(6). PMID: 29874626    Free PMC article.
Review.
The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine.
Kivilcim Ozturk, Michelle Dow, +2 authors, Hannah Carter.
J Mol Biol, 2018 Jun 18; 430(18 Pt A). PMID: 29908887    Free PMC article.
Review.
Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues.
Daniel Groelz, Christian Viertler, +2 authors, Kurt Zatloukal.
PLoS One, 2018 Sep 08; 13(9). PMID: 30192857    Free PMC article.
Microsatellite instability test using peptide nucleic acid probe-mediated melting point analysis: a comparison study.
Mi Jang, Yujin Kwon, +6 authors, Won Kyu Kim.
BMC Cancer, 2018 Dec 06; 18(1). PMID: 30514259    Free PMC article.
Panoptic View of Prognostic Models for Personalized Breast Cancer Management.
Geetanjali Saini, Karuna Mittal, +3 authors, Ritu Aneja.
Cancers (Basel), 2019 Sep 11; 11(9). PMID: 31500225    Free PMC article.
Review.
In situ analysis of Her2 DNA and RNA in retinoblastoma and adjacent retina.
Gail M Seigel, Dhaval K Shah, +4 authors, Jidong Shan.
Oncoscience, 2019 Oct 15; 6(7-8). PMID: 31608299    Free PMC article.
Oncotype DX Breast Cancer recurrence score resists inter-assay reproducibility with RT2-Profiler Multiplex RT-PCR.
Verena Schildgen, Mathias Warm, Michael Brockmann, Oliver Schildgen.
Sci Rep, 2020 Jan 01; 9(1). PMID: 31889145    Free PMC article.
Extraction-free whole transcriptome gene expression analysis of FFPE sections and histology-directed subareas of tissue.
Christy L Trejo, Miloš Babić, +6 authors, Bruce E Seligmann.
PLoS One, 2019 Feb 23; 14(2). PMID: 30794557    Free PMC article.
Oncotype DX for Comprehensive Treatment in Male Breast Cancer: A Case Report and Literature Review.
Ang Zheng, Lin Zhang, +2 authors, Feng Jin.
Am J Mens Health, 2019 May 10; 13(3). PMID: 31068065    Free PMC article.
Review.
A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer.
Rachel L Stewart, Katherine L Updike, +4 authors, Katherine E Varley.
Cancer Res, 2019 May 03; 79(13). PMID: 31048497    Free PMC article.
Toward Improving Practices for Submission of Diagnostic Tissue Blocks for National Cancer Institute Clinical Trials.
Hala Makhlouf, Mark A Watson, +11 authors, Irina Lubensky.
Am J Clin Pathol, 2019 Oct 16; 153(2). PMID: 31613330    Free PMC article.
Optimizing Tissue Preservation for High-Resolution Confocal Imaging of Single-Molecule RNA-FISH.
Nash Redmayne, Shawn L Chavez.
Curr Protoc Mol Biol, 2019 Nov 26; 129(1). PMID: 31763781    Free PMC article.
The age of paraffin block influences biomarker levels in archival breast cancer samples.
Hong Chen, Qing-Qing Fang, Bo Wang.
Oncol Lett, 2020 Jun 23; 20(1). PMID: 32565978    Free PMC article.
Quantifying mRNA levels across tissue sections with 2D-RT-qPCR.
Michael Armani, Michael A Tangrea, +2 authors, Elisabeth Smela.
Anal Bioanal Chem, 2011 May 12; 400(10). PMID: 21559756    Free PMC article.
Loss of CDKN2A and CDKN2B expression is associated with disease recurrence in oral cancer.
V G Deepak Roshan, M S Sinto, Bipin T Vargees, S Kannan.
J Oral Maxillofac Pathol, 2019 May 22; 23(1). PMID: 31110422    Free PMC article.
Gene expression analysis in formalin fixed paraffin embedded melanomas is associated with density of corresponding immune cells in those tissues.
Minyoung Kwak, Gulsun Erdag, Craig L Slingluff.
Sci Rep, 2020 Oct 29; 10(1). PMID: 33110110    Free PMC article.
Different stability of miRNAs and endogenous control genes in archival specimens of papillary thyroid carcinoma.
Daina Pamedytyte, Enrika Leipute, +4 authors, Aurelija Zvirbliene.
Mol Med, 2020 Nov 07; 26(1). PMID: 33153429    Free PMC article.
Impact of tissue preservation on collagen fiber architecture.
H N Hutson, C Kujawa, +2 authors, K S Masters.
Biotech Histochem, 2018 Oct 26; 94(2). PMID: 30354688    Free PMC article.
Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review.
Maryam Sotoudeh Anvari, Atoosa Gharib, +5 authors, Mohammad Vasei.
Iran J Pathol, 2021 Jan 05; 16(1). PMID: 33391375    Free PMC article.
Review.
Concordance of the 21-gene assay between core needle biopsy and resection specimens in early breast cancer patients.
Peng Qi, Yu Yang, +5 authors, Xiao-Yan Zhou.
Breast Cancer Res Treat, 2021 Jan 14; 186(2). PMID: 33439420    Free PMC article.
Cancer of Unknown Primary: Challenges and Progress in Clinical Management.
Noemi Laprovitera, Mattia Riefolo, +3 authors, Manuela Ferracin.
Cancers (Basel), 2021 Jan 29; 13(3). PMID: 33504059    Free PMC article.
Review.
Validation of the GenesWell BCT Score in Young Asian Women With HR+/HER2- Early Breast Cancer.
Mi Jeong Kwon, Jai Min Ryu, +12 authors, Jeong Eon Lee.
Front Oncol, 2021 Mar 13; 11. PMID: 33708625    Free PMC article.
Cell-blocks and other ancillary studies (including molecular genetic tests and proteomics).
Vinod B Shidham.
Cytojournal, 2021 Apr 22; 18. PMID: 33880127    Free PMC article.
Review.