Low Level Somatic Variant Detection by Sanger Sequencing of FFPE Samples for Precision Oncology Research
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This document describes a method for detecting low-level somatic variants in FFPE samples using Sanger sequencing and Minor Variant Finder software. It validates the method by detecting variants in 35 colon cancer FFPE samples as low as 5% allele frequency using 1 ng or less DNA input per reaction. The method provides a low-cost and fast turnaround alternative to NGS for precision oncology research applications requiring analysis of a limited number of clinically relevant targets from FFPE samples.
Low Level Somatic Variant Detection by Sanger Sequencing of FFPE Samples for Precision Oncology Research
- 1. Low level somatic variant detection by Sanger sequencing of FFPE samples for precision oncology research Arpad Gerstner, Edgar Schreiber, Steve Jackson and Kamini Varma © 2016 Thermo Fisher Scientific, Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. 180 Oyster Point Blvd. South San Francisco, CA 94080 TP53 c.517G>T in FFPE 2182 FORWARD: 8.2% REVERSE: 8.4% FORWARD REVERSE C/A C Control sample Test sample Test sample (NSS) 35 FFPE samples from colon cancer biopsies Effect of low DNA input amount on minor variant detection The recommended input amount with this workflow is 1 ng/reaction but the minor variant of interest could still be detected even at as low as 0.1 ng DNA. Comparison of minor variants detected using NGS vs. Sanger sequencing analyzed by MVF software VAFs of 35 FFPE samples from colon cancer biopsies were confirmed using the extended RAS panel for Sanger sequencing and VAFs were sorted from lowest (minor variant at 3.8%) to highest (70%). FFPE sample preparation, DNA extraction and the entire Sanger Sequencing workflow and data analysis using MVF was validated by OmniSeq LLC, Buffalo, NY, USA. Electropherograms generated by Minor Variant Finder Software Minor variant c.517G>T was detected in FFPE sample 2182 using amplicon 836916 from the TP53 panel. The variant was detected at 8.2% in the forward and 8.4% in the reverse direction by Minor Variant Finder software compared to the primary base C (or G in the corresponding reverse reaction). C (or G) was detected in the control sample at the allelic ratio of 100% (bottom electropherograms). Minor variant A in the forward reaction (similarly, the corresponding T in the reverse reaction) of the test specimen would have been easily missed by visual inspection of the electropherograms of the test sample (middle electropherograms). However, the Minor Variant Finder algorithm is able to identify the A (or T) allele as a minor variant candidate as shown in the algorithm-generated electropherograms (top) after noise subtraction and submission (NSS). PCR and sequencing reactions were performed using the Applied Biosystems™ BigDye™ Direct Cycle Sequencing Kit and a Veriti™ Thermal Cycler. Sequencing reactions were cleaned up using the Applied Biosystems™ BigDye XTerminator™ Purification Kit. Sequencing reactions were electrophoresed on the Applied Biosystems™ 3500xL Genetic Analyzer. FFPE test samples were referenced to DNA control CEPH 1347-02 sequenced in both forward and reverse directions, and processed under similar conditions throughout the entire workflow on the same Applied Biosystems™ MicroAmp™ Fast Optical 96-Well Reaction Plate sealed with MicroAmp™ Clear Adhesive Film. Pan-caner panel confirming NGS allele frequencies FFPE samples were used to screen for 14 variants represented by 10 amplicons. Allelic ratios calculated by Minor Variant Finder Software were in line with variant allele frequencies found by NGS. Highlighted cells represent variants where the variant allele frequency (VAF) was significantly different between forward and reverse Sanger sequencing reactions. This is likely due to local sequence context– specific nucleotide incorporation differences. Effect of low DNA input amount on allele frequency across different FFPE samples ABSTRACT DNA sequence variants play an important role in the initiation and progression of many different cancer types. The detection of germline variants at a fixed ratio by gold-standard Sanger sequencing has been well established; however, the detection of somatic mutations, especially in heterogeneous tumor samples where variants may be present at a lower level, has been more challenging. Minor Variant Finder Software (MVF) enables calling of low- frequency variants at a detection level as low as 5% using Sanger sequencing. We have developed gene-specific Sanger sequencing panels covering the entire coding region (all exons) of specific genes (e.g., TP53, KRAS, and NRAS) implicated in tumorigenesis. We initially determined variants of TP53 and KRAS from lung tumor FFPE samples by NGS using the Ion PGM™ System. We confirmed the identity and minor allele frequency of these variants by gene-specific Sanger sequencing panels analyzed by MVF. To demonstrate the robustness and flexibility of using Sanger sequencing for oncology research, we also included variants across many different solid tumor types in a pan-cancer panel. We tested this workflow with lower amounts of DNA input (10ng, 3ng, 1ng, 0.1ng). Additionally, we have built an extended RAS panel including eight amplicons covering the most important codons (12-13, 59-61, 117 and 146) of KRAS and NRAS genes. The entire workflow and data analysis using MVF was validated on thirty-five FFPE samples derived from colon cancer biopsies by OmniSeq LLC, Buffalo, NY. For Research Use only – Not for use in diagnostic procedures CONCLUSIONS Sanger sequencing with Minor Variant Finder software is not only the gold standard for confirmation of minor variants detected by NGS, but it is also an attractive first line screening choice when working with a limited number of targets. One of the ideal applications is precision oncology research. Depending on the tumor type, often only a few clinically relevant mutations required to be screened (e.g. extended RAS panel for colon cancer) and limited amount of DNA available from FFPE samples. This robust and simple workflow can detect as little as 5% of a minor variant in an FFPE sample using 1 ng (or less) DNA per reaction and also offers fast turnaround time (~4 hours including data analysis) at a low cost per sample. Comparison of minor variants detected using NGS vs. Sanger sequencing Minor variants originally detected in the Colon And Lung Cancer Panel and the Oncomine NGS panel by PGM Sequencer were confirmed by Sanger sequencing from both Forward and Reverse directions using Minor Variant Finder software (MVF). A simple and fast workflow for tumor genetic analysis The overall sequencing quality and the allele ratios appear to be more variable for reactions with starting materials lower than 1 ng DNA, but the minor variants of interest were still detectable even with DNA input as low as 0.1 ng.