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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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2
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Wang J, Yang X, Chen H, Wang X, Wang X, Fang Y, Jia Z, Gao J. A high-throughput method to detect RNA profiling by integration of RT-MLPA with next generation sequencing technology. Oncotarget 2018; 8:46071-46080. [PMID: 28545022 PMCID: PMC5542250 DOI: 10.18632/oncotarget.17551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/28/2017] [Indexed: 01/14/2023] Open
Abstract
RNA in formalin-fixed and paraffin-embedded (FFPE) tissues provides large amount of information indicating disease stages, histological tumor types and grades, as well as clinical outcomes. However, Detection of RNA expression levels in formalin-fixed and paraffin-embedded samples is extremely difficult due to poor RNA quality. Here we developed a high-throughput method, Reverse Transcription-Multiple Ligation-dependent Probe Sequencing (RT-MLPSeq), to determine expression levels of multiple transcripts in FFPE samples. By combining Reverse Transcription-Multiple Ligation-dependent Amplification method and next generation sequencing technology, RT-MLPSeq overcomes the limit of probe length in multiplex ligation-dependent probe amplification assay and thus could detect expression levels of transcripts without quantitative limitations. We proved that different RT-MLPSeq probes targeting on the same transcripts have highly consistent results and the starting RNA/cDNA input could be as little as 1 ng. RT-MLPSeq also presented consistent relative RNA levels of selected 13 genes with reverse transcription quantitative PCR. Finally, we demonstrated the application of the new RT-MLPSeq method by measuring the mRNA expression levels of 21 genes which can be used for accurate calculation of the breast cancer recurrence score – an index that has been widely used for managing breast cancer patients.
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Affiliation(s)
- Jing Wang
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xue Yang
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haofeng Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xuewei Wang
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangyu Wang
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi Fang
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, California, United States
| | - Jidong Gao
- Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Yeo J, Morales DA, Chen T, Crawford EL, Zhang X, Blomquist TM, Levin AM, Massion PP, Arenberg DA, Midthun DE, Mazzone PJ, Nathan SD, Wainz RJ, Nana-Sinkam P, Willey PFS, Arend TJ, Padda K, Qiu S, Federov A, Hernandez DAR, Hammersley JR, Yoon Y, Safi F, Khuder SA, Willey JC. RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPs. BMC Pulm Med 2018; 18:42. [PMID: 29506519 PMCID: PMC5838965 DOI: 10.1186/s12890-018-0603-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Background There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. Methods To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0.7, FEV1% < 80%), and 30 non-COPD controls. Targeted next generation sequencing was used to measure total and allele-specific expression of 35 genes in genome maintenance (GM) genes pathways linked to COPD pathogenesis, including seven TP53 and CEBP transcription factor family members. Shrinkage linear discriminant analysis (SLDA) was used to identify COPD-classification models. COPD GWAS were queried for putative cis-regulatory SNPs in the targeted genes. Results On a network basis, TP53 and CEBP transcription factor pathway gene pair network connections, including key DNA repair gene ERCC5, were significantly different in COPD subjects (e.g., Wilcoxon rank sum test for closeness, p-value = 5.0E-11). ERCC5 SNP rs4150275 association with chronic bronchitis was identified in a set of Lung Health Study (LHS) COPD GWAS SNPs restricted to those in putative regulatory regions within the targeted genes, and this association was validated in the COPDgene non-hispanic white (NHW) GWAS. ERCC5 SNP rs4150275 is linked (D’ = 1) to ERCC5 SNP rs17655 which displayed differential allelic expression (DAE) in BEC and is an expression quantitative trait locus (eQTL) in lung tissue (p = 3.2E-7). SNPs in linkage (D’ = 1) with rs17655 were predicted to alter miRNA binding (rs873601). A classifier model that comprised gene features CAT, CEBPG, GPX1, KEAP1, TP73, and XPA had pooled 10-fold cross-validation receiver operator characteristic area under the curve of 75.4% (95% CI: 66.3%–89.3%). The prevalence of DAE was higher than expected (p = 0.0023) in the classifier genes. Conclusions GM genes comprised by COPD-associated BEC expression patterns were enriched for SNPs with cis-regulatory function, including a putative cis-rSNP in ERCC5 that was associated with COPD risk. These findings support additional total and allele-specific expression analysis of gene pathways with high prior likelihood for involvement in COPD pathogenesis. Electronic supplementary material The online version of this article (10.1186/s12890-018-0603-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiyoun Yeo
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Diego A Morales
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Tian Chen
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA
| | - Erin L Crawford
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Xiaolu Zhang
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Thomas M Blomquist
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, HEB 219, Toledo, OH, 43614, USA
| | - Albert M Levin
- Department of Biostatistics, Henry Ford Health System, 1 Ford Place Detroit, MI, Detroit, MI, 48202, USA
| | - Pierre P Massion
- Thoracic Program, Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | | | - David E Midthun
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Peter J Mazzone
- Department of Pulmonary Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Steven D Nathan
- Department of Pulmonary Medicine, Inova Fairfax Hospital, 3300 Gallows Road, Falls Church, VA, 22042-3300, USA
| | - Ronald J Wainz
- The Toledo Hospital, 2142 N Cove Blvd, Toledo, OH, 43606, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, USA, Richmond, VA, 23284-2512, USA.,Ohio State University James Comprehensive Cancer Center and Solove Research Institute, Columbus, OH, USA
| | - Paige F S Willey
- American Enterprise Institute, 1789 Massachusetts Ave NW, Washington, DC, 20036, USA
| | - Taylor J Arend
- The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Karanbir Padda
- Emory University School of Medicine, 1648 Pierce Dr NE, Atlanta, GA, 30307, USA
| | - Shuhao Qiu
- Department of Medicine, The University of Toledo Medical Center, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Alexei Federov
- Department of Mathematics and Statistics, The University of Toledo, 2801 W. Bancroft Street, Toledo, OH, 43606, USA.,Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA
| | - Dawn-Alita R Hernandez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Jeffrey R Hammersley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Youngsook Yoon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Fadi Safi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - Sadik A Khuder
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, RHC 0012, Toledo, OH, 43614, USA
| | - James C Willey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH, 43614, USA.
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Multianalyte quantitative competitive PCR on optically encoded microspheres for an eight-gene panel related to prostate cancer. Anal Bioanal Chem 2017; 410:971-980. [PMID: 28861591 DOI: 10.1007/s00216-017-0595-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/09/2017] [Accepted: 08/18/2017] [Indexed: 10/19/2022]
Abstract
Nucleic acid-based tests have a profound impact in every medical discipline. Because multigene tests offer higher diagnostic accuracy and lower overall cost than single assays, they are especially useful for diseases, like prostate cancer, that present variability at the molecular level and diversity of available therapeutic interventions. We have developed a quantitative competitive PCR for an eight-gene panel, related to prostate cancer, that includes five genes of the human tissue kallikrein family (KLKs), prostate-specific membrane antigen (PSMA), prostate cancer antigen 3 (PCA3), and HPRT1 as a reference gene. Using PCR as a synthetic tool, a competitor was prepared for each target sequence containing the same primer binding sites as the target but differing in a short segment to enable discrimination by hybridization. The assay involves multiplex amplification of targets and competitors followed by a multiplex hybridization assay for the 16 amplification products. The assay was performed on optically encoded microspheres with oligonucleotide probes attached to their surface. The microspheres were analyzed rapidly (1 min) by flow cytometry. The signal ratio of the target and cognate competitor is a function of the target copy number in the sample prior to amplification. The multiplexing potential of the proposed method is much higher than real-time PCR and other end-point methods since there are 100 sets of commercially available microspheres.
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Zeka F, Vanderheyden K, De Smet E, Cuvelier CA, Mestdagh P, Vandesompele J. Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples. Sci Rep 2016; 6:21418. [PMID: 26898768 PMCID: PMC4761903 DOI: 10.1038/srep21418] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 01/19/2016] [Indexed: 01/10/2023] Open
Abstract
Fragmented RNA from formalin-fixed paraffin-embedded (FFPE) tissue is a known obstacle to gene expression analysis. In this study, the impact of RNA integrity, gene-specific reverse transcription and targeted cDNA preamplification was quantified in terms of reverse transcription polymerase chain reaction (RT-qPCR) sensitivity by measuring 48 protein coding genes on eight duplicate cultured cancer cell pellet FFPE samples and twenty cancer tissue FFPE samples. More intact RNA modestly increased gene detection sensitivity by 1.6 fold (earlier detection by 0.7 PCR cycles, 95% CI = 0.593-0.850). Application of gene-specific priming instead of whole transcriptome priming during reverse transcription further improved RT-qPCR sensitivity by a considerable 4.0 fold increase (earlier detection by 2.0 PCR cycles, 95% CI = 1.73-2.32). Targeted cDNA preamplification resulted in the strongest increase of RT-qPCR sensitivity and enabled earlier detection by an average of 172.4 fold (7.43 PCR cycles, 95% CI = 6.83-7.05). We conclude that gene-specific reverse transcription and targeted cDNA preamplification are adequate methods for accurate and sensitive RT-qPCR based gene expression analysis of FFPE material. The presented methods do not involve expensive or complex procedures and can be easily implemented in any routine RT-qPCR practice.
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Affiliation(s)
- Fjoralba Zeka
- Center for Medical Genetics, Ghent University, Belgium
- Cancer Research Institute Ghent, Ghent University, Belgium
| | - Katrien Vanderheyden
- Center for Medical Genetics, Ghent University, Belgium
- Cancer Research Institute Ghent, Ghent University, Belgium
| | - Els De Smet
- Center for Medical Genetics, Ghent University, Belgium
- Cancer Research Institute Ghent, Ghent University, Belgium
| | | | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Belgium
- Cancer Research Institute Ghent, Ghent University, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, Belgium
- Cancer Research Institute Ghent, Ghent University, Belgium
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Peng Z, Andersson K, Lindholm J, Dethlefsen O, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C. Improving the Prediction of Prostate Cancer Overall Survival by Supplementing Readily Available Clinical Data with Gene Expression Levels of IGFBP3 and F3 in Formalin-Fixed Paraffin Embedded Core Needle Biopsy Material. PLoS One 2016; 11:e0145545. [PMID: 26731648 PMCID: PMC4701463 DOI: 10.1371/journal.pone.0145545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 12/04/2015] [Indexed: 11/28/2022] Open
Abstract
Background A previously reported expression signature of three genes (IGFBP3, F3 and VGLL3) was shown to have potential prognostic value in estimating overall and cancer-specific survivals at diagnosis of prostate cancer in a pilot cohort study using freshly frozen Fine Needle Aspiration (FNA) samples. Methods We carried out a new cohort study with 241 prostate cancer patients diagnosed from 2004–2007 with a follow-up exceeding 6 years in order to verify the prognostic value of gene expression signature in formalin fixed paraffin embedded (FFPE) prostate core needle biopsy tissue samples. The cohort consisted of four patient groups with different survival times and death causes. A four multiplex one-step RT-qPCR test kit, designed and optimized for measuring the expression signature in FFPE core needle biopsy samples, was used. In archive FFPE biopsy samples the expression differences of two genes (IGFBP3 and F3) were measured. The survival time predictions using the current clinical parameters only, such as age at diagnosis, Gleason score, PSA value and tumor stage, and clinical parameters supplemented with the expression levels of IGFBP3 and F3, were compared. Results When combined with currently used clinical parameters, the gene expression levels of IGFBP3 and F3 are improving the prediction of survival time as compared to using clinical parameters alone. Conclusion The assessment of IGFBP3 and F3 gene expression levels in FFPE prostate cancer tissue would provide an improved survival prediction for prostate cancer patients at the time of diagnosis.
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Affiliation(s)
- Zhuochun Peng
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
| | - Karl Andersson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Ridgeview Instruments AB, Uppsala, Sweden
| | - Johan Lindholm
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Dethlefsen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Sten Nilsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Chunde Li
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
- * E-mail:
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Blomquist T, Crawford EL, Yeo J, Zhang X, Willey JC. Control for stochastic sampling variation and qualitative sequencing error in next generation sequencing. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 5:30-37. [PMID: 26693143 PMCID: PMC4673681 DOI: 10.1016/j.bdq.2015.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Clinical implementation of Next-Generation Sequencing (NGS) is challenged by poor control for stochastic sampling, library preparation biases and qualitative sequencing error. To address these challenges we developed and tested two hypotheses. METHODS Hypothesis 1: Analytical variation in quantification is predicted by stochastic sampling effects at input of a) amplifiable nucleic acid target molecules into the library preparation, b) amplicons from library into sequencer, or c) both. We derived equations using Monte Carlo simulation to predict assay coefficient of variation (CV) based on these three working models and tested them against NGS data from specimens with well characterized molecule inputs and sequence counts prepared using competitive multiplex-PCR amplicon-based NGS library preparation method comprising synthetic internal standards (IS). Hypothesis 2: Frequencies of technically-derived qualitative sequencing errors (i.e., base substitution, insertion and deletion) observed at each base position in each target native template (NT) are concordant with those observed in respective competitive synthetic IS present in the same reaction. We measured error frequencies at each base position within amplicons from each of 30 target NT, then tested whether they correspond to those within the 30 respective IS. RESULTS For hypothesis 1, the Monte Carlo model derived from both sampling events best predicted CV and explained 74% of observed assay variance. For hypothesis 2, observed frequency and type of sequence variation at each base position within each IS was concordant with that observed in respective NTs (R2 = 0.93). CONCLUSION In targeted NGS, synthetic competitive IS control for stochastic sampling at input of both target into library preparation and of target library product into sequencer, and control for qualitative errors generated during library preparation and sequencing. These controls enable accurate clinical diagnostic reporting of confidence limits and limit of detection for copy number measurement, and of frequency for each actionable mutation.
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Affiliation(s)
- Thomas Blomquist
- Department of Pathology, University of Toledo Health Sciences Campus, Toledo, OH 43614
| | - Erin L Crawford
- Department of Medicine, University of Toledo Health Sciences Campus, Toledo, OH 43614
| | - Jiyoun Yeo
- Department of Medicine, University of Toledo Health Sciences Campus, Toledo, OH 43614
| | - Xiaolu Zhang
- Department of Medicine, University of Toledo Health Sciences Campus, Toledo, OH 43614
| | - James C Willey
- Department of Pathology, University of Toledo Health Sciences Campus, Toledo, OH 43614 ; Department of Medicine, University of Toledo Health Sciences Campus, Toledo, OH 43614
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Peng Z, Andersson K, Lindholm J, Bodin I, Pramana S, Pawitan Y, Nistér M, Nilsson S, Li C. Operator dependent choice of prostate cancer biopsy has limited impact on a gene signature analysis for the highly expressed genes IGFBP3 and F3 in prostate cancer epithelial cells. PLoS One 2014; 9:e109610. [PMID: 25296164 PMCID: PMC4190108 DOI: 10.1371/journal.pone.0109610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/01/2014] [Indexed: 11/20/2022] Open
Abstract
Background Predicting the prognosis of prostate cancer disease through gene expression analysis is receiving increasing interest. In many cases, such analyses are based on formalin-fixed, paraffin embedded (FFPE) core needle biopsy material on which Gleason grading for diagnosis has been conducted. Since each patient typically has multiple biopsy samples, and since Gleason grading is an operator dependent procedure known to be difficult, the impact of the operator's choice of biopsy was evaluated. Methods Multiple biopsy samples from 43 patients were evaluated using a previously reported gene signature of IGFBP3, F3 and VGLL3 with potential prognostic value in estimating overall survival at diagnosis of prostate cancer. A four multiplex one-step qRT-PCR test kit, designed and optimized for measuring the signature in FFPE core needle biopsy samples was used. Concordance of gene expression levels between primary and secondary Gleason tumor patterns, as well as benign tissue specimens, was analyzed. Results The gene expression levels of IGFBP3 and F3 in prostate cancer epithelial cell-containing tissue representing the primary and secondary Gleason patterns were high and consistent, while the low expressed VGLL3 showed more variation in its expression levels. Conclusion The assessment of IGFBP3 and F3 gene expression levels in prostate cancer tissue is independent of Gleason patterns, meaning that the impact of operator's choice of biopsy is low.
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Affiliation(s)
- Zhuochun Peng
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
| | - Karl Andersson
- Department of Oncology, Radiology and Radiation Sciences, Uppsala University, Uppsala, Sweden
- Ridgeview Instruments AB, Uppsala, Sweden
| | - Johan Lindholm
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Inger Bodin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Sekolah Tinggi Ilmu Statistik/Institute of Statistics, Jakarta, Indonesia
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Monica Nistér
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology/Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Sten Nilsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Chunde Li
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Oncology, Karolinska University Hospital, Stockholm, Sweden
- Chundsell Medicals AB, Stockholm, Sweden
- * E-mail:
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