Philip S Bernard
Affiliation: University of Utah
- Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumorsJason I Herschkowitz
Lineberger Comprehensive Cancer Center
Genome Biol 8:R76. 2007..To address this need, we characterized mammary tumor gene expression profiles from 13 different murine models using DNA microarrays and compared the resulting data to those from human breast tumors...
- Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assayLaurent Perreard
The ARUP Institute for Clinical and Experimental Pathology, SLC, Utah, USA
Breast Cancer Res 8:R23. 2006..In the current article, we use microarray analysis and a real-time quantitative reverse-transcription (qRT)-PCR assay to risk-stratify breast cancers based on biological 'intrinsic' subtypes and proliferation...
- The molecular portraits of breast tumors are conserved across microarray platformsZhiyuan Hu
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
BMC Genomics 7:96. 2006..To overcome this problem we used publicly available breast cancer gene expression data sets and a novel approach to data fusion, in order to validate a new breast tumor intrinsic list...
- EGFR associated expression profiles vary with breast tumor subtypeKatherine A Hoadley
Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
BMC Genomics 8:258. 2007..An EGFR-associated gene expression signature was identified in the basal-like SUM102 cell line and was used to classify a diverse set of sporadic breast tumors...
- Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomesYoko S Derose
Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
Nat Med 17:1514-20. 2011..This bank of tumor grafts also serves as a publicly available resource for new models in which to study the biology of breast cancer...
- Differentiating Ewing's sarcoma from other round blue cell tumors using a RT-PCR translocation panel on formalin-fixed paraffin-embedded tissuesTracey B Lewis
Research and Development, The ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
Mod Pathol 20:397-404. 2007..Our real-time RT-PCR assay for detecting sarcoma translocations has high sensitivity and specificity for Ewing's sarcoma and has clinical utility in differentiating small round blue cell tumors in the clinical lab...
- PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markersRoy R L Bastien
The ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
BMC Med Genomics 5:44. 2012..Discrepancies between these methods may lead to different treatment decisions...
- Molecular classification of melanoma using real-time quantitative reverse transcriptase-polymerase chain reactionTracey B Lewis
Research and Development, ARUP Laboratories Inc, Salt Lake City, Utah, USA
Cancer 104:1678-86. 2005..Molecular methods are more sensitive in detecting occult lymph node metastases compared with standard histopathology and are reported to have utility in clinical diagnostics...
- ESR1 gene amplification in breast cancer: a common phenomenon?Lindsay A Brown
Nat Genet 40:806-7; author reply 810-2. 2008
- Molecular portraits and the family tree of cancerChristine H Chung
Division of Hematology Oncology, University of North Carolina at Chapel Hill, CB 7305, 3009 Old Clinic Building, Chapel Hill, North Carolina 27599, USA
Nat Genet 32:533-40. 2002..The early results are painting a detailed portrait of cancer that illustrates the individuality of each tumor and allows familial relationships to be recognized through the identification of cell types sharing common expression patterns...
- Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissuesMichael Mullins
Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
Clin Chem 53:1273-9. 2007....
- State of the science: molecular classifications of breast cancer for clinical diagnosticsJohn E Robison
Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
Clin Biochem 37:572-8. 2004..This manuscript reviews the current standards of care, presents progress that is being made in the development of genomic assays for breast cancer and discusses options for implementing these new tests into the clinical setting...
- Statistical modeling for selecting housekeeper genesAniko Szabo
Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USA
Genome Biol 5:R59. 2004..We present appropriate models for selecting the best housekeepers to normalize quantitative data within a given tissue type (for example, breast cancer) and across different types of tissue samples...
- Real-time PCR technology for cancer diagnosticsPhilip S Bernard
Department of Pathology, University of Utah School of Medicine, 30 North 1900 East, Salt Lake City 84132, USA
Clin Chem 48:1178-85. 2002..The challenge for pathology will be the development and implementation of these molecular classifications for routine clinical practice...
- Color multiplex polymerase chain reaction for quantitative analysis of epidermal growth factor receptor genes in colorectal adenocarcinomaLester J Layfield
Department of Pathology, University of Utah School of Medicine, and ARUP Laboratories, Inc, Salt Lake City, Utah 84132, USA
J Surg Oncol 83:227-31. 2003..Possible mechanisms for over expression of EGFR include gene amplification, transcriptional upregulation, or decreased degredation of the EGFR protein...
- High-throughput amplicon scanning of the TP53 gene in breast cancer using high-resolution fluorescent melting curve analyses and automatic mutation callingRoy Bastien
Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112 5550, USA
Hum Mutat 29:757-64. 2008..The TP53 scanning assay can be performed from a variety of specimen types with high sensitivity/specificity and could be used for clinical and research purposes...
- Discriminate gene lists derived from cDNA microarray profiles of limited samples permit distinguishing mesenchymal neoplasia ex vivoDavid E Joyner
SAR Lab, Sarcoma Services, Department of Orthopedics, Huntsman Cancer Institute and Primary Children s Medical Center, University of Utah, Salt Lake City, UT 84112, USA
J Cancer Res Clin Oncol 131:137-46. 2005..This technique may enable an eventual molecular classification schema based on expression profiles that can complement current clinical and pathologic diagnostic procedures in mesenchymal tumors...
- Homogeneous amplification and mutation scanning of the p53 gene using fluorescent melting curvesHaleigh Millward
Idaho Technology Inc, Salt Lake City, UT 84105, USA
Clin Chem 48:1321-8. 2002..In malignancy, gene mutations frequently occur in tumor suppressor genes such as p53 and are sporadically located. We describe a homogeneous method for amplification and mutation scanning, and apply the method to the p53 gene...