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Genetic Testing for Keratoconus – Avagen


the first and leading personalized genetic eye test. AvaGen quantifies the risk or presence of keratoconus and other corneal genetic disorders caused by gene variants. AvaGen delivers a valuable tool for early and accurate decision-making that protects vision for patients and their families.

Home » Center of Keratoconus » Genetic Testing for Keratoconus – Avagen

Next Generation Sequencing (NGS) AvaGen delivers:

  • A new level of targeted and personalized eyecare
  • Objective polygenic keratoconus risk score -data based on multiple gene clusters that have a high correlation with keratoconus -to inform early and accurate management decisions
  • Definitive diagnosis of specific corneal dystrophies based on monogenic data from the TGFBI gene and 70 TGFBI gene variants providing YES/NO diagnosis of corneal dystrophies including:
    • Epithelial Basement Membrane
    • Granular Type 1
    • Granular Type 2 (Avellino)
    • Lattice Type 1
    • Lattice Type IIIA
    • Reis-Bucklers
    • Schnyder
    • Theil-Behnke
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Easy to Understand Reporting

Every AvaGen test report is organized into actionable sections plus other supporting information:

  • Patient and Order Information
  • Keratoconus risk assessment
    • Polygenic risk score, categorized as low, medium, or high risk of keratoconus
    • Relevant variant analysis
    • Detailed variant interpretation
  • Corneal dystrophy detection
    • YES/NO diagnosis of corneal dystrophies based on monogenic data from TGFBI gene
    • Relevant variant analysis
    • Detailed variant interpretation

Genetic Counseling

Avellino also provides the services of genetic counselors to assist doctors and patients with added expert support.

  • Counseling is available for those with at-risk or positive test results
  • Genetic counseling gives you information about how genetic conditions might affect you or your family and may be used to determine how likely it is that you or your family member has a genetic condition. Genetic counseling after testing can help you better understand your test results and treatment options, help you deal with emotional concerns, and refer you to other healthcare providers, advocacy, or support groups.

Collection, Ordering, and Results

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Simple buccal (mouth) swab to collect sample

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Ship to Avellino for analysis in high-throughput CLIA-certified lab

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AvaGen report uploaded to HIPAA-compliant portal

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Genetic counselors available to provide additional layers of support for ECPs and patients

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Genetics & Eyecare Today™ is a go-to resource helping eyecare professionals understand and proactively apply genetic data in the management of ocular diseases and conditions.

Genetics & Eyecare Today™ is a go-to resource helping eyecare professionals understand and proactively apply genetic data in the management of ocular diseases and conditions.

Explore AvaGen methodology

A next-generation sequencing platform uncovers rare variants associated with keratoconus

Keratoconus, a corneal ectatic disorder, is a complex disease characterized by genetic heterogeneity requiring a comprehensive sequencing method able to detect rare DNA variants. Here, we present a representative case study where a targeted next-generation sequencing (NGS) platform was used to uncover rare variants.


Whole exome sequencing (WES) was carried out on a sample cohort of 218 cases and 68 controls. The WES results were used to design a custom NGS panel. 119 case samples, including the case study described here and 79 controls, were sequenced with the targeted NGS panel. DNA was extracted from buccal swab samples and functionalized libraries were constructed prior to all sequencing. Variant call format files (VCFs) were filtered, and a risk score based on prediction software tools was developed to predict the pathogenicity of suspect variants. The case study presented here was clinically diagnosed as keratoconus with secondary amyloid deposits.


Five rare, missense single nucleotide variants found in LOX, LTBP2, MAP3K- 19, and ZNF469 were uncovered in the subject’s DNA. Variants in the LTBP2 and MAP3K-19 genes are reported here for the first time in association with keratoconus. Variations known to result in corneal dystrophic amyloid deposition were not present.


NGS can identify a range of genetic variants for keratoconus. The variants uncovered in LTBP2 and MAP3K-19 strengthen the evidence for linkage of keratoconus to chromosomal loci 14q24.3 and 2q21.3. Providing physicians with a test to determine genetic factors can help assess the risk of developing keratoconus before symptoms appear.

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