Biomedical Engineering Reference
In-Depth Information
Proton (now part of Life Technologies), fall under the rubric of a single paradigm
termed cyclic array sequencing (Chap. 2 ; Fig. 1.1 ; Metzker 2010 ). Cyclic array
platforms achieve low costs by “massively parallel” sequencing, meaning that the
number of sequence reads from a single experiment is vastly greater than the 96
obtained with modern capillary electrophoresis-based Sanger sequencers. At pres-
ent this very high throughput is achieved with substantial sacrifi ces in length and
accuracy of the individual reads when compared to Sanger sequencing. Nonetheless,
assemblies of such data can be highly accurate because of the high degree of
sequence coverage obtainable. They are most readily applied to sequencing, in
which sequence data is aligned with a reference genome sequence in order to look
for differences from that reference. A few examples of enrichment and NGS
sequencing technologies are discussed in Chaps. 2 and 3 , respectively. Other
technologies are under development and all of these methods will undoubtedly
continue to improve.
Within the last 5 years, high-throughput sequencing technologies have success-
fully identifi ed mutations in novel genes for a number of genetic conditions, includ-
ing Sensenbrenner syndrome, Kabuki syndrome, and Miller syndrome (Fig. 1.1 ;
Gilissen et al. 2010 ; Ng et al. 2010 ). NGS facilitates target sequencing for rapid,
accurate, and lower cost diagnostic applications. However, with several target
enrichment strategies, including microarray-based capture, in-solution capture, and
polymerase chain reaction (PCR)-based amplifi cation (Albert et al. 2007 ; Gnirke
et al. 2009 ; Hodges et al. 2007 , 2009 ; Kirkness 2009 ; Nikolaev et al. 2009 ; Okou
et al. 2007 ; Tewhey et al. 2009 ), and NGS sequencing platforms, selection and vali-
dation of the technologies becomes crucial for clinical applications (Metzker 2010 ;
Voelkerding et al. 2009 ). In the last 2 years, a number of clinical NGS panels have
been developed for mutation detection of genes in a number of phenotypic and/or
genetically heterogeneous disorders including muscular dystrophies and hearing
loss (Schrauwen et al. 2013 ; Sivakumaran et al. 2013 ; Valencia et al. 2012 , 2013 ).
Moreover, three large-scale clinical studies were published showing results that
NGS of maternal DNA of pregnant women is a powerful molecular diagnostic tool
for diagnosis of fetal aneuploidies (Chiu et al. 2011 ; Ehrich et al. 2011 ; Palomaki
et al. 2011 ). The clinical applications are discussed in more detail in Part II, Chaps.
4 , 5 , 6, 7 , 8 , and 9 , of this topic.
1.7
Future Trends
In the coming years, molecular diagnostics will continue to be of critical importance
to public health worldwide. Molecular genetic testing will facilitate the detection
and characterization of disease, as well as monitoring of drug response, and will
assist in the identifi cation of genetic modifi ers and disease susceptibility. Massively
parallel methods are likely to dominate clinical high-throughput sequencing appli-
cations for the next few years. However, a variety of other approaches are being
investigated that may eventually be developed into practical methods (Chan 2005 ).
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