FAQ - Our services

Exome sequencing diagnostics - Why choose our laboratory?

  • ISO15189 accredited laboratory
  • Experience of close to 4000 (probands) clinical exomes
  • Proven track record
  • 16 involved clinical laboratory geneticists and >20 clinicians
  • Expert team of >10 bio-informaticians
  • Clinical interpretation and comprehensive reporting of results
  • Turnaround time of 4 months
  • Median read depth of 75x

Exome sequencing diagnostics - The advantage compared to a targeted analysis?

The usage of the use of in-silico gene lists is that these gene lists are updated on a frequent basis with newly identified causative genes. An additional advantage is that, if the disease panel analysis does not reveal the genetic cause of the disorder we can proceed with an exome wide analysis as a second step.

Exome sequencing diagnostics - Our current quality standards

For clinical exome sequencing we demand Q30 base scores of >80%, a median coverage of at least 75x or more, and 90-95% of all targets is sequenced with at least >20x.

Exome sequencing diagnostics - Trio-sequencing versus singleton sequencing?

Trio-sequencing of an affected individual and parents is typically done for isolated cases, in order to detect putative de novo events. Besides the analysis of de novo mutations we also look at dominant and recessive mutations occurring thoughout the exome.
If a disorder is likely to be recessive, trio-sequencing will have very limited additional value. Due to the increased costs of a trio-sequencing study, it is only recommended for isolated cases (e.g. Intellectual Disability).

Exome sequencing diagnostics - Data storage and data retrieval

The BAM-files will be stored for a minimum of two years and the VCF-files are stored for at least three generations. The VCF-files (the unannotated files) can be obtained, if a document of permission of the patient will be provided. For the data retrieval of raw data an additional charge will apply (please contact us, for more details).

Exome sequencing diagnostics - Incidental Findings

We generated gene panels with known disease-causing genes for each condition tested by exome sequencing. In case no causative mutation has been found in the chosen gene-panel we can proceed with an open exome analysis. One of the main issues in case of an open exome analysis involves the potential identification of unsolicited, incidental or secondary findings - genetic variants that are medically relevant but not for the disease for which the patient visited the clinic [Johnston JJ et al. Am J Hum Genet. 2012]. An example of this could be a gene alteration associated with an increased risk of cancer or cardiovascular disease in the counselee. This could have important consequences for the counselee and/or other family members. International discussion on the reporting of unsolicited findings keeps ongoing. The American College of Medical Genetics, among others, recommends that a limited number of medically relevant variants should be specifically sought and reported in each patient undergoing exome or genome sequencing. We do not follow the ACMG guideline regarding the active seeking of mutations in specific genes, but follow the recommendations by the European Society of Human Genetics [van El et al. Eur J Hum Genet. 2013], and the guidelines for diagnostic next generation sequencing as published by Eurogentest (www.eurogentest.org). This means that secondary findings will be assessed by an independent expert panel which determine 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. Secondary findings are described in a separate report issued to the referring medical doctor. In all situations, the counselee will be informed of the results of exome sequencing by their physician.

To view our policy on disclosing incidental findings click here

Mutation Diagnostics - Familial mutation(s)

We can perform carrier testing of a known familial mutation and familial segregation of a variant found by WES. Costs for this test are 350 euro and 50 euro for each additional family member (if send together in one batch). The test includes sequencing of the full coding region, in wich the mutation is located, and generation of clinical report. TAT is approximately 4 weeks.

Mutation Diagnostics - Prenatal Testing

Regarding prenatal analysis of a known familial mutation; Costs for this test are 800 euro. The test includes sequencing of the full codin region, in wich the mutation is located, + the exclusion of maternal contamination. The TAT of prenatal testing is 2-3 weeks.
Please inform our administration via gen@umcn.nl when you plan to send the sample, so we can start the analysis immediately upon it's arrival.

Regarding prenatal analysis of a unknown familial mutation / prenatal full gene sequencing please contact us for pricing information.

Whole genome sequencing

We do not offer diagnostic genome sequencing yet, but hope to be able to offer this at the end of 2016 / beginning 2017. Instead, we do offer diagnostic exome sequencing.
For more information please take a look at our exome sequencing diagnostics page.

NIPT

At present, we do not offer Non Invasive Prenatal Testing (NIPT) for foreign patients. We are only allowed (due to a Dutch law) to offer this test to our national patients under strict regulations.

Need advice?

Please contact us via info@genomediagnosticsnijmegen.nl for any questions related to:

  • Portfolio
  • Prices
  • TAT
  • Status of analysis
  • Advice on wich test to request for your patient
  • etc..

FAQ - Our laboratory

Laboratory opening times

MON to FRI

08:30 – 16:30

Weekend

-

Out Of Hours Delivery

YES

Sample conditions

Single gene diagnostics, multiple gene diagnostics and mutation diagnostics

  • We prefer EDTA blood (10/20 ml in unbreakable tubes)
  • Or at least 10µg unpurified DNA
  • In case of neonate: EDTA blood (at least 3ml) / Heparin blood (at least 1-2 ml)

Exome sequencing diagnostics

  • We prefer EDTA blood (10/20 ml in unbreakable tubes)
  • Or at least 3µg purified DNA (Qubit measured)
  • Or at least 10µg unpurified DNA

Shipment details

Postal / Courier address:

Radboud university medical center
Department of Human Genetics
Division Genome Diagnostics Nijmegen, route 815
P.O. Box 9101
6500 HB Nijmegen
The Netherlands

What about quality control (lab-accreditation)?

We are an ISO 15189:2012 certified laboratory. This means, that our lab meets high level quality requirements. Audits and EQA schemes (CEQAS, UKNEQAS, EMQN & CF Network) take place on a yearly basis.

FAQ - Ordering and payment

How can i pay the invoices?

Usually, on the invoice, the referring physician will be stated. In case another billing address should be used, please indicate this clearly. 
The following methods of payment are accepted; wire transfer, checks or PayPal. When using PayPal as the payment method, please use info@genomediagnosticsnijmegen.nl as e-mail address.

For all our single gene diagnostics, multiple gene diagnostics and mutation diagnostics (carrier testing) a final report and invoice will be sent out as soon as all the results are obtained and interpreted.
Our exome sequencing diagnostics service needs to be pre-paid, unless agreed otherwise. Tests will only be initiated after receiving the pre-payment. A pre-payment invoice will be generated at our administration and send to you via e-mail.

Can i use S2 / E112 forms?

We do not accept S2/E112 forms. We offer genetic testing rather than hospital treatment, therefore we are not obligated to accept these forms. As we perform more genetic tests than covered by our contracts with the Dutch health insurance companies, our costs for genetic services for people from abroad are not compensated by the health insurance companies.

Instead of an S2/E112 we send an invoice together with the final results to the referring physician (or to another billing address, if indicated clearly).