DNA sequencing is the process of finding the order of the building blocks (i.e. nucleotides) of the genetic code of an individual. Whole exome sequencing (WES) is a widely used next-generation sequencing (NGS) method that involves sequencing the protein-coding regions (exome) of the genome. The human exome represents 1-2% of the genome, and mutations within the exome are known to cause about 85% of the diseases caused by genes. Therefore WES is thought to be a cost-effective method to check for disease-causing mutations.
Reasons for doing prenatal WES
Increasingly, prenatal WES is being performed via fetal cells obtained from amniocentesis or placental cells obtained from chorionic villus sampling when:
1. there are multiple and many isolated fetal structural abnormalities detected by detailed ultrasound scans.
2. there are certain isolated fetal structural abnormalities or certain ultrasound markers (e.g. increased nuchal translucency >= 4.5 mm)
3. past history of pregnancies where the fetus(es) was / were affected with genetic syndromes
WES is cheaper than whole genome sequencing (WGS), and produces a smaller and more manageable data set for faster and easier data analysis than WGS. More and more researchers are now finding that mutations outside the exome may also cause diseases. WES would miss these mutations.
Limitations of prenatal WES
1. The biggest limitation of WES is that it does not sequence 100% of the genes in the genome, instead focusing only on the exons or the parts of the genome that code for proteins which make up 1-2% of the entire genome.
Some parts of the exome are not examined, and some types of mutations are not detectable by WES. Disease-causing genes outside of what is checked for could still be undetected, despite the WES being already a test with very high resolution. It may therefore miss many mitochondrial genome mutations, large rearrangements, epigenetic factors, large deletions or duplications, and structural variations e.g. inversions, translocations and many copy number variants.
2. Possible difficulty in interpretation of the results.
An individual that has already been born may present with intellectual disabilities, behavioural abnormalities and structural abnormalities. WES in such cases may allow genetic mutations detected to be matched to all these abnormalities. For such cases, the individual's genetic sequence could be analysed by WES. If there were any results that would be classified as VOUS, the genetic code of the parents could be tested to determine if the parents also carry similar VOUS mutations. Such a process of discovery could take months of testing and analysis.
A fetus, on the other hand, may only present on ultrasound with certain structural abnormalities; intellectual disabilities, behavioural abnormalities and many structural abnormalities would not or may not be detectable on ultrasound scan. In order to avoid over-interpretation of mutations that may be found, it is only responsible for clinicians and laboratories to interpret the genetic mutations that can be matched with the abnormalities that had been detected on ultrasound scan. Very often, a proper interpretation can only take place after a consultation with an expert fetal medicine specialist to interpret the scan findings, a laboratory to explore the available libraries for the different mutations detected, and a clinical geneticist to interpret the likelihood that the mutations can cause a disease and the possible range of diseases that the mutations can cause. Our clinic provides the expert fetal medicine assessment based on detailed ultrasound scans +/- referrals to paediatric cardiologists for fetal echocardiography +/- fetal MRI, counselling and procedures like amniocentesis / chorionic villus sampling, and we tie up with top genetic laboratories around the world and also refer you to local expert clinical geneticists for pre- and post-test counselling.
WES (trio) or WES (single)
For fetal assessment, it is recommended that the fetus and both parents be analysed with WES (trio) as speed is of the essence for analysis during the pregnancy. If the fetus has a VOUS detected and one of the parents carries similar VOUS mutations and do not manifest any disease, then it is more reassuring. If the fetus has a VOUS detected and none of the parents carries similar VOUS mutations, then it is a de novo mutation and could be more worrying in terms of the predicted outcome. Doing a WES (single) on the fetus only and then doing the parents' WES only if VOUS is detected may be a cheaper strategy but the proper interpretation of the results would be delayed as then the geneticist could be waiting a further few weeks for the parental WES results. Experts agree that WES (trio), rather than WES (single), should be performed for prenatal samples.
Potential unintended consequences of performing prenatal WES:
It may reveal information about family relationships e.g. that the husband of the mother may not be the biological father of the child, or that the couple may be related by blood.
It may reveal that a parent of the affected fetus is also affected by the same genetic condition, which may have medical consequences for the parent (even if he/she is currently asymptomatic) and his/her family members. This may have negative implications on the insurability of the parent with the genetic condition.
It may reveal unexpected / incidental medical information (known as secondary findings) about the child or the parents. Such secondary findings are not related to the reason for doing the test. The American College of Medical Genetics and Genomics has recommended that consideration be given for mutations in 57 specific genes (e.g. inherited cancer syndromes, connective tissue disorders associated with sudden cardiac events, certain types of heart disease, high cholesterol, rare genetic susceptibility to complications from anaesthesia when certain drugs are used) generally unrelated to the presenting problem to be reported as these may benefit you to know as there could be certain interventions that could reduce the complications of the genetic condition in the affected individuals. Knowing about these secondary findings could also cause anxiety / stress to the family and possibly affect the insurability of the individuals adversely. Knowledge of certain secondary findings may lead to more medical screening, procedures and testing for your child, you and possibly other family members. One may choose not to receive secondary findings specifically in your child's report or your report. You could also choose to receive the child's report only after the child has been delivered. If you had chosen not to receive report about any secondary findings, this information would then not be available to you or your health insurance company.
The sequenced exome will be compared to libraries with known normal and abnormal "reference" DNA sequences. WES results may be classified as:
2) likely pathogenic
3) variation of unknown significance (VOUS)
4) likely benign
The report would include:
Primary result where genetic changes that are likely related to your child's condition will be discussed in detail
Secondary findings (see above). In addition to ACMG's 57 medically actionable genes, different laboratories may also report different sets of other secondary findings.