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3 Diagnostic Genetic Tests for Eye Disease You Must Know

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Recent innovations have made genetic testing more accessible, now, ophthalmologists can use it as a helpful tool for identifying inherited eye diseases.

3 Diagnostic Genetic Tests for Eye Disease You Must Know
As an eyecare provider, your patients may come to you with clinical presentations that can confound and masquerade as underlying diagnoses. With current advancements in genetic testing for inherited eye diseases, providers have additional tools and information accessible to them to enhance patient care.
Here, we will discuss the different types of genetic testing available for some of the more common eye disorders likely to be encountered in clinical practice.

Overview of genetic testing for eye diseases

The primary purpose of genetic testing is to identify pathogenic genetic changes that drive the underlying pathogenesis that patients present with. These diseases include macular and retinal dystrophies, corneal dystrophies, optic neuropathies, and early-onset (i.e., congenital and juvenile) cataracts. Overall, genetic testing contributes to a better understanding of disease prognosis and facilitates treatment via clinical trial access.1

Clinical studies have identified over 500 gene mutations linked to the development of inherited eye diseases.

Moreover, through whole-genome sequencing, which is the process of analyzing specific DNA nucleotides in an entire genomic sequence, the extent that these mutations contribute to disease development can be further investigated. Genomic analyses allow genotype-phenotype correlations to be assessed, which helps guide treatment options targeting specific genetic pathogenic mechanisms.2
As a result, genetic testing has been used as a source of information by clinical providers to further facilitate diagnostic and therapeutic treatment plans for their patients.

Common eye diseases with known genetic components

The Centers for Disease Control and Prevention (CDC) reports that approximately 4.2 million individuals in the United States aged 40 and above are either legally blind or have low vision. Moreover, the CDC identifies that the leading causes of blindness and low vision stem from age-related eye diseases.3
In clinical practice, this means that some of the most common eye diseases that providers diagnose have a genetic component that contributes to clinical outcomes. With the expansion of genetic testing capabilities, researchers and providers can now target specific genetic factors that contribute to eye disease pathogenesis with the goal of delaying or terminating disease onset.

AAO Task Force recommendations for genetic testing

The American Academy of Ophthalmology (AAO) Task Force on Genetic Testing has established recommendations for providers who plan to enroll their patients in genetic testing.
AAO recommendations on genetic testing for eye disease include:4
  1. Offer genetic testing to patients where the causative gene(s) for the heritable eye disorder has been identified.
  2. Utilize approved laboratories that report their clinical data according to peer-reviewed medical literature and databases that define disease-causing and non-disease-causing variants.
  3. Provide patients with all necessary reports and findings of the genetic testing.
  4. Avoid direct-to-consumer genetic testing kits and provide patients with the necessary information to seek approved testing facilities.
  5. Order the most specific genetic test according to the patient’s clinical findings.
  6. Avoid repetitive testing for complex genetic diseases unless a clear treatment plan has been established.
  7. Avoid the testing of asymptomatic minors unless all parents consent or justifiable cause is established.

Genetic tests ophthalmologists can use to identify eye diseases

Genetic testing is a very detailed and carefully executed process. Due to the complex nature of genetic testing, it should be the goal of every eyecare provider to offer patients a simplified explanation of the advantages and disadvantages behind each test, as well as the cost of each genetic test. Clinicians should educate their patients on the testing process and the availability of genetic counseling.
The genetic testing process involves simplified steps that should be explained to patients seeking genetic testing options. The process begins with a collection of DNA samples (i.e., blood or saliva), which then get sent to a research laboratory for further analysis. It is important to note that clinicians should only utilize the recommended collection tools provided by accredited genetic laboratories to collect DNA samples.
After the DNA results are interpreted, clinicians should establish a return visit with their patients to review and discuss the findings. During this return visit, it is pertinent to address why the genetic test was conducted, the test's purpose, the results, and the steps moving forward based on the findings. Additionally, if available, clinicians may provide targeted therapy options that can be utilized in the future.

Next-generation sequencing

Next-generation sequencing (NGS) utilizes gene panel assays to detect nucleotide sequences in whole genomes or targeted regions of DNA or RNA strands. By detecting predetermined genetic components specific to genes of interest, NGS provides detailed results that outline potentially harmful genetic variants related to inherited eye diseases.
NGS has evolved from decades of genetic sequencing technologies, which now allows researchers to obtain data in a faster, more cost-effective manner.5 Through these advancements, researchers have the ability to analyze thousands of data points to understand the genetic factors and variants related to some of the most common eye pathologies treated by everyday providers.
Previous sequencing research was centered around the Sanger sequencing technology, which provided similar data analyses to NGS. However, Sanger sequencing was more costly and took approximately a decade to provide detailed genomic sequencing results. NGS revolutionized sequencing methods and can provide DNA sequencing of the entire human genome in less than one day.6

How is NGS conducted?

The process of NGS involves collecting and cleaving DNA/RNA strands to yield desired nucleic acid fragments, which serve as the starting point for testing. Next, researchers generate a sequencing library through one of two methods.
Researchers generate sequencing libraries with the following methods:
  • PCR amplification using radiolabeled nucleotides
  • Adding radiolabeled sequencing adapters to enlarge genetic sequences to the desired size
Using radiolabeled sequencing adaptors allows parallel sequencing to take place. In parallel sequencing, the library of radiolabeled nucleotides representing desired genomic sequences is loaded in a parallel fashion through an NGS reader. The NGS reader, which uses fluorescence scanning, analyzes each parallel nucleotide one by one.
The collected data is then compared to previously documented reference genomic sequences to identify variant nucleotide patterns that are potential contributing factors to disease onset.7

NGS in clinical research

NGS has many clinical applications, and it is currently being used in laboratories to understand the impact of genetic variants on patients’ vision. Patel et al. utilized NGS gene assays to examine a variety of genetic and developmental eye diseases in the pediatric population.
The data of this study showed that NGS was able to detect 429 known eye disease genes through parallel sequencing analysis, which detected various mutations compared to reference sequences. This shows how NGS functions as an additional tool for the detection of molecular defects to establish targeted therapies in the near future.
The data showed that variant mutations were contributing to the following pediatric eye diseases:8
  • Glaucoma (59 gene variants)
  • Microphthalmia-anophthalmia-coloboma (86 gene variants)
  • Congenital cataracts and lens-associated conditions (70 gene variants)
  • Retinal dystrophies (235 gene variants)
  • Albinism (15 gene variants)
  • Optic atrophy and strabismus (10 gene variants)

Weighing the pros and cons of NGS

The following information offers advantages and disadvantages of next-generation sequencing that providers can share with their patients for a greater understanding of genetic testing and its role in hereditary eye diseases.

Advantages of NGS:

  1. NGS has higher sensitivity compared to previous genetic sequencing technology.
  2. It provides a greater workflow to obtain fast and accurate genomic sequence readings.
  3. NGS can yield the sequence of millions of DNA fragments in less than one day.
  4. NGS offers specific information on genetic mutations that include gene insertions, deletions, duplications, inversions, translocations, amplification, etc.
  5. Previous genetic testing over the last three decades has cost $20 to $25 million; NGS has lowered the price tag to an average of $1,000 per genetic sequence examination. This has allowed for the more widespread use of genomic sequencing to assess genetic variants related to disease.9

Disadvantages of NGS:

  1. Although NGS outlines genetic variants expressed throughout genomic sequences, many of these variants and their functions are not fully understood and require future testing.
  2. There are limited research institutions with the necessary technology and funding to utilize NGS analysis.
  3. Approximately 3% of NGS data on genetic variants has a clinical application connected to genetic diseases. This finding leaves the door open for future research to further understand the correlation between genetic variants and inherited eye diseases.9

Genetic Eye Diseases test

The Genetic Eye Diseases (GEDi) test is an enhanced testing application that utilizes a targeted approach of next-generation sequencing to investigate known genetic variants connected to inherited eye diseases.
Currently, 226 gene mutations have been discovered to cause inherited retinal diseases; this number expands when including additional ocular pathologies such as strabismus, optic atrophy, and glaucoma.

Why use GEDi?

The purpose of using the GEDi test rather than NGS is to further refine data analysis to investigate the specific effects of identified gene mutations and the extent to which these mutations catalyze disease progression. GEDi testing shows 98% accuracy in detecting genetic variants within a genomic sequence.
In comparison, other methods of sequencing, such as whole-genome sequencing, yield an 88% accuracy rating.10 As a result, the GEDi test has allowed for an expansion of the testing capabilities of researchers and a more specific analysis of the reported 226 gene mutations related to inherited retinal diseases.

How does GEDi work?

GEDi testing utilizes a targeted enrichment bait library design, which is similar to the process of library sequencing in NGS. The target enrichment bait library design allows researchers to obtain DNA or RNA nucleotides present in coding exons, the 5’-/3’-untranslated regions, and select introns that harbor known genetic mutations that cause eye disorders.
After obtaining the desired library of known variants, the process of genetic sequencing for the GEDi test follows the NGS steps previously discussed.10 GEDi testing allows researchers to begin their experimental investigation with a very specific subgroup of mutation-causing genetic material. Consugar et al. expanded the clinical use of GEDi testing to detect single-nucleotide variants within whole-genome sequences.
The data from this study identified that the GEDi test had increased rates of sensitivity, specificity, reproducibility, and clinical sensitivity when compared with traditional whole-genome sequencing methods. This study that the GEDi test is preferable over whole-exome sequencing and that more clinical benefits, such as targeted therapies, can evolve from the results of the GEDi test.11

Weighing the pros and cons of the GEDi test

The GEDi test has many advantages and disadvantages that can play a vital role in the care of patients’ inherited eye diseases.

Advantages of the GEDi test:

  1. The GEDi test has a faster turnaround time (approximately 1 day) for genetic sequencing results compared to traditional whole-genome sequencing methods.
  2. The cost of the GEDi test ($430) is much cheaper per patient compared to whole-exome sequencing ($1,325).
  3. GEDi yields a very strong sensitivity and specificity, which allows for a higher probability of obtaining statistically meaningful results.11

Disadvantages of the GEDi test:

  1. DNA sequences of the targeted enrichment library may resist accurate variant detection when high concentrations of guanine-cytosine (GC) nucleotides and/or repetitive nucleotide elements are present.
  2. Nucleotides with insufficient sequencing depth are prone to failure of detection during radiolabeled scanning of nucleotide bases.
  3. For some genetic mutations of inherited eye diseases, expansion methods to augment nucleotide sequencing depth remain limited, thereby preventing further analysis of specific mutation subgroups.11

Polymerase chain reaction-single strand conformational polymorphism

Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) is an experimental method aimed at analyzing genomic sequences and identifying coexisting genetic mutations. Specifically, PCR-SSCP can detect nucleotide insertions, deletions, rearrangements, etc., that can predispose patients to a variety of heritable diseases, including inherited eye diseases.

Why use PCR-SSCP?

PCR-SSCP is used in molecular laboratories to identify polymorphisms that contribute to inherited eye diseases and to address the risk factors that augment mutation rates. The findings of each PCR-SSCP have been used by researchers to develop treatment options specific to DNA polymorphisms and to identify patient carriers relative to the general population.12

How does PCR-SSCP work?

The process of PCR-SSCP begins with the screening of genetic sequences to detect DNA base pair variants. If variants are identified, traditional PCR methods are utilized, beginning with gene amplification to produce a viable number of mismatched sequences.
When gene amplification is complete, double-helix DNA strands are enzymatically separated into single-stranded DNA (ssDNA) that contain the mismatched base pairs that represent the genetic variant. The ssDNA strands get further fragmented into smaller nucleotides to allow for gel electrophoresis analysis.
Gel electrophoresis separates the DNA fragments according to size and weight. The purpose of using gel electrophoresis was built on the notion that ssDNA folds into specific conformational shapes when denatured. As a result, gel electrophoresis allows researchers to differentiate mutant base pairs from normal base pairs according to these folded structures to determine their prevalence and location within the genomic sequence.13
PCR-SSCP is another form of genetic testing utilized by molecular laboratories to identify the genetic factors that cause inherited eye diseases. This genetic test offers clinicians a valuable source of information on the causes of patients’ eye pathologies so that further attention can be directed toward these identified genetic factors.

Weighing the pros and cons of PCR-SSCP

Clinicians can share the following advantages and disadvantages of PCR-SSCP with their patients as part of their treatment plans.

Advantages of PCR-SSCP:

  1. PCR-SSCP is a fast, inexpensive technique that can be done in many laboratories with PCR technology.
  2. PCR-SSCP has a high sensitivity and specificity rate for detecting single-strand polymorphisms within genomic sequences.
  3. This technique utilizes radiolabeled primers during gene amplification, which allows for the use of gel or capillary electrophoresis, which yields precise, reproducible, and thorough data results.14

Disadvantages of PCR-SSCP:

  1. Although the cost of running each PCR-SSCP analysis is low, the upfront expense of purchasing the technology is relatively costly. The DNA sequencer that detects radiolabeled nucleotides is the most expensive component of the technology.14
  2. Larger DNA fragments under investigation can be cleaved with restriction enzymes, which could lead to unidentified base substitutions contributing to disease onset. This may mask data results and prevent an identifiable genetic mutation from being assessed.15

Additional resources for genetic testing

Genetic Testing Registry

The Genetic Testing Registry of the National Institutes of Health (GTR) is a free online resource available to researchers and eyecare providers to help them understand the role of genetic testing in various pathologies, including inherited eye diseases.
With the advent of advanced genetic testing and its widespread availability, the GTR offers a pooled database of genetic test information voluntarily submitted by previous test providers. The goal of the GTR is to expand the clinical use of genetic testing and to offer providers information on the different test options available for their patients.16

Genetic counseling

Genetic counseling should also be recommended to patients, as certified genetic specialists/counselors can serve as an additional source of information on genetic testing. Furthermore, genetic counseling can enhance patients’ understanding of their clinical diagnoses, as well as expand upon the recommendations suggested by their eyecare provider.
During genetic counseling sessions, a specialist may review the test results, which include the number of mutated genes, chances of disease development, risk factors, treatment options, and whether other family members should seek genetic testing. The information that can be provided by a team of genetic specialists offers the patients a valuable second source of care in addition to their eyecare provider, and allows for an optimal treatment plan to be established.1


Diagnostic genetic testing has shown promising results in detecting, assessing, and treating various genetic mutations that contribute to poor vision outcomes. The availability of genetic testing has increased substantially over the last decade, which has allowed researchers and clinicians to expand their understanding of the role that genetics plays in eye disorders.
Some of the most common eye disorders in clinical practice have been shown to be largely influenced by genetic mutations that can affect the timing of disease onset. However, with the implementation of the Genetic Testing Registry, data can be further shared between researchers and clinicians, enabling them to be more prepared to detect markers of disease and provide necessary resources in a timely manner.
As a result, genetic testing has become a promising component of the patient care process and a vital tool in diagnosing various inherited eye diseases.
  1. Foundation Fighting Blindness. (n.d.). Genetic testing for retinal degenerative diseases: Information and resources for affected individuals, families and health care providers. Foundation Fighting Blindness. Retrieved November 19, 2022, from
  2. Frontiers. (2022). Molecular diagnosis and disease mechanisms in rare genetic eye disease. Frontiers. Retrieved November 20, 2022, from
  3. Centers for Disease Control and Prevention. (2020, June 3). Common eye disorders and diseases. Centers for Disease Control and Prevention. Retrieved November 20, 2022, from
  4. Stone EM, Aldave AJ, Drack AV, et al.  Recommendations for genetic testing of inherited eye diseases: report of the American Academy of Ophthalmology Task Force on genetic testing.  Ophthalmology. 2012;119(11):2408-2410.
  5. Illumina. (n.d.). Next-generation sequencing (NGS). Next-Generation Sequencing (NGS). Retrieved November 21, 2022, from
  6. Behjati S, Tarpey PS. What is next generation sequencing? Arch Dis Child Educ Pract Ed. 2013 Dec;98(6):236-8. doi: 10.1136/archdischild-2013-304340. Epub 2013 Aug 28. PMID: 23986538; PMCID: PMC3841808.
  7. iRepertoire. (2020, October 5). NGS overview: from sample to sequencer to results. iRepertoire. Retrieved November 21, 2022, from
  8. Patel A, Hayward JD, Tailor V, et al. The Oculome Panel Test: Next-Generation Sequencing to Diagnose a Diverse Range of Genetic Developmental Eye Disorders. Ophthalmology. 2019 Jun;126(6):888-907. doi: 10.1016/j.ophtha.2018.12.050. Epub 2019 Jan 14. PMID: 30653986.
  9. Singer, M. (2022, May 18). Exploring the pros and cons of next-generation sequencing. Market Business News. Retrieved November 22, 2022, from
  10. Panel-based genetic diagnostic testing for Eye Disease. Harvard Medical School Department of Ophthalmology. (2014, December 1). Retrieved November 22, 2022, from
  11. Consugar, M., Navarro-Gomez, D., Place, E. et al. Panel-based genetic diagnostic testing for inherited eye diseases is highly accurate and reproducible, and more sensitive for variant detection, than exome sequencing. Genet Med 17, 253–261 (2015).
  12. Kakavas VK, Plageras P, Vlachos TA, Papaioannou A, Noulas VA. PCR-SSCP: a method for the molecular analysis of genetic diseases. Mol Biotechnol. 2008 Feb;38(2):155-63. doi: 10.1007/s12033-007-9006-7. Epub 2007 Oct 13. Erratum in: Mol Biotechnol. 2008 Nov;40(3):316.
  13. Goodall, R. (2014). Molecular clinical biochemistry. Clinical Biochemistry: Metabolic and Clinical Aspects, 844–873.
  14. Menounos, P. G., & Patrinos, G. P. (2010). Mutation detection by single strand conformation polymorphism and heteroduplex analysis. Molecular Diagnostics, 45–58.
  15. Bailey, A. L. (1995). Single-stranded conformational polymorphisms. PCR Strategies, 121–129.
  16. U.S. Department of Health and Human Services. (n.d.). Genetic testing registry. National Institutes of Health. Retrieved November 22, 2022, from
Vincent Gallub, M3
About Vincent Gallub, M3

Vincent Gallub is a third-year medical student at the Touro College of Osteopathic Medicine- Harlem. He graduated summa cum laude from George Washington University with a bachelor’s degree in Psychology and a concentration in Cognitive Neuroscience.

Prior to starting medical school, Vincent served as an ophthalmic technician, where he discovered his passion for ophthalmology and the treatment of advanced eye diseases. Additionally, during his undergraduate studies, Vincent served as a research intern at the George Washington University Cancer Center and Children’s National Medical Center, both located in Washington, D.C. Outside of his academic and research pursuits, Vincent enjoys traveling, exploring New York City, and watching his favorite sports team, the New York Yankees.

Vincent Gallub, M3
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