genedx-review

GeneDx review – Accessible clinical genetic testing for rare diseases?

Rating based on our GeneDx review

7 Facts from our GeneDX review

  1. Location: Gaithersburg, Maryland
  2. Products: wide variety of clinical genomic test
  3. Reports: detailed health reporting for specific medical conditions
  4. Result delivery: up to 16 weeks
  5. Privacy: reports anonymized data to ClinVar
  6. Cost: highly variable, but can be covered by insurance
  7. Alternatives: Nebula Genomics (non-diagnostic whole genome sequencing for $299), GeneSight, Invitae, Myriad Genetics, Ambry Genetics, Color Genomics, Veritas Genetics

Summary

This is a review of GeneDx is a clinical genomics company with expertise in rare and ultra-rare disease diagnostics located in Gaithersburg, MD. GeneDx Inc is a subsidiary of BioReference Laboratories, Inc., an OPKO Health company. The hybridization-based or next-generation sequencing tests have to be ordered by an MD, a DO (or in some states a genetic counselor). These results are returned directly to the clinician.

GeneDx offers their test results as actionable information for patients. According to the site, GeneDx is a world leader in genomics with an acknowledged unparalleled comprehensive genetic testing system. But many user reviews complain about the high costs. 

Their FDA approved tests are covered by many national insurance companies but the out-of-pocket expenses can vary significantly. 

FDA approved rare disease diagnostic tests can alternatively be sought through Centogene

Are you interested in a test that decodes 100% of your DNA instead of testing only a few genes? Nebula Genomics offers Whole Genome Sequencing for only $299! This is the most complete DNA test that decodes all 20,000 genes and all regulatory genomic regions. In comparison, GeneDx sequences just a few genes at a much higher price. Click here to learn more!

Company Overview

GeneDx is an FDA approved clinical diagnostic testing company with acknowledged expertise in rare disease diagnostics. GeneDx was founded in 2000 as a subsidiary of Bio reference Laboratories by two scientists from the National Institutes of Health (NIH), Drs. Sherri Bale and John Compton. The company is owned by Okpo Health.

GeneDx believes in responsible testing and diagnostics. The company focuses on diagnosing rare and ultra-rare genetic disorders. The company tries to buck the traditional diagnostic advice of, “When you hear hoofbeats, think horses, not zebras” by only focusing on the rare “zebras”.

The company’s first diagnostic test in 2007 used comparative genomic hybridization to look for variations ranging in size from single-gene duplications or deletions to whole chromosome abnormalities. 

In 2008 they started using next-generation sequencing which gives much better resolution: this allows for the detection of changes in the DNA, called variants, that only affect a single letter of the DNA alphabet. 

GeneDx began their next-generation sequencing with targeted gene panels for specific rare diseases. This allows a doctor to verify if a disorder is caused by a specific broken gene. 

In 2012, they began offering whole-exome sequencing, which looks at all of the genes, although not all of the DNA. As of 2017, GeneDx also offers whole-genome sequencing. This allows a doctor to take a more exploratory approach to rare disease diagnostics.

Review of how GeneDx works

GeneDx works directly with clinicians. A licensed healthcare provider is required to order the DNA test and the results are returned to the provider. Co-founder Dr. Sherri Bale refers to clinicians as the “clients” and the patients as “our patients” even though “we don’t see the patients ourselves.” 

First, a patient would need to meet with their healthcare provider. If the clinician suspects the patient’s symptoms may be caused by a specific genetic disorder, the doctor or genetic counselor can order the testing of a specific gene or set of genes. If the specific disorder is undetermined, all of the genes can be sequenced. 

Example of GeneDx genetic testing menu (from the Mayo Clinic)
Example of GeneDx genetic testing menu (from the Mayo Clinic)

Next, the patient then needs to submit a sample. Different tests have different requirements, but GeneDx works with anything they can pull enough DNA from blood, cheek swabs, skin biopsies, and even amniocentesis for prenatal screening.

Finally, the clinician will receive a report. This can take up to 16 weeks for full genome sequencing. 

You can browse the site to learn more about how to use GeneDx. 

Review of GeneDx Sample Report

Below is an example of a positive result. The report states what panels were requested, what genes were tested, and which known disease-causing mutations were found.

Annotated testing report from Northwell Health
Annotated testing report from Northwell Health

The top part of the report here left blank, are the patients’ information. Following this is a detailed list of the panels ordered and genes tested. Here, as the clinician was not certain which syndrome matched the patient’s symptoms, multiple panels were ordered.

This led to the sequencing of 11 of the roughly 20,000 different genes.

Here the result is positive. The patient has a mutation in the RAF1 gene. The change in the DNA happens in the 1423rd position of the cDNA, changing it from a T to a C. This changes the protein from having phenylalanine to leucine in the 475th position. 

The patient has one good copy of the gene and one broken copy, meaning they are heterozygous. 

The most important part here is that this mutation is “disease-causing” — based on previous patients GeneDx has examined, it is known that this mutation causes the symptoms the patient has.

This diagnosis is restated in plain language in the interpretation section. Although many disease panels were ordered, the genetic testing concludes that the patient has a Noonan syndrome spectrum disorder caused by a mutation in the RAF1 gene.

The report goes on to explain why the mutation is believed to be disease-causing and medical recommendations for the patient and their family. In this example, the broken gene is associated with heart problems, so the patient’s heart should be evaluated.

Finally, the report states exactly how the test was performed. Here, the 11 genes were isolated and sequenced with next-generation sequencing. This provides some limitations of the test: it’s possible the patient also has mutations elsewhere that were not tested.

The report can also come back negative, which does not mean there is not a genetic cause to the disorder. GeneDX also clarifies this result here:

It is also possible that a mutation is found in the tested gene but it hasn’t previously been associated with the patient’s symptoms. Results are based on established medical literature, but not every possible variant has been documented. 

These “Variants of Uncertain Significance” (VUS) are reported but are not considered a positive result — there isn’t enough information to say that that mutation is causing the patient’s disease. 

Sequencing family members can add information: if unaffected family members also have the same mutation, it is unlikely to be causative.

GeneDx uses all of this information in their analysis. They provide a very detailed report and explanation of results through medical professions.

Review of GeneDX Clinician Oversight

In a direct to consumer DNA test, the consumer requests the test, submits their own DNA sample, pays for the analysis, and receives the results. 

For GeneDx, the order is submitted by the clinician. The sample submitted by the patient. The payer is primarily a health insurance company, and the results are sent back to the clinician. 

Only a clinician can order a GeneDx test — either an MD, a DO, or, in some states, a genetic counselor. The tests may only be ordered in accordance with established medical guidelines as a diagnostic tool.

The results are only returned to the clinician. GeneDx does employ genetic counselors, but they are laboratory genetic counselors that do not work directly with the patient. Their role is to work on the cases and possibly provide education to an ordering clinician. 

Genetic counseling services are recommended but not provided through GeneDx.

Review of GeneDx Costs

GeneDx aims to be completely transparent with their pricing so that patients, clinicians, and payers know the cost of the test. However, because the test is a medical diagnostic procedure, the price varies by test specifics and insurer.

The billing page of GeneDx’s website states that they will attempt to contact a patient if the out-of-pocket expense will be over $100. 

Financial assistance is offered based on household income and size, including a compassionate care price and payment plans. Details on pricing are not publically available.

Review of GeneDx Privacy

As a medical diagnostics company, GeneDx is required to comply with the European Union’s General Data Protection Regulation (GDPR) and the United State’s Health Insurance Portability and Accountability Act (HIPAA) and the Health Information Technology Act (HITECH).

GeneDx does report variants they find to ClinVar, a publically available database. The data is not personally identifiable but helps other geneticists link together changes in the DNA with their medical outcome in humans. 

This helps reduce the number of Variants of Uncertain Significance by providing evidence that they are pathogenic, likely to cause a disease, or benign, just a normal part of human variation.

GeneDx Reviews

GeneDx reviews on Yelp have an average 1-star rating. Reviews complain about unexpected costs, delays in testing, high-pressure sales tactics, and changes in results

Google Reviews of GeneDx average to 2.1 out of 5 with similar complaints of insurance issues as well as complaints from former employees.

The Better Business Bureau gives GeneDx an A+ rating, but please note that this does not take into account customer reviews. 

Pros and Cons

Pros

  • FDA approved diagnostic testing for many rare diseases
  • Orthogonal variant validation
  • Contracted with most major insurances

Cons

  • No direct patient education
  • Slow turn arounds
  • Insurance complications and unexpected bills

Nebula Genomics

We finish our GeneDx review with a comparison to Nebula Genomics and other DNA testing companies.

Nebula Genomics is not an FDA approved diagnostic test but does offer higher coverage DNA sequencing, works to educate and empower the user, and costs considerably less.

Nebula Genomics 30x Whole Genome Sequencing

Whole-exome sequencing covers about 2% of the genome. GeneDx’s whole exome sequencing is performed such that at least 95% of the DNA is sequenced at least ten times (called 10x coverage) and at least 98% is sequenced at least once. 

Nebula genomics goes beyond that — not only is all of the genome sequenced, but each piece is also sequenced on average 30x coverage. Higher sequencing coverage provides better accuracy for finding DNA variants.

Nebula Empowers the User to Learn About Their Own DNA

Nebula actually wants people to be able to learn about their health, personality, and ancestry. Nebula is committed to explaining the cutting edge science simply and accurately. Nebula believes individuals are capable of taking charge of their genomic information. This includes being able to use Nebula Research Library to go through curated research studies and Nebula Explore to receive weekly updates with the most recent scientific advances.

Nebula also allows users to access all of their own data. Users can download their raw genomic data and look at it themselves. Nebula even provides information on how to get started and explanations for what it all means.

Nebula’s Pricing is Straightforward and Affordable

There is no ambiguity in Nebula’s pricing. Whole-genome 30x coverage is $299. Access to the Nebula explore with its weekly updates is $9.99 a month or $700 for a lifetime of access. 


GeneDx
23andMe
AncestryDNANebula Genomics
DNA Testing MethodNext Generation (Single gene, multiple genes, all genes, or whole genome) or hybridization Microarray-based genotypingMicroarray-based genotypingNext generation (Whole Genome Sequencing with 30x coverage)
Able to upload raw DNA dataNoNoNoYes (23andMe and Ancestry)
Downloadable data accessNoYes (23andMe format file)Yes (Ancestry format file)Yes (FASTQ, BAM, and VCF files)
FDA approved Yes, for all testYes, for some testsYes, for some testNo
Physician orders needed for FDA approved testsYesNoYesNA
Informative and educational explanationsNoYes YesYes
Simplified Report Finding ToolsNoYesYesYes
CostVariable and often unpredictable$99, $199, or $499$99 or $149$0 – $299
GeneDx vs 23andMe vs AncestryDNA vs Nebula Genomics

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