PerkinElmer eBook - Next-Gen Sequencing - 11

Next-Gen Sequencing * The Next Next Thing in Sequencing

Dr. Sachidanandam says that his group has
only scratched the surface of what MSeek might
eventually reveal: "Although a current limitation
is that MSeek requires at least 4 μg of intact total
DNA, we expect that many applications will follow,
not just in therapeutics, but also in areas such as
forensics."
Isolating Pure Tumor Cell
Populations from FFPE
Molecular analysis of tumors is often problematic
because of their heterogeneity, according to
Raimo Tanzi, Ph.D., chief commercial officer, Silicon
Biosystems. "The introduction of digital analytical
methods, such as NGS and digital PCR, has helped
tease out minority populations," Dr. Tanzi points out.
"Ultimately, however, only a homogeneous sample
provides for the clearest interpretation."
To address this issue, Silicon Biosystems applied its
new digital technology, called the DEPArray™, to the
isolation and sorting of pure populations of cells
from a heterogeneous tumor sample. "This semi-

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conductor-based technology uses dielectrophoresis
(DEP) to bind single cells to single microelectrodes
on a CMOS chip," explains Dr. Tanzi. "It leverages the
absolute precision of semiconductors for sorting
cells in absolute purity."
"FFPE samples are initially transformed into cell
suspensions, stained with appropriate markers, and
then loaded onto a single-use microfluidic cartridge,"
Dr. Tanzi continues. "Once inside the flowcell, each
single cell is first captured by one of the 30,000
CMOS chip-controlled electrodes (that is, a DEP
cage) and then scanned with a microscope to
obtain fluorescent and bright field images.
"Based on these images, each cell is allocated in a
specific category (tumor, stromal, etc.). Eventually,
all cells belonging to one same category are delivered in 100% purity, moving via software control
of the corresponding electrodes toward a recovery
chamber in the chip."
The new technology can isolate pools of tens
to hundreds of pure cells available for up to

whole-genome analysis. Pools may include
epithelial-mesenchymal transition cells, tumorinfiltrating lymphocytes, and stromal cells.
"The DEPArray is the first automated technology
that can isolate 100% pure populations of cells from
heterogeneous FFPE samples," asserts Dr. Tanzi.
"This provides many advantages, some of which are
particularly relevant for cancer research, such as
uniformity of samples, clear identification of copy
number variants, and loss of heterozygosity.
Another possible use is for performing genetic
analysis of very small samples such as fine needle
aspiration samples and tumors with low cellularity."
Clearly, investigators are making exciting progress
in the NGS field. The future should feature faster,
more precise, and novel technologies. n

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PerkinElmer eBook - Next-Gen Sequencing

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