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Logistics of Genetic Testing: An Overview for Retina Specialists

What you need to know about genetic testing laboratories to help your patients.

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With a multitude of gene therapy trials currently under way, genetic testing has become a critical component of diagnosing and managing the patient with inherited retinal disease (IRD). As a retina specialist with a particular focus in IRD, I have taught an instructional course on IRD and gene therapy for the past several years at the American Society of Retina Specialists as well as the American Academy of Ophthalmology, and without a doubt the most frequently asked question during the panel discussion regards the logistics of genetic testing.

Many retinal dystrophy clinics are associated with academic institutions and may have a genetic counselor on staff who can facilitate the collection and shipment of blood or saliva, completion of paperwork, selection of laboratories, and insurance preauthorization. Pre- and posttesting genetic counseling is done by a certified ophthalmic genetic counselor in many academic institutions. Without infrastructure in place to support these considerations, trying to coordinate genetic testing in a private practice setting can be overwhelming.

The goal of this article is to give an overview that is both comprehensive and accurate, but by no means will this be all inclusive. I will describe available genetic testing options in the light of my personal experience clinically working with some of these genetic testing laboratories in the past few years. I have no financially related bias or personal relationship to any labs.

Christine Kay, MD, is a vitreoretinal specialist with Vitreoretinal Associates in Gainesville, Florida. Dr. Kay has no financial disclosures related to genetic testing laboratories, but states that she is a clinical trial investigator and consultant for AGTC, clinical trial investigator for Alkeus, clinical trial investigator for Foundation Fighting Blindness, and consultant for Astellas. Reach her at christinenkay@gmail.com. Dr. Kay would like to acknowledge Karmen Trzupek, MS, genetic counselor, for her contribution to this article.

ROLE OF GENETIC TESTING IN A RETINA CLINIC

The field of retinal genetics and gene therapy has been exploding in the past several years. Multiple phase 1/2 trials are ongoing in the US and in Europe for IRDs, including Stargardt disease, X-linked retinoschisis, X-linked retinitis pigmentosa (RP), Usher syndrome (MYO7A associated), achromatopsia (both CNGA3 and CNGB3 associated), choroideremia, and MERTK-associated autosomal recessive RP. With the first phase 3 trial in retinal gene therapy now complete for RPE65-associated Leber congenital amaurosis (LCA), and results recently published in The Lancet,1 as well as an expedited 6-month US Food and Drug Administration (FDA) review in progress (with a unanimous vote in favor by an FDA advisory committee on October 12, 2017 and a formal FDA response expected in January 2018), we are living in a new reality of the possibility of genetic therapy for retinal eye disease.

The importance of genetic testing has become imminent, and awareness of this importance is growing not only in our retina community but also in our referral community of general ophthalmologists and optometrists. Retina specialists are increasingly expected to be aware of updates in the field of retinal genetics and retinal gene therapy and should be able to facilitate discussions with patients involving the importance of diagnosis, confirmation of genotype, and options for relevant clinical trials.

This is not to say that we all need to be able to accurately diagnose and follow progression of patients with IRDs. Those of us who specialize in IRDs believe that we can offer these patients specialized care, optimal opportunity for confirmation of diagnosis, and counseling regarding natural history and pertinent clinical trial opportunities, with the correct tools in specialized IRD clinics (electrophysiology, microperimetry, kinetic perimetry) to follow progression. But, realistically, with a prevalence of 1 out of 4,000 for RP2 and 1 out of 8,000 for Stargardt disease,3 we are all going to be seeing and even managing these patients in our clinics, and the better prepared we are to deal with the question of genetic testing in this subset of patients the better we will be able to take care of these patients.

Many patients likely ask about genetic testing, given an increased public awareness of the importance of genetic confirmation of disease and awareness of gene therapy trials. I would argue that if patients are not bringing up genetic testing, we as retina specialists should be initiating this conversation.

WHICH PATIENTS BENEFIT FROM TESTING?

In 2016, an American Academy of Ophthalmology task force released a position statement regarding the role of genetic testing in retinal disease: At this time, clinicians should avoid routine genetic testing for genetically complex/multifactorial diseases such as AMD; instead, genetic testing should be used in Mendelian disease (monogenetic disease) such as RP or Stargardt disease.4

Within the list of inherited retinal dystrophies, I have a priority list of diseases I feel most critically require genetic confirmation, based on (1) inheritance pattern and family counseling/risks and (2) existence of gene therapy or other clinical trials that depend on genotype confirmation. Regarding inheritance pattern, X-linked disease and autosomal-dominant disease imply substantial risks to other family members and future offspring, and genetic testing in the affected individual may be useful to identify other at-risk relatives. Therefore, if I am suspicious for these inheritance patterns when I elicit a family history, I absolutely encourage proceeding with genetic testing and spend considerable time counseling the patient and family as to possible risks for other relatives (including carrier state in unaffected women in the extended family for X-linked disease), children, or future offspring.

Regarding existence of therapies or trials, possible therapies for Stargardt disease, for example, are currently being evaluated in gene therapy trials (NCT01367444), stem cell therapy trials,5 and oral drug trials (NCT02402660); so, if there is any suspicion of a genetic diagnosis of ABCA46 (the most common genotype for autosomal-recessive Stargardt disease, or STDG1), I point the patient to genetic testing and counsel the patient regarding updates in relevant ongoing clinical trials. Similarly, given the existence of ongoing clinical trials for these diseases, I highly suggest proceeding with genetic testing if there is suspicion for Leber congenital amaurosis,1 choroideremia,7 X-linked retinoschisis (NCT02317887, NCT02416622), X-linked RP (NCT03116113), achromatopsia (NCT02935517, NCT02599922), or Usher syndrome (NCT01505062).

SELECTING A TESTING LABORATORY

When considering which genetic testing laboratory to use, there are multiple considerations:

  • Is the lab Clinical Laboratory Improvements Amendment (CLIA) certified? If not, don’t use it! Certification is a mandatory criterion for clinical genetic testing in the United States. This certification is the first requirement in lab selection.
  • Does the lab bill insurance directly? Does the lab attempt preauthorization by requesting clinic notes and directly working with insurance companies?
  • Who analyzes the results? Does the genetic analysis follow ACMG (American College of Medical Genetic and Genomics) standards? With next-generation sequencing, results can be quite messy, requiring skilled interpretation of “pathogenicity” of the identified variants (mutations).
  • Is testing allele specific (looking only for known mutations) or full sequencing (looking for any mutations)? Along these lines, does the analysis include the detections of deletions and duplications, not just mutations? These types of genetic errors are common in Ush2A and EYS, 2 common genes associated with Usher syndrome or RP. Does testing look for deep intronic mutations, which are quite common in the ABCA4 gene (Stargardt disease)?
  • “Panel” selection: targeted vs comprehensive, and for comprehensive, how many genes are tested? Does the lab offer a comprehensive large “retinal dystrophy” panel (ie, Blueprint Genetics’ 181-gene panel for $1,700 or Mass. Eye and Ear’s 267-gene panel for $2,850) or does the lab specialize in directed disease-targeted panels? For example, Molecular Vision Lab, in addition to a large comprehensive retinal dystrophy panel, has a targeted “macular dystrophy panel” that costs $500 and tests 13 genes with next-generation sequencing (ABCA4, BEST1, CDH3, DRAM2, EFEMP1, ELOVL4, IMPG1, IMPG2, PROM1, RDS, RP1L1, TIMP3, TTLL5).
  • What is the lab’s detection rate? Does it have available validation data for specific conditions or genes? Mutations in RPGR, for example, associated with X-linked RP, can be difficult to detect. Some laboratories have much higher detection rates than others.
  • What is the turnaround time for results? This can vary widely, from a few weeks for the fastest labs to months or years for the slower labs.
  • Logistics of sample collection: Are both saliva and blood accepted for DNA retrieval? Does the company provide collection kits and FedEx shipping labels? These are important logistical considerations.

GENETIC TESTING LABORATORIES

This section will review some of the categories of laboratories and mention a few specific laboratories, focusing on the labs I have had the most personal experience using.

Commercially Available Options

These companies offer comprehensive large next-generation sequencing retinal dystrophy panels and rapid turnaround of results. Companies also provide interpretation of results, with analysis of pathogenicity and clinical significance of mutations. Typically, companies mail a specimen collection kit to patients.

Nonprofit Laboratories

The John and Marcia Carver Nonprofit Genetic Testing Laboratory at the University of Iowa (carverlab.org ) offers diagnosis-driven “smart panels” and tier testing models, which may lower the cost of testing. Turnaround depends on panel tested and averages 14 to 16 weeks. Mass. Eye and Ear Infirmary also has a nonprofit lab (oculargenomics.meei.harvard.edu ).

Research-Based Testing

Some universities as well as nonprofit laboratories may offer research-based options for genetic testing. For example, patients seen at University of Iowa may be offered research-based genetic testing as part of their clinical exam with Dr. Edwin Stone. Turnaround time can be longer and more variable with research-based testing options.

Externally Funded Options

In 2016, Spark Therapeutics, a gene therapy pharmaceutical company, launched an initiative to provide access to genetic testing free for eligible IRD patients, The Identify Your Inherited Retinal Disease, or ID YOUR IRD, initiative (idyourird.com ). Thirty-one genes are tested, including most of the genes associated with LCA, choroideremia, and early-onset, rod-dominated RP. Importantly, the genes associated with X-linked RP, most types of adult-onset RP, and macular dystrophies (including Stargardt disease) are not included.

GENETIC COUNSELING

For both legal and ethical reasons, it is important that we recognize our limitations as physicians and explain these limitations to our patients — and document that we have explained them. We are not (or at least most of us are not) certified ocular genetic counselors ourselves. We have not completed a 2-year master’s degree in an accredited genetic counseling program. Even for those of us who are experienced in seeing and managing patients with IRDs, it is important to highly recommend to patients that they utilize the widely available genetic counseling options, which includes offering them an appointment with a geneticist (medical doctor) or offering them ocular genetic counseling at a local academic institution or through a telemedicine-based counseling service.

Telephone counseling has become more widely available and allows genetic counseling to be readily available to patients regardless of demographic or location. I typically point my patients in the direction of a pediatric or adult geneticist if I have any concerns about a systemic or syndromic disease with other potential systemic risks (ie, Bardet-Biedl syndrome, Batten disease, Senior-Loken syndrome). These syndromic diseases involve multiple systems and often severe systemic risks/morbidity and even mortality. Ophthalmologists are certainly not capable of managing these diseases and must recruit the help of our internal medicine counterparts and geneticists.

I encourage patients to consider using Informed DNA, an excellent ocular genetic telemedicine service based in St. Petersburg, Florida (informeddna.com ). This company bills the patient’s insurance for a genetic counseling appointment and can eradicate logistical issues of genetic testing from your clinic by offering the entire package: pretesting genetic counseling including obtaining a detailed history and inheritance pattern, post-test counseling explaining results and prevalence/prognosis if known, preauthorization of insurance for testing, and selection of appropriate genetic testing laboratories. Lastly (and this is my favorite part), this company works with genetic testing labs that ship specimen collection kits to patients so that the specimen can be collected at a convenient time by your patient from the comfort of home. The specimen is typically saliva, which can easily be obtained by a patient at home, although blood samples are also accepted.

REGISTRY

With the explosion in clinical trials for IRDs, it is important that patients register their diagnosis and genotype with a national registry. My Retina Tracker (myretinatracker.org ) is a free online registry provided by the Foundation for Fighting Blindness as part of its mission to drive the research that will provide preventions, treatments, and cures for people affected by IRDs. The My Retina Tracker protocol is approved by Western Institutional Review Board. Participants in My Retina Tracker provide informed consent to share their deidentified data in the registry, and this deidentified data are accessible to both researchers and industry.

Privacy is a high priority and participants only display a unique, anonymous registry number in the viewable database. To contact participants with a profile of interest, researchers need to demonstrate they have an IRB-approved protocol and contact letter, and provide the registry number of the participants they wish to contact. Registry staff then share the contact information with the participants, who then decide if they wish to engage.

SUMMARY

With the recent explosion in the field of retinal gene therapy, retina specialists need to keep up with counseling, managing, or appropriately referring patients with an IRD. Genetic testing is a huge component of the work-up. It requires not only logistical consideration if this service is going to be offered in a clinic setting but ethical and legal considerations.

For physicians who are not interested in making genetic testing service a part of their clinic, ocular genetic telecounseling service companies can provide this. For physicians who are ready to embark on offering genetic testing within the busy retina clinic practice, this article hopefully provided some useful tips, considerations, and advice from someone who has been experienced some of the pitfalls and logistical challenges. My own preferences in genetic testing services have evolved dramatically over the past several years. Suffice it to say that genetic testing for inherited retinal disease is here to stay, and as retina specialists we are going to become increasingly engaged in the process of facilitating this process for our patients. RP

Table 1: Labs That Offer Comprehensive Large Retinal Dystrophy Panel
NUMBER OF GENES TESTED IN RETINAL DYSTROPHY PANEL COST DIRECTLY BILLS INSURANCE? TESTING TURN-AROUND TIME
Molecular Vision Lab 280 $1,500 Yes 4-6 weeks
Blueprint Genetics 181 $1,700 Yes 4-6 weeks
Mass. Eye and Ear 267 $2,850 No 90 days
Prevention Genetics 80 $2,890 Yes 4 weeks
GeneDx 201 $3,000 Yes 8 weeks
Baylor Genetics 66 $4,060 Yes 72 days

REFERENCES

  1. Russell S, Bennett J, Wellman JA, et al. Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial. Lancet. 2017;26;390(10097):849-860.
  2. Haim M. Epidemiology of retinitis pigmentosa in Denmark. Acta Ophthalmol Scand Suppl. 2002;(233):1-34.
  3. Walia S, Fishman GA. Natural history of phenotypic changes in Stargardt macular dystrophy. Ophthalmic Genet. 2009;30(2):63-68.
  4. American Academy of Ophthalmology. Recommendations for genetic testing of inherited eye diseases – 2014. Available at https://www.aao.org/clinical-statement/recommendations-genetic-testing-of-inherited-eye-d .
  5. Schwartz SD, Regillo CD, Lam BL, et al. Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies. Lancet. 2015;385(9967):509-516.
  6. Zhang K, Kniazeva M, Hutchinson A, et al. The ABCR gene in recessive and dominant Stargardt diseases: a genetic pathway in macular degeneration. Genomics. 1999;60(2):234-237.
  7. MacLaren RE, Groppe M, Barnard AR, et al. Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial. Lancet. 2014;383(9923):1129-1137.