Application of Next-Generation–Sequencing to the Diagnosis of Genetic Disorders: A Brief Overview - Next Generation Sequencing Technologies in Medical Genetics - page 38

4.8 Primary Ciliary Dyskinesia

These are autosomal recessive disorders characterized by abnormalities of motile
cilia, which result in phenotypes ranging and including situs inversus, neonatal
respiratory distress at full-term birth, recurrent otitis media, chronic sinusitis,
chronic bronchitis that may result in bronchiectasis, and male infertility. It can be
caused by mutations in nine different genes ( DNAH5 , DNAH11 , DNAI1 , DNAI2 ,
KTU , LRRC50 , RSPH9 , RSPH4A , and TXNDC3 ). Immunohistochemistry can be
used to detect loss of specifi c proteins as these disorders have defective dynein arms
or other axonemal components, but this will not point towards a specifi c genetic
etiology. Hence multiplexing on an NGS platform is highly desirable (Berg et al.
2011 ). A pilot study of four individuals with primary ciliary dyskinesia mutations
was conducted using a custom array (NimbleGen), to capture 2,089 exons from 79
genes associated with primary ciliary dyskinesia or ciliary function, and sequencing
was performed on the GS FLX Titanium (Roche 454) platform. Three out of three
substitution mutations and one of three small insertion/deletion mutations were
readily identifi ed using this methodology. Importantly, this process failed to detect
two known mutations: one single-nucleotide insertion and a whole-exon deletion.
Similar to primary ciliary dysplasia are the nephronophthisis-associated ciliopa-
thies (NPHP-AC; Otto et al. 2011 ). These comprise a group of autosomal recessive
cystic kidney diseases that includes nephronophthisis (NPHP), Senior-Loken syn-
drome (SLS), Joubert syndrome (JBTS), and Meckel-Gruber syndrome (MKS).
Just like PCD, a number of genes have been implicated in NPHP-AC ( NPHP1 ,
INVS , NPHP3 , NPHP4 , IQCB1 , CEP290 , GLIS2 , RPGRIP1L , NEK8 , TMEM67 ,
INPP5E , TMEM216 , AHI1 , ARL13B , CC2D2A , TTC21B , MKS1 , and XPNPEP3 ).
Otto et al. examined 120 patients with severe NPHP-AC phenotypes by PCR ampli-
fying all 376 exons of 18 NPHP-AC genes and subjecting the amplicons to sequenc-
ing on Illumina Genome Analyzer. DNA from patients with known mutations were
used and detection of 22 out of 24 different alleles (92 % sensitivity) was demon-
strated. NGS led to the molecular diagnosis in 30/120 patients (25 %) and 54 patho-
genic mutations (27 novel) were identifi ed in seven different NPHP-AC genes.

4.9 Urea Cycle Disorders

Urea cycle disorders (UCDs) are caused by defects in the enzymes, which are
involved in the transfer of nitrogen from ammonia to urea. This can lead to toxic
hyperammonemia. There are a total of six genes involved in coding for six enzymes,
which include carbamoylphosphate synthetase I (CPS1), ornithine transcarbamy-
lase (OTC), argininosuccinic acid synthetase (ASS1), argininosuccinic acid lyase
(ASL), arginase (ARG), and N -acetyl glutamate synthetase (NAGS). Biochemical
analysis of intermediary metabolites (plasma amino acids and urine orotic acid) is
used to diagnose inborn UCDs and genetic mutation testing is commonly used to