June 2021
Volume 62, Issue 8
Open Access
ARVO Annual Meeting Abstract  |   June 2021
Highly sensitive and specific in silico program to detect RP1 Alu insertion from short-read sequencing data
Author Affiliations & Notes
  • Jinu Han
    Department of Ophthalmology, Yonsei University College of Medicine, Seodaemun-gu, Seoul, Korea (the Republic of)
  • Suk Ho Byeon
    Department of Ophthalmology, Yonsei University College of Medicine, Seodaemun-gu, Seoul, Korea (the Republic of)
  • Junwon Lee
    Department of Ophthalmology, Yonsei University College of Medicine, Seodaemun-gu, Seoul, Korea (the Republic of)
  • Christopher Suengkyu Lee
    Department of Ophthalmology, Yonsei University College of Medicine, Seodaemun-gu, Seoul, Korea (the Republic of)
  • Min Kim
    Department of Ophthalmology, Yonsei University College of Medicine, Seodaemun-gu, Seoul, Korea (the Republic of)
  • Hyun Taek Lim
    Department of Ophthalmology, University of Ulsan College of Medicine, Songpa-gu, Seoul, Korea (the Republic of)
  • Footnotes
    Commercial Relationships   Jinu Han, None; Suk Ho Byeon, None; Junwon Lee, None; Christopher Suengkyu Lee, None; Min Kim, None; Hyun Taek Lim, None
  • Footnotes
    Support  Supported by the Korea Centers for Disease Control and Prevention (Grant No. 2018-ER6902-02 and 2019-NG-051-01), and partially supported by National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2020R1C1C1007965).
Investigative Ophthalmology & Visual Science June 2021, Vol.62, 1564. doi:
  • Views
  • Share
  • Tools
    • Alerts
      ×
      This feature is available to authenticated users only.
      Sign In or Create an Account ×
    • Get Citation

      Jinu Han, Suk Ho Byeon, Junwon Lee, Christopher Suengkyu Lee, Min Kim, Hyun Taek Lim; Highly sensitive and specific in silico program to detect RP1 Alu insertion from short-read sequencing data. Invest. Ophthalmol. Vis. Sci. 2021;62(8):1564.

      Download citation file:


      © ARVO (1962-2015); The Authors (2016-present)

      ×
  • Supplements
Abstract

Purpose : To investigate mobile element insertions (MEIs) in exon 4 of RP1 and develop a simple approach to detect RP1 MEIs by searching unprocessed short reads.

Methods : A total of 494 unrelated patients with inherited retinal diseases were genotyped. Proband-only whole-genome sequencing (WGS) or trio WGS was performed in 16 unsolved families after targeted or whole exome sequencing. WGS revealed an RP1 Alu insertion in exon 4 in 2 families. The Linux program grep was developed to search for common MEIs in RP1 exon 4. A 26-bp “probe” sequence containing the known junction sequence of the MEI and corresponding wild-type 26bp sequence was used (See https://github.com/jin0008/RP1_aluinsertion). Additional screening for this mutation was performed in 273 unrelated patients.

Results : Among the 273 patients, 5 families had a heterozygous RP1 Alu insertion. In patients with heterozygous RP1 Alu insertion, 3 patients with the compound heterozygous c.5797C>T:p.(Arg1933*) variant had macular dystrophy and 2 patients with more proximal truncating variants (c.4196del and c.4582_4584del) had early-onset cone-rod dystrophy. The AluY insertion resulted in c.4052_4053ins:p.(Tyr352Alafs*9), which was confirmed by polymerase chain reaction and gel electrophoresis. No homozygous RP1 Alu insertion was found in our cohort. A simplified grep search code revealed a variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results in 120 control samples.

Conclusions : The MEI in RP1 exon 4 is common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1 Alu grep program detected AluY insertion in RP1 efficiently without preprocessing of raw data or complex installation processes.

This is a 2021 ARVO Annual Meeting abstract.

 

(A–E) Pedigree and retinal images of patients carrying RP1 Alu insertion. (F, G) Next-generation sequencing data displayed from the Integrative Genomics Viewer at the Alu insertion junction from whole-genome sequencing of B.II-1 and one control sample. Integrative Genomics Viewer with “show soft-clipped bases” revealed multiple reads with aberrant alignments on the right side corresponding to an Alu Y insertion. (H) Alu insertion confirmed by PCR and gel electrophoresis. DNA fragments containing Alu insertion were distinguished from DNA fragments not containing Alu insertion by size. (I) Schematic presentation of Alu insertion in exon 4 of RP1.

(A–E) Pedigree and retinal images of patients carrying RP1 Alu insertion. (F, G) Next-generation sequencing data displayed from the Integrative Genomics Viewer at the Alu insertion junction from whole-genome sequencing of B.II-1 and one control sample. Integrative Genomics Viewer with “show soft-clipped bases” revealed multiple reads with aberrant alignments on the right side corresponding to an Alu Y insertion. (H) Alu insertion confirmed by PCR and gel electrophoresis. DNA fragments containing Alu insertion were distinguished from DNA fragments not containing Alu insertion by size. (I) Schematic presentation of Alu insertion in exon 4 of RP1.

×
×

This PDF is available to Subscribers Only

Sign in or purchase a subscription to access this content. ×

You must be signed into an individual account to use this feature.

×