Abstract
Purpose :
In previous literatures, mobile element insertions (MEIs), including LINE-1 and Alu element, have been known to cause human genetic diseases. However, in various type of MEIs, LINE-1 has not been diagnosed in inherited retinal degeneration (IRD), and also, they are not easy to map and often missed in annotations of non-canonical transcripts. Here, we established a capture-based next generation sequencing (NGS) analysis workflow applied for our IRD cohort for detecting who had genetic variations originated from LINE-1 insertion.
Methods :
253 unsolved probands from Taiwan inherited retinal degeneration project (TIP) cohort recruited from 2015 to 2020 have been screened for MEIs using capture-based NGS retinal dystrophy panel which included 233 disease-related genes following by SCRAMble tool. The computational analysis results were viewed by clusters of soft clipped reads in a BAM file by means of Integrative Genomics Viewer (IGV) and the possible variations were verified by traditional experiments using long-range PCR. All probands were evaluated regarding the clinical examination, which mainly includes best-corrected visual acuity, fundus autofluorescence, color photo, optical coherence tomography, electroretinogram, visual field, and other clinical routine.
Results :
In our cohort, two IRD probands were diagnosed caused by LINE-1 insertion. Proband 1 was a 54-year-old woman who was initially partially-diagnosed with a single nucleotide variant, c.6416G>A, in EYS. After MEIs analysis, she was then found to have a LINE-1 insertion in the exon 26 of EYS. There is no other patient in her family. Proband 2 was a 25-year-old man carried a heterozygous truncating mutation, c.11704C>T, and a LINE-1 insertion in exon 8 in ALMS1 gene, and both mutations were simultaneously found in his brother. They had similar phenotypes and the same age of onset. With the information, we can make sure that he was affected with ALMS1 genetic defects and diagnosed with recessive Alström syndrome.
Conclusions :
To our knowledge, this is the first case report about pathogenic LINE-1 insertion in IRD patients. This study highlights the value of systematically conducting for MEIs detection of NGS data in IRDs cohort.
This abstract was presented at the 2023 ARVO Annual Meeting, held in New Orleans, LA, April 23-27, 2023.