More information - exome sequencing diagnostics

Why choose our laboratory for your diagnostic exome sequencing?
  • ISO15189 accredited laboratory
  • Experience of over 10.000 clinical exomes
  • Proven track record
  • 16 involved clinical laboratory specialist and >20 clinicians
  • Expert team of bio- informaticians
  • Comprehensive reporting of results

Exome sequencing in general

Rater than be limited to analysing single genes, or predefined panels of genes, exome sequencing is aimed to cover the human exome, the coding region of all (20000) human genes. All types of mutations are potentially detectable by this assay. Due to this, exome sequencing has proven to be a diagnostic test with a very high diagnostic yield.
Advantages of exome sequencing:

  • The diagnostic yield of exome sequencing is higher than achieved by Sanger sequencing
  • Exome sequencing can solve complex clinical cases
  • Exome sequencing can lead to a quicker genetic diagnosis
Our exome sequencing approach 

Exome Sequencing Diagnostics has been developed and implemented in our laboratory in 2011, in close collaboration with clinicians, clinical laboratory geneticists and scientists. In an initial phase, the test was focused on the 5 specializations of our laboratory, but rapidly expanded to other disorders. Since 2011 we have processed over 10000 clinical exome requests. Our current sample load exceeds 500 samples per month.
Our Exome sequencing Diagnostics consists of 3 major steps:

  • Exome Sequencing
  • Exome Data Analysis
  • Clinical Interpretation & Reporting


Step 1: Exome sequencing


To sequence the exome, a sample of the patient is required. In some cases it may also be necessary to test samples from the parents (trio-based sequencing). After the isolation of DNA from the sample, it is enriched for exonic DNA and sequenced on a NGS platform. This process is performed under strict quality requirements. High quality standards are applied:

  • Q30 base scores of >80%
  • A median coverage of at least 75x
  • 90-95% of all targets is sequenced with at least >20x


Step 2: Exome data analysis

In-silico exome gene panels

After exome sequencing, the raw data are analysed. We have developed a post-sequencing bioinformatic pipelin that uses in-silico exome gene panels (gene lists) for filtering of the exome data. Per disorder type, a specific exome gene panel has been developed, wich contains all the known disease-causing genes and is used to filter the data for this specific disorder. As a result, the number of variants to be assessed is decreased dramatically. For example, by using the vision disorders gene panel the number of variants is decreased form >1000 to <10 variants. The in-silico gene panels are updated on a regular basis with newly identified causative genes to ensure adequate mutation detection. Current and past gene panels, including coverage data per gene, are available at our website.

In-house bionformatics

With the in-house developed bioinformatic pipeline, variants are annotated, selected and prioritised for pathogenicity. This can be done using one gene panel at a time, but it is also possible to use multiple gene panels simutaneously.
Initially, only variants in genes of a selected gene panel are assessed and analysed. If this gene panel analysis has not revealed causative mutations, the analysis can be repeated with less strict filtering or an exome-wide analysis can be initiated.
Copy number variant (CNV) analysis is routinely performed on each exome in order to also identify structural variants of >3 exons, thereby increasing the change of finding a cause for the patient's disorder.exome data analysis

Trio-analysis

A specialised analysis is the trio analysis, wich is used to identify de novo mutations by studying variants
from both the patient as well as the unaffected parents.(Raw data are stored and can be retrieved)


Step 3: Clinical interpretation & reporting

The variants identified will be interpreted in the clinical context provided by the referring clinicians.

There are several possible outcomes:

  • One or more pathogenic variants are identified that may explain the disorder of the patient
  • One or more variants are identified of wich the significance is not immediately clear; additional testing in family members, or other (biochemical) testing, may be required
  • No variants are identified that might explain the disorder; after a gene panel analysis, an exome-wide analysis can be considered

The initial analysis is focused on known or predicted deleterious varaints in genes known to be associated with the disorder the patient was referred for (analysis of one or more exome gene panels).
However , if no causative mutation is found within the gene panel, we can proceed with the analysis of the rest of the exome data. The interpretation in the exome-wide analysis is focused on likely-disruptive variants in all genes. Besides the identification of causative mutations in disease genes not (yet) suggested in a particular patient (broadening the phenotype) or the identifcation of novel (candidate) disease genes, exome-wide analysis does bear the risk of the identification of medically relevant variants for other (late onset) disorders; for example a variant associated with an increased cancer risk. These so called unsolicited findings could have important consequences for the patient and/or other family members. The risk of such unsolicited findings is reduced by variant filtering using gene panels or trio analysis.

Unsolicited findings will be discussed by a dedicated committee, which determines the clinical relevance. In general, the committee decides only to report (likely) pathogenic variants indicative of a treatable or preventable health problem, when it is regarded to be in the counselee's best interest to be informed. Unsolicited findings are described in a separate report issued to the referring medical doctor. In all situations, the patient will be informed of the results of exome sequencing by their physician.

What is included in our exome sequencing diagnostics?

blokjes exome  STEP 1: Sequencing of the exome

      * Sample collection
      * DNA isolation
      * Sequencing of the human exome

  STEP 2: Exome data analysis

      * Read alignment, variant calling
      * Variant annotation using an in-house developed bionformatic pipeline
      * Variant filtering according to the requested in-silico gene panel(s)
      * And/or Exome wide analysis: analysis of the full pre-existing dataset, limited to likely-disruptive variants, both nucleotide variants and CNVs (>3 exons)

  STEP 3: Clinical interpretation and reporting

      * (Sanger) sequening validation of disease causing variants
      * Clinical interpretation of the variants by a clinical laboratory geneticist
      * A comprehensive report with the clinical interpretation, a conclusion and putative recommendations for further testing


Raw data (raw reads) are stored standard for one year and can be obtained for an additional charge (please contact us).

Diagnostic interpretation of exome data

The diagnostic interpretation of exome data can be requested seperately in case you already have exome sequencing data, but stil lack the diagnostic interpretation.
For instructions on how to send us your exome sequencing data, please contact us via info@genomediagnosticsnijmegen.nl

Diagnostic yield of Exome Sequencing Diagnostics

The diagnostic yield of exome sequencing diagnostics varies per exome gene panel used. See below for a schematic representation of these diagnostic yields.

The variation in diagnostic yield may be caused by several factors, inlcuding:

  • The genetic heterogeneity of the disorders
  • The fraction of genes already known for a certain disorder (versus those still to be identified)
  • Pre-testing of the patient for genes involved in the disorder
  • Referral policies
  • Technical limitations of exome sequencing for identifying specific types of mutations (i.e. repeat expansions and mitochondrial DNA mutations)

Diagnostic yield of each exome gene panel