Which Whole Exome Sequencing (WES) tests are available ?
- WES analysis of patient only
- WES analysis of patient and 2 parents to detect de novo variants
- WES analysis of 2 siblings and 2 parents to detect autosomal recessive variants
- WES analysis of 3 affected family members to detect autosomal dominant variants
Which patients should be tested by “whole exome” next-generation sequencing (NGS)?
- Patients who have exhausted currently available genetic testing and do not yet have a molecular diagnosis
- Patients with a long differential diagnosis or genetically very heterogeneous disorder (eg deafness, retinitis pigmentosa, cardiomyopathy) that makes sequential testing cost-prohibitive
Which analysis is performed?
- Approximately 37 Mb (214.405 exons) of the Consensus Coding Sequences (CCS) are enriched from fragmented genomic DNA by > 340.000 probes designed against the human genome (Nextera Rapid Capture Exome, Illumina)
- The generated library is sequenced on an Illumina NextSeq or HiSeq 4000 platform (Illumina)
- All exons and intron boundaries (+/-20 bp) were analyzed
- Relevant variants identified by NGS are Sanger sequenced to exclude NGS artefacts
- All relevant variants are in-house analyzed for their possible pathogenicity and clinical relevance
Which analysis is not performed?
- Analysis of introns
- Analysis of the mitochondrial genome
- Deletion-duplication testing
- Analysis of repeats (eg FMR1 repeat)
What will be in the report?
- Pathogenic variants and variants of unknown significance (VUS) in genes that are:
- Previously implicated in a human disorder similar to the affected individual
- Could be hypothesized to be related to the cause of the disorder due to their relationship to other genes or particular function
What will not be in the report?
- Non-paternity, unless specifically requested
- Carriership of recessive variants, unless specifically requested
- Late-onset dominant variants not related to the proband’s disorder (eg BRCA1)
- Benign and likely benign variants
What is required?
- 30 µg of DNA or 10 ml EDTA blood of proband and both parents
- Informed consent if needed locally
- Clinical information about the patient
- A pedigree
Why should you send samples of the parents together with that of the proband?
- Comparing the proband’s exomic data to that of the parents will significantly increase the sensitivity of the test as it will maximize the likelihood of identifying the disease-causing variant(s), and decrease the chance of obtaining variants of unknown significance (VUS)
The TAT is less than 2 months.
- WES analysis of patient only: 1500 Euro
- WES analysis of patient and 2 parents to detect de novo variants: 2500 Euro
- WES analysis of 2 siblings and 2 parents to detect autosomal recessive variants: 2700 Euro
- WES analysis of 3 affected family members to detect autosomal dominant variants: 2700 Euro
Whole Exome Sequencing (WES)