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

100 Applying Pharmacogenomics in Therapeutics
which is also known as Philadelphia chromosome (Nowell and Hungerford 1960).
Translocations can be balanced (in an even exchange of chromosome materials, with
no extra or missing genes, and ideally full functionality) or unbalanced (where the
exchange of chromosome materials is unequal, resulting in extra or missing genes).
Translocation can be detected by chromosome study (also known as standard cytogenetics
or a karyotype) of the affected cells or by fluorescence in situ hybridization
(FISH) if probes are available.
Genes may also be amplified or overexpressed. One example is HER2 (human
epidermal growth factor receptor 2) amplification in breast cancer (Owens et al.
2004; Slamon et al. 1987; Yaziji et al. 2004). Common methods of detecting gene
amplification include reverse transcription-polymerase chain reaction (RT-PCR),
FISH, and SNP assay using next-generation sequencing (NGS) technologies.
A mutation, small deletion, or duplication can be detected by direct sequencing.
Two most widely used sequencing technologies in genetic testing laboratory are
Sanger sequencing and NGS. Sanger sequencing was developed by Frederick Sanger
and colleagues in 1977, and it has become the classic DNA sequencing method (Sanger
et al. 1977a, 1977b). This sequencing method is based on the selective incorporation
of chain-terminating dideoxynucleotide (ddATP, ddGTP, ddCTP, or ddTTP) during
in vitro DNA replication by DNA polymerase. Compared to NGS and other more
recently developed sequencing technologies, Sanger sequencing is time consuming
and expensive, but it is highly accurate. In contrast, the NGS technologies allow massive
parallel sequencing of many DNA strands simultaneously; therefore they are
faster and cheaper than Sanger sequencing. But the length of reading sequence is
shorter, usually less than 300-bp compared to more than 500-bp by Sanger sequencing.
However, NGS needs significantly less DNA and is more accurate and reliable.
Larger deletion and duplication can be detected by FISH or traditional cytogenetics
(chromosome study or karyotyping). FISH can only detect deletion or duplication
specifically targeted by the probe used, and the deletion or duplication is required
to be larger than the probe size, usually lager than 100 kb. FISH can also be used
to detect gene fusion, gene amplification, chromosome translocation, and inversion.
Standard cytogenetic study (chromosome analysis) usually cannot detect deletions
<5 Mb. Chromosomal microarray analysis (CMA) or comparative genomic hybridization
(CGH) microarray testing is a technology that compares patient DNA with
reference DNA from normal individuals to detect copy-number variation (CNV) at
higher resolution than G-band chromosome analysis. Dependent on the purpose of
genetic testing, these technologies are often used in combination to provide the best
testing results.
PHARMACOKINETICS
Interindividual differences in genetic makeup can affect variability in drug responses
at both pharmacokinetic and pharmacodynamic levels. Pharmacokinetics is the study
of the absorption, distribution, metabolism, and excretion as well as transport of
the drug. Pharmacodynamics studies the biochemical and physiological effects of
the drug. Drug metabolism can be divided into three phases. Phase I metabolism
often refers to oxidation, hydroxylation, and hydrolysis of the drug in the liver,