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Tumor Genomic Proling Reports from Different Vendors: A...
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CLINICAL NEXT­GENERATION SEQUENCING
3
FOR SOMATIC MUTATION DETECTION- ADVANCEMENTS AND COMMERCIALIZATION STRATEGIES
Andrew Hesse, Christopher Chen, and Honey V. Reddi
Transgenomic, Inc, 5 Science Park, New Haven, CT, USA 06477.
ABSTRACT
Advancements in next-generation sequencing, variant-calling software, and mutation enrichment are facilitating the detection of rare genetic variants. In doing so, these methods have enabled identification of somatic disease, and more specifically cancer, representing as little as 0.01% of bulk genetic material. This improved sensitivity reduces false negative results, and in cancer, allows earlier detection. Such early detection will greatly improve monitoring and treatment of these diseases, especially in the context of liquid biopsies. This review aims to encapsulate the growing spectrum of technology and software currently being utilized to improve the sensitivity of somatic variant detection. Furthermore, industry adoption of these techniques will be summarized.
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Keywords: Somatic mutation; Sequencing methods; Liquid biopsy
Advances in Molecular Diagnostics
BACKGROUND
Unlike germline mutations, which are present in all cells of the body, somatic mutations are mosaic [1] and therefore can be present in very low number relative to healthy cells [2,3]. This makes detection of these rare variants problematic by increasing the diagnostic cost and complexity, as well as presenting new technological challenges. Much of the analytical difficulty is caused by the innate error rate of DNA sequencing methods. These errors behave as sequencing noise, making it difficult to discriminate between genuine rare mutations and mistakes made during in vitro DNA amplification. Next-generation sequencing (NGS) methods, like those run on Illumina and Ion Torrent platforms, are a significant improvement over 1st generation technology, but still cannot easily detect mutations with allelic fractions below 10% [4]. Similarly, false negative results of variants with low allelic fractions pose a problem for clinical laboratories by limiting diagnostic efficacy. In this regard, current sequencing methods show an improvement over the previous gold standard, Sanger sequencing, which has a limit of detection (LOD) of 20% [5] for non-confirmatory testing. The other major problem with current sequencing methods, perhaps the most concerning to the patient, is that solid tissue biopsies are needed to genotype cancer-specific tissue. However, increasing the sensitivity of these technologies and implementing newer, non-invasive enrichment techniques will open doors in clinical molecular diagnostics to safe and early disease screening and monitoring.
An emerging solution to combat both the sensitivity limitations of NGS and the invasiveness of acquiring solid tumor samples is enriching liquid biopsies. Liquid biopsies are blood samples from which either circulating tumor cells (CTC) or circulating cell-free DNA (cfDNA) from tumors can be isolated. Respectively, these are either cancerous cells themselves or DNA from cancerous cells that have been shed into circulation [6]. Currently, the most viable sample type for use with liquid biopsies is blood plasma. It is important to have the plasma isolated as early as possible after the blood draw to mitigate further dilution of mutant
Clinical Next-Generation Sequencing for Somatic Mutation Detection...
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DNA by wild-type DNA from continued lysis and breakdown of healthy blood cells [7]. The ability to readily obtain minimally invasive samples without needing to know tumor location makes liquid biopsies attractive for early disease detection. After detection, these methods can be used to track disease regression or recurrence following treatment [8]. Existing sequencing methods have limits of detection above 10% tumor cells, which in the context of liquid biopsies corresponds to severe disease [6]. Reducing the limit of disease detection would allow clinicians to identify and treat earlier disease states.
Figure 1: Overview of workow.
Pathologists can readily score sections from biopsies to identify
samples with greater than 10% tumor burden [9], but the emerging eld
of liquid biopsies will enable far more sensitive detection methods. To lower the limit of mutation detection, researchers have developed ways to simplify extraction of liquid biopsies, improve sequencing technology, enrich for mutant populations, and enhance bioinformatics software (Figure 1). This review will focus on the latest developments within each of these methods and discuss the utilization of combinations of technologies and strategies for commercialization.
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Advances in Molecular Diagnostics
SEQUENCING METHODS
Whole exome sequencing will typically identify more than 20,000 variants [10], but most of these are clinically insignificant polymorphisms, non­pathogenic missense mutations or false positive calls resulting from sequencing errors. The simplest way to sift through the noise of NGS data is to perform deeper sequencing. This method of adding coverage to increase base call reliability was verified by Izawa et al. in a 2012 study which demonstrated that a variant with a 1% allele fraction can be detected with statistical confidence at 700x coverage comprised of 350 reads from each strand [11]. The drawback of deep sequencing is the increase in cost. A most practical way to increase coverage is to focus sequencing on a small panel of genes relevant to the disease state rather than whole genome or exome. Accordingly, for Cancer, many companies are beginning to introduce panels tailored to a “broad spectrum” common mutation cancer panel or a typespecific cancer. Another simple way to reduce the noise from NGS is to perform “paired tumor-normal” sequencing. This technique involves orthogonally sequencing (independent, simultaneous runs of paired specimens) somatic and normal tissue sample from whole blood. Common experimental designs produce independent sequence files that are imported into analysis software that compare the germline and somatic data to eliminate non-specific variants [12]. Further refinement is accomplished with customized bioinformatics pipelines and confirmation of suspect mutations on an alternate technology. Illumina and Ion Torrent are the current market leaders in NGS platforms, having been largely adopted by industry due to lower error rates compared to Pacific Biosciences and Oxford Nanopore, making them more suitable for somatic mutation sequencing.
Illumina
Currently, Illumina is the most widely used NGS technology with 74% market share (www.marketsandmarkets.com/Market-Reports/ next­generation-sequencing-ngs-technologies-market-546.html). Compared to other available sequencing technology, Illumina offers the largest data output, the lowest cost per-base and relatively fast turn-around time. Illumina products amplify fragments by clonal bridge amplification and sequence by synthesis using reversible dye terminators. Three “off the
Clinical Next-Generation Sequencing for Somatic Mutation Detection...
55
shelf ” somatic cancer panels are available: the TruSight Tumor Panel™,
the TruSight Myeloid PanelTM, and the TruSeq Amplicon Cancer
Panel™. The TruSight Tumor Panel consists of 26 genes spanning 21kb
of sequence and achieves a minimum coverage of 1,000x per amplicon at 7,000X mean coverage (illumina/ datasheet.pdf). The TruSeq Amplicon Cancer Panel is composed of 48 genes spanning more than 35kb of sequence with an average coverage of 1,000x per run [13]. The TruSight Myeloid PanelTM covers approximately 141kb from 15 full genes (exons only) and hotspots from 39 additional genes. In this panel, sequencing depth is 500X for 95% of amplicons with an LOD as low as 3% (illumina_trusight_tumor.pdf).
Illumina recently released the NextSeq 500 v2. This kit is compatible with the TruSight Myeloid and TruSeq Ampicon Cancer Panels run on NextSeq sequencers. It improves upon the previous sequencing reagents and clustering chemistry with error rates in line with those seen on MiSeq or HiSeq.
Thermo Fisher
Ion Torrent products amplify DNA fragments by emulsion PCR, and sequencing is performed directly on a silicon chip that detects changes in pH from the release of a proton during DNA polymerization. The Personal Genome Machine (PGM) and the Ion Proton exhibit the quickest run time, the former in little as 3 hours [14] and yield roughly 1-2 GB and 10-15 GB of data per run, respectively. Ion Torrent has recently released several cancer panels including the 50-gene Ampliseq Hotspot Cancer Panel v2 which is an update of the previous Ampliseq panel adding an additional 4 genes and about 2000 COSMIC mutations (2,800 total). This assay has been validated using various carcinomas, gastrointestinal stromal tumors, melanoma, and brain tumors [13,15]. The panel is composed of a relatively small panel (less than 13.5 kb of sequence), allowing for scalable runs generating as much as 5,000x coverage using Ion Torrent’s 316 chip (www.edgebio. com/ampliseq-cancer-panel). Using a smaller “hotspot” panel on the Ion Torrent further increases the speed of sequencing and
allows for faster reporting. The AmpliSeq™ Comprehensive Cancer
Panel is a larger panel that covers 409 genes and, when coupled with the Ion Proton sequencer, generates more than 10GB of data. The clinical utility of the Ion Proton and AmpliSeq Comprehensive Cancer Panel was
56
Advances in Molecular Diagnostics
demonstrated in a study by Singh et al that utilized these tools to discover somatic variation in multiple cancer types from formalin-fixed paraffin­embedded biopsy samples. Finally, there is a more specialized AmpliSeq Colon and Lung Cancer Research Panel v2. This panel covers hotspots from 24 genes and was validated on 155 unique FFPE samples from the OncoNetwork Consortium.
Ion Torrent recently upgraded their sequencing chemistry for the
PGM with the launch of the Hi-Q™ sequencing kit. In developing the
Hi-Q kits, mutated polymerases were screened to identify a novel enzyme that reduces the false positives caused by insertion/deletion polymerase errors by 90%. Furthermore, the new chemistry supports 400 base pair read lengths. Ion Torrent technology offers lower cost equipment and faster turnaround times than Illumina, but more expensive sequencing runs. Comparison of the Illumina and Thermo Fisher commercial cancer sequencing kits and technologies is listed in Tables 1 and 2.
Table 1: Commercial sequencing Kit comparison.
*Up to 96 samples pooled using v3 kits (mean coverage remains 1000X) **AmpliSeq CP contains the following additional genes EZH2 and IDH2
compared to TruSeq CP