Exome Sequencing as a Discovery and Diagnostic Tool - Next Generation Sequencing Technologies in Medical Genetics - page 71

the causal variants remain elusive for many disorders that cannot use these two
approaches. These disorders include (1) “extremely rare” Mendelian disorders,
where only a small number of cases are available, (2) unrelated cases from different
families, and (3) sporadic cases due to de novo variants (Ku et al. 2011 ). However,
WES now offers new opportunities to study extremely rare disorders and sporadic
cases as well as complex diseases.

8.3 Exome Sequencing Necessity for Gene Discovery

The linkage study design is unsuitable for the de novo variants and extremely rare
Mendelian disorders because of the diffi culty in collection of an adequate number of
affected individuals (of multigenerational pedigree) and families for a statistically
powerful study (Ku et al. 2011 ). For example, the candidate gene for Kabuki syn-
drome remained unknown until recently because it is an extremely rare (incidence 1
in 32,000) autosomal-dominant Mendelian disorder (Ng et al. 2010a ). To address
these issues, WES was performed on ten individuals affected with Kabuki syndrome
and causal variants were found in MLL2 (Ng et al. 2010a ). Similarly, Schinzel-
Giedion syndrome cases are mostly sporadic. Through WES de novo causal variants
were identifi ed in SETBP1 in four affected individuals with this syndrome (Hoischen
et al. 2010 ). Moreover, the causative variants of Miller syndrome, an extremely rare
disorder, were recently reported in DHODH (Ng et al. 2010b ). Collectively, these
studies have demonstrated the advantages of WES over the linkage study design in
situations where a small number of unrelated samples or sporadic cases are available.
In contrast to linkage study designs, WES is more robust for disorders with pre-
sumably genetic and phenotypic heterogeneity (Ku et al. 2011 ). These problems are
well depicted in Kabuki syndrome which is likely a genetically heterogeneous dis-
order because not all the affected individuals have causal variants in the single can-
didate gene ( MLL2 ; Ng et al. 2010a ). However, causal variants in other genes have
not been identifi ed. By accounting for the genetic and phenotypic heterogeneity, the
investigators successfully identifi ed causal variants in MLL2 in a subset of individu-
als. WES has now become technically feasible and more cost-effective due to the
recent advances in high-throughput sequence capture methods and NGS technolo-
gies, which have offered new opportunities for Mendelian disorder research.

8.4 Exome Sequencing Gene Discovery Applications

8.4.1 Sequencing of Unrelated Individuals

The WES approach has been clearly demonstrated to be useful for identifi cation of
causative variants of extremely rare Mendelian disorders, especially for de novo
variants that were not addressed by linkage studies, by sequencing the exomes of