RESOURCE GUIDE F F P E R N A S a m p l e P reparat i o n R es o u r c e G u i d e FFPE RNA Sample Preparation Resource Guide The development of molecular diagnostics, drugs and, ultimately, personalized treatment for complex diseases such as cancer depends on clinical utilization of robust biomarkers. Expression profiling using FFPE samples has proven to be a valuable approach for such a molecular test. NuGEN’s FFPE RNA sample preparation workflow represents a significant technological breakthrough, supporting both retrospective analysis of archived FFPE tissues for the initial discovery as well as making it possible to implement the test in a clinical setting on a routine basis following current standardized pathologist practice. This assay is compatible with a variety of FFPE RNA isolation kits and supports analysis on different analytical platforms. Figure 1 RNA Extraction NuGEN’s FFPE RNA Sample Preparation Workflow RNA Amplification qPCR Sample QC (optional) Fragmentation & Labeling Genomic Analysis NuGEN Tech Rept #1 Encore Biotin Molecule Affymetrix 3´ Expression Arrays Fast track your expression biomarker discovery and diagnostic test development by choosing NuGEN as your sample preparation partner. • QIAGEN • Roche • Beckman Coulter Genomics • Life Technologies WT-Ovation FFPE System WT-Ovation Exon Module Encore Biotin Molecule Affymetrix Exon/Gene Arrays Encore BiotinIL Molecule Illumina BeadChips Unique Features of the NuGEN FFPE RNA Sample Prep Workflow NuGEN Agilent App Note Agilent Expression Arrays qPCR or other detection platforms Simple, robust and reliable • Starting with 50 ng input FFPE total RNA • Compatible with multiple microarray, qPCR and additional detection platforms • Automatable • Highly reproducible Fast • Total assay time from total RNA to array hybridization in one day Proven • Customer publications in major peer-reviewed journals • Dx partners choosing NuGEN solutions for their test development cGMP certified • Expediting regulatory approval path to molecular diagnostics Introduction Formalin fixation coupled with paraffin-embedding (FFPE) is the most common method of clinical tissue sample storage comprising the major percentage of all archived specimens in the world. These archives are of significant value to today’s biomarker discovery efforts since they are readily available and are often associated with in-depth patient clinical records regarding diagnosis, prognosis, response to treatment and outcome. In addition, it is a standard procedure for pathologists to use FFPE samples for established immunohistochemical analysis. Consequently, it is highly desirable to utilize the same tissue collection for molecular Dx tests in order to better correlate the various test results and reduce the barrier of adoption in the clinic. Working with nucleic acids isolated from FFPE samples, however, has been challenging. These FFPE samples exhibit marked degradation and change in response to fixation methods and long-term storage. Until recently, in spite of their desirability, these sample sets have been viewed as unlikely candidates for global gene expression analysis using microarrays or large-scale qPCR analysis. NuGEN’s unique FFPE RNA Sample Preparation Workflow takes an innovative approach by employing the WT-Ovation™ FFPE System for RNA amplification of formalin-fixed, paraffin-embedded samples through a simple, robust and easily automatable 1 F F P E R N A S a m p l e P reparat i o n R es o u r c e G u i d e In addition to providing superior-quality technical results, adopting a new technology in a clinical setting requires the tests to pass stringent regulatory approvals and the process can be lengthy and time consuming. To help facilitate and expedite the regulatory approval process essential for molecular Dx test development, NuGEN has also implemented rigorous quality programs for reagents manufacturing and is one of the first sample preparation companies to receive the cGMP certification. NuGEN’s cGMP certification, which complements the company’s ISO 13485 compliance, demonstrates NuGEN’s quality infrastructure and its ability to develop and manufacture highly reproducible genomic sample preparation products that meet the “ …microarray analysis is possible, precise, and reliable from small amounts of RNA extracted after microdissection of tumor cells from FFPE tissue specimens processed for routine histopathological diagnostics. ” “ Our approach is feasible and reliable for a molecular pathological laboratory in a clinical environment, as demonstrated by performing the laboratory protocol at different time points for different samples and by applying a practicable microdissection step… ” Lassmann, S. et al (2009) J. Mol. Med, 87:211-224 Figure 2. cDNA Amplification Yields 10 cDNA Yields (µ) µg 9 8 Array Minimum solution from as little as 50 ng input of total RNA. In combination with labeling reagents, the single-day workflow can be tailored for analysis on the researcher’s detection system of choice to fit on a variety of microarray platforms. Alternatively, the amplified products can be analyzed by qPCR or a range of other detection platforms, or archived for future analysis. The data generated using the NuGEN workflow are reliable, sensitive, highly reproducible and biologically relevant (see the list of selected customer publications in this document and available at www.nugeninc.com). 7 6 5 4 3 2 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 Sample # 41 FFPE-derived Ovarian tumor samples are shown. A minimum of 5.8 µg is required for analysis on GeneChip arrays (shown by the red bar) a criterion met by all amplifications in this study. Ta b l e 1 . Array Metrics No. of Arrays %P Background Signal 40 36.3 ± 8.5 28.8 ± 3.1 Scaling Factor cDNA Yield (µg) 26 ± 14 7.8 ± 0.88 Array metrics for the same set of Ovarian FFPE samples shown in Figure 1, obtained from analysis on the GeneChip HG-U133A Plus 2.0 GeneChip Arrays. % Present calls ranged from 18-50% for this set of 2- to 15-year-old samples. premium standards required for diagnostic tests. As a result, NuGEN eases diagnostic customers’ path to integrating sample preparation into Dx tests and eventual regulatory approval. SPIA® - Single Primer Isothermal Amplification Central to NuGEN’s FFPE RNA sample preparation solution is the RiboSPIA technology that provides both oligo(dT)- and random primer-initiated amplification. It offers the benefit of whole transcriptome amplification for degraded samples. The system yields sufficient amplified product (cDNA) for analysis of at least one microarray as well as qPCR and QC analysis, in about six hours. This amplification system can also be used in archiving strategies where the amplified cDNA serves as a more stable source of experimental samples for use with various analytical platforms and for sharing among collaborators. This solution’s low input requirement for RNA allows the preservation and archiving of the original FFPE block for future studies. Highly Robust, Reliable and Reproducible Array Results In a collaborative study with the Moffitt Cancer Center & Research Institute, a large set of ovarian tumor samples were amplified and labeled using the NuGEN FFPE RNA sample preparation workflow and analyzed on Affymetrix GeneChip® HG-U133 Plus 2.0 Arrays. The amount of amplified cDNA recommended for one array analysis is 5.8 μg, denoted by a red bar on the histogram in Figure 2. In this study, sufficient material was produced for array analysis for all samples regardless of the age of the 2 F F P E R N A S a m p l e P reparat i o n R es o u r c e G u i d e Array performance averages across all individuals in this study were also consistent despite the wide range of sample ages and the expected variability among different individuals (Table 1). To demonstrate the technical reproducibility of the workflow, five replicates were amplified from a three-year old breast tumor FFPE sample. As shown in Table 2, a high level of consistency was obtained with the R2 average of 0.986, call concordance average of 85.0% and a %P range of 52.0% – 54.4%. The NuGEN FFPE RNA sample preparation workflow is robust across a wide range of samples independent of the age. It effectively amplifies the FFPE RNA enabling highly reproducible and reliable results on microarrays. Maintaining Biological Significance from FFPE Samples To illustrate the integrity of the biological data, RNA extracted from FFPE tissue was amplified, labeled, hybridized to microarrays and analyzed using Principal Components Analysis (PCA) (Figure 3). Targets were prepared from FFPE RNA from one donor (pink) and fresh frozen tissue from a second donor (blue). Each sample was amplified in quadruplicate and hybridized to GeneChip HG-U133A 2.0 Arrays. This result indicates a statistically significant separation of samples based on the tissue disease state for both fresh frozen and FFPE samples, demonstrating the amplification system has clearly maintained the biological data integrity. In an independent study, the differential expression correlation was assessed comparing the FFPE samples with the matching fresh frozen tissues. As shown in Figure 4, the correlation of differential expression was high, indicating the faithful representation of the transcriptome using the NuGEN FFPE RNA sample preparation workflow, which is extremely critical for biomarker discovery and diagnostic test development. Similar concordance results were also obtained on other microarray Ta b l e 2 . Array Metrics A. Signal R2 1 2 0.985 3 0.983 0.986 4 0.981 0.987 0.991 5 0.987 0.989 0.987 0.986 % Call Concordance 1 2 3 4 2 84.6 3 85.3 84.4 4 84.8 84.5 85.0 5 85.7 85.0 85.5 2 3 4 B. 85.4 C. Array Metrics SF Bkgd %P GAP Act RawQ Average 6.8 29.0 53% 0.8 12.0 0.8 SD 0.58 1.13 1.1% 0.03 0.48 0.05 Five replicate amplifications performed on 50 ng of total RNA derived from a three-year old breast tumor FFPE sample were analyzed on GeneChip arrays. Results show highly reproducible and robust array performance. Signal R2 and Call Concordance shown in panels A and B have an average of 0.986 and 85.0%, respectively. The %P shown in panel C was in a range of 52.0% – 54.4%. Figure 3. Principal Components Analysis (PCA) of Colon Tumor and Normal Adjacent Tissue (NAT). 60 48 NAT 36 24 PCA #2 samples, indicating the robustness of the amplification technology. 12 0 -12 -24 Tumor -36 -48 -60 -230 -184 -139 -94 -49 -4 41 86 132 177 222 PCA #1 Targets were prepared from RNA extracted from formalin-fixed, paraffin-embedded tissue (FFPE) from one donor (red) and fresh frozen tissue from a second donor (blue). Each sample was amplified in quadruplicate and hybridized to Affymetrix GeneChip HG-U133A 2.0 Arrays. PCA was performed using Partek Genomics Suite software. The green and blue ellipses (NAT and Tumor, respectively) define the boundary of 2 standard deviations from the centroid of each cluster, indicating a statistically significant separation of samples based on the disease state of the tissue. This demonstrates that the amplification systems maintain the integrity of the biological data. 3 F F P E R N A S a m p l e P reparat i o n R es o u r c e G u i d e platforms such as Affymetrix GeneChip Exon/Gene Arrays, Illumina BeadChips and Agilent Whole Genome Expression Arrays (data not shown). Figure 4. Highly Concordant Differential Expression Analysis Results Between FF and FFPE Samples Signal Log Ratio: FFPE vs. FF Signal Log Ratios (P>.0001, N=815) 3 Unique qPCR-based Sample QC Method for Sample Qualification FF SLR Due to the expected wide range of quality and integrity for FFPE-derived RNA, there is a pressing need for tools that allow assessment of sample quality so researchers can determine the level of performance expected with the samples under study. The more tradi- 2 y = 1.2x - 0.042 R2= 0.92 1 0 -2.5 -2 -1.5 -1 -0.5 2 2.5 -3 Using the WT-Ovation FFPE System, total RNA isolated from lung cancer and normal FFPE samples (50 ng) as well as matching fresh frozen (FF) tissues (2 ng) were amplified, labeled and hybridized to Affymetrix GeneChip® HG-U133A Arrays. 815 genes were detected to be highly differentially expressed (signal log ratio, SLR) between the cancer and normal samples. Highly concordant results are demonstrated between FF and FFPE samples. Figure 5. RNA Quality Assessment of qPCR Assay A 60 R2 = 0.97 50 R2 = 0.75 40 R2 = 0.82 30 20 10 0 0 Briefly, the NuGEN FFPE sample QC method was developed after surveying a panel of amplicons from housekeeping genes across diverse tissues and comparing their expression level normalized to a reference RNA sample (HeLa RNA). Amplicons that correspond to portions of the beta actin and 1.5 FFPE SLR Tanney, A. and Kennedy, RD. (2010) Personalized Medicine, 7(2):205-211 2 4 6 8 10 12 gACTB delta Ct (FFPE - HeLa) B 60 R2 = 0.99 50 R2 = 0.79 40 R2 = 0.89 %P tional method of correlating Bioanalyzer trace or sample age with microarray expression analysis outcome has been shown to be ineffective. As a result, NuGEN has developed a new sample QC method immediately following reverse transcription and second-strand cDNA synthesis of RNA extracted from FFPE blocks that are predictive of the performance of the microarray assay in a given sample set. 1 -2 %P “ In the future, the use of molecular subtyping and companion diagnostics to guide patient care will become standard practice. FFPE remains the standard method for sample storage in routine clinical practice. The ability to work with FFPE samples will therefore be a key component to biomarker discovery, validation and, ultimately, delivery in the clinic. ” 0.5 -1 “ In our own experience, it has been possible to extract good quality transcriptional data from samples as old as 17 years using the Roche High Pure FFPE extraction kit and the NuGEN WT-Ovation FFPE system. ” 0 30 20 10 0 -5 0 5 10 15 18S delta Ct (FFPE - HeLa) Delta Cts between FFPE and control RNAs show high correlation to array performance (%P). Delta Cts for three different sample sets were calculated and plotted versus the %P for the corresponding arrays. A correlation for the gACTB amplicon is shown in Figure 5A and for the 18S rRNA amplicon in Figure 5B. Blue represents a 21-sample lymphoma set, green represents a 40-sample ovarian tumor set and yellow represents a 2-sample breast tumor set (with 5 replicates of each plotted). 4 F F P E R N A S a m p l e P reparat i o n R es o u r c e G u i d e 18S rRNA transcripts were selected because they exhibited stable expression pattern across multiple tissues and high correlation to array performance, as measured by %Present call on Affymetrix GeneChip U133 Arrays in the 63 FFPE RNAs tested (Figure 5). Detailed design and sequences of the amplicons are described in the NuGEN WT-Ovation FFPE v2 Technical Note #1 (download at www.nugeninc.com). This novel RNA sample quality assessment assay correlates qPCR results to the quality of microarray results generated with these samples. This in-process quality assessment assay, in conjunction with a pilot study approach described in the FFPE Validation Guidelines (NuGEN Bulletin 9, download at www.nugeninc.com), can predict the performance of a given set of FFPE samples, allowing researchers to utilize these valuable samples to their fullest potential. “ With several commercially available kits for nucleic acid extraction that appear to work equally well, and a robust RNA amplification kit such as the NuGEN Ovation FFPE System, we achieved functional, reproducible, and reliable microarray data from FFPE material from multiple tissues. ” Abdueva, D. et al (2010) J. Mol. Diagnostics, 12(4):409-417 Conclusions Expression profiling from FFPE samples has been recognized to play a pivotal role in discovery of biomarkers and development of molecular diagnostic tests for complex diseases such as cancer. To meet the challenges of working with this sample type that is both important for retrospective studies and standard practice in established pathology setting, NuGEN has developed a robust, reliable, and flexible sample preparation workflow. Since NuGEN has also established rigorous manufacturing processes (achieving both ISO 13485 and cGMP certification). These methods can be used to generate reproducible, biologically significant data for signature development and use in a clinical setting. These qualifications make it easier and faster for the diagnostic partners to integrate NuGEN reagents as a part of their Dx tests expediting the path to regulatory approval. Fast track your expression biomarker discovery and diagnostic test development by choosing NuGEN as your sample preparation partner. NuGEN WT-Ovation FFPE System Technical Report #2 – The WT-Ovation FFPE System Performance NuGEN Technologies Bulletin 9 – WT-Ovation FFPE System Validation Guidelines and the RNA Sample Quality Assessment Tool Pilot Study Selected Customer Publications (For a more complete list of publications and web seminars, visit www.nugeninc.com) Lassmann, S. et al (2009) J. Mol. Med, 87:211-224 Abdueva, D. et al (2010) J. Mol. Diagnostics, 12(4):409-417 Tanney, A. and Kennedy, RD. (2010) Personalized Medicine, 7(2):205-211 Customer Support NuGEN provides worldwide technical support. To learn more, call us at (888) 654 6544 or (650) 590 3600, or visit us on the web at www.nugeninc.com. Ordering Information Related References Part No. Product Name NuGEN Agilent Application Note 3400 WT-Ovation™ FFPE System V2 4200 Encore™ Biotin Module 4210 Encore™ BiotinIL Module 2000 WT-Ovation™ Exon Module NuGEN WT-Ovation FFPE System Technical Report #1 – RNA Sample Quality Assessment Test for the WTOvation FFPE System NuGEN Technologies, Inc. Headquarters USA Europe 201 Industrial Road, Suite 310 San Carlos, CA 94070 USA Toll Free Tel: 888.654.6544 Toll Free Fax: 888.296.6544 [email protected] [email protected] P.O. Box 149 6680 AC Bemmel The Netherlands Tel: +31-13-5780215 Fax: +31-13-5780216 [email protected] For our international distributors contact information, visit our website www.nugeninc.com ©2010 NuGEN Technologies, Inc. All rights reserved. The Ovation® and Applause™ families of products and methods are covered by U.S. Patent Nos. 6,692,918, 6,251,639, 6,946,251 and 7,354,717, and other issued and pending patents in the U.S. and other countries. NuGEN, the NuGEN logo, Ovation, SPIA, Ribo-SPIA, WT-Ovation, Applause, Encore, Prelude and Imagine More From Less are trademarks or registered trademarks of NuGEN Technologies, Inc. Other marks appearing in these materials are marks of their respective owners. For research use only. M01172 5
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