Exome Sequencing as a Discovery and Diagnostic Tool - Next Generation Sequencing Technologies in Medical Genetics - page 70

While family-based analysis designs allow for disease gene discoveries, the data
from these efforts provides the name of the gene and better molecular description of
the human exome by contributing to the frequency information of known and novel
SNPs. In addition, the increase in sequencing data output (depth of coverage) has
increased the sequencing accuracy and improvement of exome enrichment methods
has opened the opportunity to use the exome as a clinical diagnostic tool and the
clinical exome test is now being offered by several clinical laboratories. To continue
the data curation, bioinformatic procedures include reduction or correction of
sequencing errors by intra- and inter-sample comparisons.
A major challenge in WES is narrowing down the number of variants to a
manageable potentially causative gene list. The exome analysis pipeline can be used
in research to discover new genes associated with disease as well as its clinical appli-
cation to medical genetics. Previous chapters have covered the sequencing (Chap. 2 )

and enrichment technologies (Chap. 3 ) in depth; thus, the focus here is to summarize
the reported applications of WES to research and the molecular diagnostic fi elds. In
addition, we briefl y describe the bioinformatic procedures that are performed to iden-
tify the potential causative genes and tools used in the interpretation of variants.

8.2 Classic Gene Discovery Approaches and Limitations

In the past, traditional linkage studies have been used to identify causal variants or
mutation for Mendelian (single gene or monogenic) disorders (Botstein and Risch
2003 ). Examples of Mendelian disorders include Freeman-Sheldon syndrome,
Fowler syndrome, autosomal-dominant amyotrophic lateral sclerosis, and hyper-
cholesterolemia (Ng et al. 2009 ; Lalonde et al. 2010 ; Johnson et al. 2010a ; Rios
et al. 2010 ). Thus far, causal variants for approximately 3,000 Mendelian disorders
have been discovered and are cataloged by the Online Mendelian Inheritance in
Man (OMIM; http://www.ncbi.nlm.nih.gov/omim ).
Due to the perfect segregation (high penetrance), genome-wide linkage studies
followed by positional cloning have also identifi ed causal variants of Mendelian
disorders. In principle, genome-wide linkage studies assume no prior hypothesis
because the genetic markers will evenly cover the whole genome. Only a limited
number of recombination events are observed within a family or pedigree. The
genetic markers will reveal genomic regions which co-segregated in affected indi-
viduals. This could then be followed up by positional cloning to identify the causal
variants and candidate genes within the genomic regions, which can be up to tens of
centimorgans (cM). On the contrary, candidate gene-based linkage studies require a
prior hypothesis and are not designed to reveal novel genomic regions for Mendelian
disorders (Botstein and Risch 2003 ).
Classical linkage studies have been the main approach for discovering causal
variants of Mendelian disorders; however, not all of these disorders are amendable
to this study design. Homozygosity mapping, on the other hand, is a more powerful
and effective approach to study recessive disorders in consanguineous families
(Harville et al. 2010 ; Collin et al. 2010 ; Pang et al. 2010 ; Iseri et al. 2010 ). However,