Feng, Xiaodong_ Xie, Hong-Guang - Applying pharmacogenomics in therapeutics-CRC Press (2016)

42 Applying Pharmacogenomics in Therapeutics
are attached to a solid surface by a covalent bond via epoxy-silane, amino-silane,
lysine, polyacrylamide, or other chemical matrix. The solid surface can be a glass,
plastic, or silicon biochip (Affymetrix) or microscopic beads (Illumina).
The biological principle behind microarrays is the property of complementation
between the probe and the nucleic acid target. More complementary base pairs
in the target sequence mean stronger hydrogen binding between the probe and the
target, while the presence of mismatches reduces this binding. Thus, only strongly
paired targets will remain hybridized to their probes after several rounds of washing
from a mild to stringent condition. The total strength of signals generated from
fluorescence-labeled targets is determined by the amount of targets bound to the
probes on a given spot.
Since an array can contain tens of thousands of different microscopic probes,
a microarray experiment can accomplish many genetic tests in parallel and therefore
dramatically expand the scope of investigation. The Affymetrix Genome-Wide
Human SNP Array series serves as a good representative for the application of
microarray in detection of whole-genome SNPs and CNVs. The latest version (6.0)
of this array features 1.8 million genetic markers and has demonstrated impressive
performance in detecting genetic variations (www.affymetrix.com). Therefore, such
microarrays and similar ones have enabled GWASs with a larger sample size in the
initial screen and replication phases, and significantly increased the overall genetic
power of these studies.
NGS Technology
Microarray-based technology has been remarkably successful at high-throughput
detection of genetic variations and expression profiles. However, both sensitivity
and specificity are limited with microarrays. More importantly, microarrays are
restricted to known genetic annotations with little ability to detect novel genetic
variations.
The demand for sequencing technologies that are capable of delivering faster, less
expensive, and massive genomic information has led to the invention of NGS technologies.
NGS technologies can generate millions or billions of sequences (Church
2006; Schuster 2008) at a much faster speed and at an extremely low cost compared
to the standard Sanger sequencing method, which underlies the decoding of
the first human genome (Lander et al. 2001) that costs about US$3 billion (http://
www.genome.gov/11006943). The first example of NGS was the massively parallel
signature sequencing technology developed over a decade ago (Brenner et al. 2000).
The polony sequencing method (Shendure et al. 2005) developed in the laboratory
of George M. Church was a more applicable, early NGS system. This method combines
emulsion PCR (a type of digital PCR), automated microscope system, and
ligation-based sequencing chemistry (sequence by ligation) and was used to sequence
a full genome of the Escherichia coli bacteria at an accuracy of >99.99% and a cost
approximately one-ninth of that of the Sanger method (Shendure et al. 2005). The
same strategy was used in a meta-genomic study that sequenced the whole genomes
of single bacterial cells and provided critical tools for systematic characterization of
genome diversity in the biosphere (Zhang et al. 2006).