Exome sequencing

Difficulties in identifying epilepsies without diagnostic hypotheses with non-specific symptoms are quite common. The diagnostic efficacy of exome sequencing in patients with epilepsy is variously reported to be between 34 and 49% (Tumienė, B., et al.,2018, Forman E.B., 2018, Helbig KL., et al., 2016) compared to 8% when chromosome microarray analysis is used (Kozhanova T.V., 2019). Exome sequencing is 1.9 times more effective than the diagnostic output of the Hereditary Epilepsies panel (diagnostic efficiency 19.0%; P=0.0018)(Costain G., 2019). Establishing a genetic diagnosis can influence treatment choice, as has been demonstrated in patients with abnormalities in the SCN1A, SCN8A, SLC2A1 genes (Snoeijen-Schouwenaars, F. M., et al., 2018). 

To date, genetic testing in epilepsy is recommended to start with sequencing of a few genes and/or target panels and finally perform exome sequencing in the remaining undiagnosed cases.

Congenital muscular dystrophies (CMDs) are a heterogeneous group of disorders characterised by a predominantly early childhood or adolescence onset, with signs of dystrophy primarily in the proximal muscles of the upper and lower extremities. The frequency of genetic diagnosis of CMD remains low, at around 24%. Families with undetected pathogenic variants of CMD face uncertainty about the risk of disease progression as well as transmission to offspring and the need for continued medical monitoring. The exomic genetic diagnosis rate of patients with muscular dystrophy, for whom targeted Sanger sequencing failed to identify the genetic cause of the disorder, was 40% for single probands and 34% to 60% for the ''trio'' sequencing (Ghaoui R., et al., 2015; Harris, E., et al., 2017).

Dementia is the most common neurodegenerative disorder, affecting between 1% and 3% of the population worldwide. Large genetic heterogeneity is challenging to diagnose, as the phenotype in many patients is either not syndromic or the molecular genetic cause is still unknown.

Exome sequencing is the gold standard in the diagnosis of neurodegenerative disorders. According to literature, exome sequencing has a diagnostic efficacy between 22% and 27% in patients who could not be diagnosed after a panel study (E Chérot, et al.,2018; Bojan Zalar, et al., 2018).

Approximately 2-4% of pregnancies are complicated by significant foetal malformations. The prenatal testing strategy and choice of tests should be individualised and correlated with ultrasound findings and family history. Current options include: karyotype analysis, fluorescent in situ hybridisation (FISH) and chromosomal microarray analysis (CMA) for analysis of chromosomal abnormalities.

Various karyotypic methods provide a diagnostic efficiency of about 35% (Zhang S., 2017, Hillman S.C., 2013). Thus, when these techniques are used, more than half of fetuses with structural abnormalities go undiagnosed. 

Two recent major studies have reported the results of exome trio sequencing performed on fetuses with malformations and normal karyotype (Petrovski S., et al., 2019, Lord J., et al., 2019). Both studies show that exome sequencing increases the diagnostic yield of fetuses with congenital malformations by approximately 8-19% after karyotyping and CMA results, and the frequency of detection of pathogenic variants is strongly correlated with the number of fetal anomalies. 

Exome sequencing is a phenotype-dependent test, so the physician must provide the laboratory with adequate information necessary to obtain the most accurate interpretation of the results. Clinical information should include detailed reports of fetal magnetic resonance imaging (MRI) and/or fetal ultrasound, preliminary results of combined screening, ethnicity, reproductive history and family history, including parental consanguinity.

The «trio» analysis is preferable to the fetus-only or fetal and single parent analysis. The «trio» analysis has higher diagnostic coefficients (by 20%) (Retterer K., 2016).

If fetal abnormalities are significantly suggestive of a specific diagnosis, single gene testing or a phenotypic gene panel is more appropriate as a first-line test. Prenatal exome sequencing can only be performed if there is a clinically relevant indication for such a test. In the absence of such indications, interpretation of the data obtained is not possible.

According to WHO, 4-6% of newborns worldwide are born each year with severe congenital malformations. Congenital malformations are estimated to be present in 13% of all neonatal intensive care unit admissions in developed countries (Widmann R., et al., 2017) and remain the leading cause of neonatal mortality. A literature review shows that exome sequencing has a high diagnostic yield (36-48%) in the diagnosis of infants with very severe congenital malformations in the absence of molecular cytogenetic abnormalities (Trujillano, D., et al.,2017, Meng L., et al., 2017, QI Zhi-Ye., et al.,2019).

An atypical and previously undescribed form of genetic disorder seen in young children challenges the traditional paradigm of multilevel genetic testing in intensive care units. Targeted panels are reasonable in most cases, but failure or duration in detecting causative variants in critically ill children is a significant challenge that can be overcome by exome sequencing.

Having minimal clinical information, i.e. only one single symptom, reduces the specificity of the results. As it is difficult to detect the full clinical picture in the first days of life, it is recommended to do a 'trio' analysis only when standard diagnostic methods such as karyotype analysis, gene panels and CMA are not feasible.