Application of Next-Generation–Sequencing to the Diagnosis of Genetic Disorders: A Brief Overview - Next Generation Sequencing Technologies in Medical Genetics - page 34

4.3 Colon Cancer

Hereditary colon cancers are caused by a number of genes and have overlapping
clinical features (Pritchard et al. 2012 ). Lynch syndrome, also called hereditary non-
polyposis colorectal cancer, is caused by defects in mismatch repair (MMR) genes,
namely, MLH1 , MSH2 , MSH6 , PMS2 , and EPCAM . Mutations in these genes are
inherited in an autosomal dominant manner. Similarly, mutations in APC cause
autosomal dominant familial adenomatous polyposis syndrome. Additionally,
mutations in APC can also cause Gardner's syndrome, Turcots syndrome, and atten-
uated familial adenomatous polyposis. MUTYH mutations are the cause of autoso-
mal recessive MUTYH -associated polyposis syndrome. Although a number of
clinical guidelines have been proposed to differentiate these conditions, it can still
be very diffi cult to get an accurate and early diagnosis. The most common diagnos-
tic problem lies in differentiating attenuated familial adenomatous polyposis and
Lynch syndrome. The most common diagnostic approach to Lynch syndrome starts
with tumor-based screening tests. This includes testing for microsatellite instability
(MSI) and using immunohistochemistry to check for protein expression. However,
these tests have false negatives. No tumor-based testing is available for polyposis
syndromes.
An NGS panel, ColoSeq, is being offered clinically for such clinical scenarios
where a clear diagnosis of hereditary colon cancer cannot be established (Pritchard
et al. 2012 ). Technically, targeted capture and NGS on the Illumina HiSeq 2000
instrument was performed. The test assesses for single nucleotide and deletion/
duplication analysis of mutations in MLH1 , MSH2 , MSH6 , PMS2 , EPCAM , APC ,
and MUTYH . In blinded specimens and colon cancer cell lines with defi ned muta-
tions, ColoSeq correctly identifi ed 28/28 (100 %) pathogenic mutations. This panel
now includes additional genes such as CDH1 , PTEN , STK11 , TP53 , SMAD4 , and
BMPR1A . The increase in gene number demonstrates the fl exibility with respect to
panel size and such panel expansion is necessary as genes become newly associated
with diseases. Moreover, to increase the clinical sensitivity of this panel, deletion/
duplication analysis of individual genes has been added. ColoSeq offers a powerful,
cost-effective means of genetic testing for Lynch and polyposis syndromes that
eliminates the need for stepwise testing and multiple follow-up clinical visits.

4.4 Mitochondrial Diseases

Mitochondrial diseases have the most varied presentation. This is because of the
unique inheritance pattern of mitochondrial diseases. They can originate from muta-
tions in either the nuclear or mitochondrial genome (Calvo et al. 2012 ). Their esti-
mated prevalence is 1 in 5,000. Clinical presentation is usually as a primary skeletal
and cardiomyopathy, neurologic disease, or multisystem disorder. Initial investiga-
tion may include blood and/or CSF lactate concentration, neuroimaging, cardiac