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

Applying Pharmacogenomics in Drug Discovery and Development
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but also increases the likelihood of identifying novel targets. It can also enhance
our understanding of disease pathophysiology through identification of previously
unknown mediators. Evidence supports this: the genomic profiling approach has
led to major advances in drug target identification for Crohn disease and rheumatoid
arthritis by allowing for the identification and delineation of the inflammatory and
autoimmune pathways that drive these diseases. 10,11 Disadvantages of genomic profiling
include increased cost of analysis compared to target gene analysis and, due
to generation of very large data sets, the need for subsequent complex biostatistical
and bioinformatic analyses. 9 In addition, generation of false positives is of concern
due to the large number of genes being surveyed.
Similar technologies can be employed for both target gene and genomic profiling
approaches, and these technologies can be used to assess either DNA or RNA
samples. The former are much easier to collect and work with; however, the latter
are often more relevant to drug target discovery because they provide information
regarding genes that are being actively expressed and are therefore more likely to be
causative in the disease process. Quantitative real-time polymerase chain reaction
(qRT-PCR) and microarray can be used to survey the presence of and/or expression
levels of genetic alterations in both small and large formats (between one gene and
thousands of genes assessed). Sequencing can also be used. Again, anywhere from
a single gene to an entire genome may be sequenced. The benefit of sequencing
versus using qRT-PCR or microarray is that many different types of genetic alterations
can be detected simultaneously, including single nucleotide polymorphisms
(SNPs), copy-number variants (CNVs), and structural variants (SVs), and that sensitivity
of detection is higher. 12,13 Disadvantages are increased costs and the technical
challenges posed by a generation of such large and complex data sets. Genomewide
association studies (GWASs) and next-generation sequencing (NGS) have been
widely employed for genomic profiling analyses. GWASs typically use microarray
technology and screen samples for the presence of common genetic variants (genetic
alterations, most often SNPs, that occur within >1% of the population). While the
entire genome is not interrogated by GWASs, thousands of representative SNPs (Tag
SNPs) are assessed, and this strategy has enabled the identification of multiple novel
potential drug targets. 14 For example, GWASs identified the complement factor H
(CFH) allele as being associated with age-related macular degeneration (AMD). 15
As a result of these studies, several complementary component inhibitors are being
developed to treat AMD patients. 16,17 The rapidly decreasing cost of sequencing
analyses has allowed NGS to play an important role in drug target discovery. For
example, NGS analyses identified DHODH, a gene that encodes an enzyme needed
for de novo pyrimidine biosynthesis, as playing a role in Miller syndrome, a rare
Mendelian disorder whose cause is poorly understood. 18 An overview of the genomic
profiling methodologies that can be employed to identify different genetic alterations
is shown in Figure 4.1. 19
Ideally, patient specimens (biospecimens) should be used for genomic-based
identification of drug targets; however, in some cases, panels of immortalized cell
lines that are derived from patient samples are used for screening purposes. Either
way, samples that originate from patients with, versus without, the disease of interest
need to be assessed. A problem with the cell line approach is that cell lines