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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.
Check back soon for additional data on variant confirmations in relation to their individual impacts to the
disease.