Introducing Amsterdam UMC

Since June 2018, Amsterdam UMC (University Medical Centers; AMC and VUmc) represents the largest academic hospital in the Netherlands. AGDx is the genomic laboratory of Amsterdam UMC and we are developing the best genetic tests for patients, for disease prevention, disease diagnosis and treatment. AGDx performs at the top of international scientific research and we make medical breakthroughs available, as Amsterdam UMC is one of the leading international centers in the field of academic medicine. AGDx performs tests under government license. Better be safe than sorry: for the vast majority of our genetic panels, we garantee 100% coverage, plus CNV analyses. This coverage percentage of 100%, is called Quality A.

Due to new regulations, there are new prices for genetic testing. As you may have noticed, prices for some tests went up, other prices went down. The price of the test can be found in the catalog. Please contact us if you have questions about the price of a specific test. Special prices are available for large amounts of test requests and regular customers. We do our best to perform at competitive prices and turn-around times, however quality and academic test interpretation is our first priority. We are happy to share our knowledge and experience of clinical genetic testing with you. Info@amsterdamgenomedx.com.

Dyslipidemia Panel

Dyslipidemia and Familial Hypercholesterolemia (FH)

As an European reference center for genetic testing in FH we have designed an utmost economic and high quality and very sensitive 29-gene panel coding- and flanking regions of genes that have been repeatedly shown to cause lipid disorders. This panel covers most dyslipidemias, including FH, hypo-alphalipoproteinemia (low HDL-cholesterol), hyper-alphalipoproteinemia (high HDL-cholesterol), hypo-betalipoproteinemia (low LDL-cholesterol), dysbetalipoproteinemia (APOE-genotyping) and hypertriglyceridemia (high triglycerides), but also rare diseases including chylomicron retention disease and cerebrotendinous xanthomatosis.

Broad coverage of dyslipidemias is efficient and indispensable, as the phenotypic heterogeneity is large and different dyslipidemic phenotypes are closely connected. This often hinders correct diagnosis. This broad panel of dyslipidemias is therefore encouraged to minimize miss-and under-diagnosis. This sensitive Dyslipidemia panel is a targeted NGS plus CNV-analyses and has a coverage of 100%.

The test is strongly recommended for patients:

  • That present with abnormally high or low lipid levels, such as LDL-cholesterol, HDL-cholesterol, triglycerides, apolipoprotein B or apolipoprotein A1.
  • That present with typical clinical phenotypic features of lipid disorders, such as xanthomas.
  • That have experienced coronary heart disease and have a strong family history of heart diseases.
  • That need to be screened before entering clinical trials.

Next to the Dyslipidemia panel, we offer simple and fast genetic analyses of single variants in those genes. This is recommended for individuals with first-degree relatives that carry a known pathogenic variant.

Epigenetics

Order Episign: one Assay, three options.

Epigentics Episign is offered as three different tests to suit the needs of your patient.

Epigenetics for diagnostic purposes, read for in-dept information our publication: EpiSign AJHG 2020

See Episign on  ASHG  TV 2019:

 

Epigenetic signatures for genetic disorders can identify for example CHARGE syndrome, Cornelia de Lange syndrome, Down syndrome, Kabuki syndrome, Sotos syndrome, Williams syndrome, ATRX syndrome, autosomal dominant cerebellar ataxia with deafness and narcolepsy (ADCADN), BAFopathies (Coffin-Siris syndrome , Nicolaides-Baraitser syndrome, Chr6q25del), Claes-Jensen syndrome, Genitopatellar syndrome, Floating Harbor syndrome, ADNP-related syndrome/Hellsmoortel-VanDerAa syndrome, and Chr7q11.23dup.

This technology provides information on epigenetic changes, a new level of analysis beyond the genome. Bekim Sadikovic

 

Obesity Panel

Amsterdam UMC Genome Diagnostics offers now targeted gene testing for obesity.

See Obesity Genetics on  ASHG  TV  October 2019:

The involvement of genetic factors in the development of obesity is estimated to be 40-70%. Clinical relevant genes may influence obese patient’ response to weight management. The obesity panel was previously performed using a WES based virtual gene panel including 52 genes. Obesity panel has been further developed as a NGS-based capture panel for economic and reliable screening for inherited obesity. The coverage of this obesity gene-panel is 100%. The purpose of this AGDx NGS – Obesitome panel is to offer relevant diagnostic testing. Since we have many requests for this panel, you can order this panel for a very special economic price. Upon request the WES based virtual gene panel of 52 genes (or including specific other obesity related genes) can be performed. For this test, please order custom WES. In case your patient has both ID and obesity a trio WES can be performed. In this case both the ID panel as well as the large obesity gene panel (including 52 genes) can be analyzed.

Ordering More than one Test

Question

I would like to order more than one test on a patient. Do I need to fill in more than one request form?

Answer

No, different tests can be ordered for one patient.

Adding another Test for a Previous tested Patient

Question

I would like to order another test on a patient who was tested previously. Do I need to submit another specimen?

Answer

No. Generally, Amsterdam GenomeDx obtains enough DNA from one specimen to allow completion of a number of tests. A second specimen is not necessary, when requested within 5 years.

Question

What is the procedure for adding on further testing to a sample already at Amsterdam GenomeDx?

Answer

An additional test can be added on to a sample already at Amsterdam GenomeDx by submitting a new order form for the new test to be performed. Please reference the Amsterdam GenomeDx lab number, patient’s name and date of birth.

Results and Analysis

Question

When can I expect the test results?

Answer

Our goal is to provide you with an accurate result in a reasonable time period. The majority of our tests takes approximately 6-8 weeks to complete. Analysis of NGS-panels can take longer, due to the higher number of genes analysed and the complexity of the interpretation. The time it takes to complete a test varies depending on a number of factors. The size of the gene, the complexity of the interpretation, the occasional need to redesign or repeat a test, and other factors can increase the turn around time. Testing can take from 2-10 weeks depending on which genetic test was ordered. The information tag for each condition (see Test catalog) indicates an estimated time frame for completion of the test. These estimates are based on the average amount of time it has taken us to complete the test in the past. As soon as a test is completed the results are mailed to the referring physician or ordering facility. Prenatal testing usually takes 2-3 weeks and test results can be communicated by phone, fax or email according to the physician’s preference.

Question

The test result has been lost or was never received, can you resend it?

Answer

Amsterdam GenomeDx can provide you with a duplicate copy of the test result if you are the ordering physician or are from the ordering facility. We cannot send results to the patient or other physicians involved in the care of the patient without a signed release from the patient authorizing us to do so.

Question

Can a test be expedited?

Answer

All prenatal tests are expedited.  Other common indications for expediting a test in the lab are a scheduled or necessary procedure (e.g. surgery) and  follow up treatment. If there are other medical indications for expediting a test, please let us know and we will do our best to get a result out as quickly as possible. Please note that for all expedited tests an extra charge of € 240 will be applied.

Billing

Question

How is billing done?

Answer

An invoice will be sent to the ordering physician’s address or to the address indicated on the test requisition form. Please pay within 30 days by bank money transfer to the bank account indicated on the invoice. Please always refer to the Test code (see order form) and PO number of your financial department.

Shipping

Question

Where do I send a specimen?

Answer

Amsterdam GenomeDx
Amsterdam UMC
Dept. Clinical Genetics, H01-114
Meibergdreef 9
1105 AZ AMSTERDAM – The Netherlands

Question

How do I send a specimen?

Answer

A specimen should be packed in materials that prevent its container from being damaged during shipment. Specimen tubes should be labeled with patient name and date of birth. Unlableled specimen tubes will be rejected by Amsterdam GenomeDx. DNA and buccal swabs specimens can be sent through the regular postal mail. Blood can also be sent through regular mail, provided that the shipment does not take longer than 4-5 days. Prenatal specimens should be shipped to us using an express delivery service.  All specimens should be shipped to us with a completed requisition form. For more information visit our Specimen Requirements page or contac us.

Question

Does Amsterdam GenomeDx pay for shipping?

Answer

No, the cost of shipping is the responsibility of the sender.

Specimen Requirements

Question

I am drawing a specimen from an infant. What is the minimum amount of blood required?

Answer

For infants, we would like 5-10 ml whole blood in EDTA (purple top tube) to perform any test.

Question

Do you accept buccal swabs specimens?

Answer

We do accept buccal swabs specimens under special circumstances. For nearly all of our tests, the quality of DNA obtained from a buccal swab specimen is not sufficient to complete the testing ordered. We actually prefer blood specimens for all our tests. Please contact us to check whether buccal swabs can be used for the test you wish to order.

Question

If more than one test is being ordered on the same patient, is it better to provide a tube of blood for each test?

Answer

No. Amsterdam GenomeDx obtains enough DNA from one specimen to complete a number of tests. Unused DNA material is stored for prolonged periods of time, unless we receive specific instruction to send the material back or to destroy it. For further details please contact us .

Question

What are the specimen requirements for prenatal testing?

Answer

The following specimens are necessary for completion of a prenatal test:

  • Maternal blood (1-4 ml in a purple-top EDTA tube) is required for maternal cell contamination (MCC) studies. The maternal sample should accompany the prenatal specimen or be shipped to arrive prior to or concurrently with the prenatal sample.
  • Maternal and Paternal blood is required for prenatal array testing.
  • If one prenatal test is ordered, one of the following is required: 10-15 ml of Amniotic fluid, 30 mg of Chorionic villi, min. 1 T25 flasks of cultured amniocytes or cultured chorionic villi. If more than one prenatal test is being ordered on a specimen, one of the following is required: 30 ml of Amniotic fluid, 30 mg of Chorionic villi, 3 T25 flasks of cultured amniocytes or cultured chorionic villi. Please note that orders for prenatal diagnostics will be accepted only upon notification to our office.

Question

Can I send DNA?

Answer

Yes. Please send a minimum volume of 20 µl and minimum concentration of 50 ng/µl (50 µg/ml). For testing on a single exon, we require 1-2 ug of DNA. If we are testing 2-10 exons, we require 5-10 ug and for tests with more than 10 exons, we need 20 ug.