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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.

52
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...
53
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 workow.
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.

54
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
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