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Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder  Alu  insertion in exon 4 of  RP1  has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the  Alu  insertion in exon 4 of  RP1  using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating  RP1  variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed  Alu Y c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in  RP1  exon 4. This  Alu Y insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this  Alu Y insertion in  RP1  exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results using 120 control samples. The MEI in  RP1  exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The  RP1 - Alu  grep program efficiently detected the  Alu Y insertion, without the preprocessing of raw data or complex installation processes.

In Silico identification of a common mobile element insertion in exon 4 of RP1