WES & CES: the differences

What’s the difference between Clinical Exome Sequencing and Whole Exome Sequencing?

There are several misconceptions around Exome Sequencing. The first one is that Clinical Exome Sequencing (CES) is synonym for Whole Exome Sequencing (WES). There is actually a big difference between doing CES and doing WES, both in terms of lab efforts and data interpretation.

How many genes are actually associated with human diseases?

While several genetic conditions have been fully characterized at the clinical and molecular level, most human genes are not actually related to human diseases. It is estimated that the genome contains approximately 20,000-25,000 genes. Of these, just less than 5,000 have been found to be mutated in human diseases and a handful more have shown to be involved in drug response. This means that whenever it comes to get the molecular confirmation of a genetic disorder, CES is usually more convenient and more suitable than WES.

CES: 150x is better.

In fact, CES enables a rapid and cost-effective analysis of all disease-associated genes, unburdening the amount of work needed from sequencing library preparation to variant calling and filtering, all the way down to the clinical interpretation of the results. Furthermore, the sensible rationalization of the enrichment phase (i.e. the work needed to isolate and sequence argeted regions) allows the lab to reach high levels of coverage when doing CES. A high level of coverage ensures a dramatic decrease in rates of false positives and false negatives, giving the whole process of CES a touch of perfection. A coverage of 50x is normally considered o be a high standard, but it’s possible to do more: according to the most ambitious requirements currently in force in Italy and other European countries, we always perform CES at the impressive coverage of 100x-150x.

When is WES recommended?

There are a few, particularly arduous clinical cases in which even CES may fail in identifying the disease-causing mutation. In such cases, it may be worth considering a larger effort by sequencing all 20,000 genes, plus consistent tracts of the regulatory sequences at the beginning (5’UTR) and at the end (3’UTR) of each gene. Like our EXOME 50MB does, a good WES analysis also includes long traits of at least 200 nucleotides at the exon/intron junctions. As a plus in comparison to WES offered by other labs, our EXOME 50MB includes even mitochondrial DNA (mtDNA) analysis. Other situations where WES is well indicated are: large association studies in multi-factorial disorders, personalized medicine and precision oncology. In these cases, thanks to the multiplexing technique, WES can be performed on several samples in parallel.

What should you check before ordering CES or WES at any lab?

1. Ask the lab if they really do Whole Exome Sequencing or Clinical Exome Sequencing. By doing WES, all (all!) the genes of the genome are sequenced. Therefore any lab offering exome sequencing without explicitly doing all genes will very likely perform just CES.

2. Guessing if it’s CES or WES from the price. The technical costs of doing Clinical Exome Sequencing (CES) aren’t in the order of thousands of euros (lab costs only, bioinformatic analysis and medical report excluded). Therefore make sure that any lab offering exome sequencing for several thousands of euros is actually doing WES and not CES.

3. Ask for the level of coverage offered. Several labs today offer WES or CES with very low levels of coverage. The level of coverage is crucial for the quality of the results but also for the costs of the run. The cost of WES varies dramatically on the level of coverage, as it may double or even triple. Therefore we recommend requesting specific information on the coverage offered. In general, we do not rate as acceptable any coverage below, but we always do 100x-150x for CES and not less than 90x for WES.