摘要：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
AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in
RP1 exon 4. This
AluY 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
AluY 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
AluY insertion, without the preprocessing of raw data or complex installation processes.
