EYS is a major gene involved in retinitis pigmentosa in Japan: genetic landscapes revealed by stepwise genetic screening

Abstract

Next-generation sequencing (NGS) has greatly advanced the studies of causative genes and variants of inherited diseases. While it is sometimes challenging to determine the pathogenicity of identified variants in NGS, the American College of Medical Genetics and Genomics established the guidelines to help the interpretation. However, as to the genetic screenings for patients with retinitis pigmentosa (RP) in Japan, none of the previous studies utilized the guidelines. Considering that EYS is the major causative gene of RP in Japan, we conducted stepwise genetic screening of 220 Japanese patients with RP utilizing the guidelines. Step 1–4 comprised the following, in order: Sanger sequencing for two major EYS founder mutations; targeted sequencing of all coding regions of EYS; whole genome sequencing; Sanger sequencing for Alu element insertion in RP1, a recently determined founder mutation for RP. Among the detected variants, 2, 19, 173, and 1 variant(s) were considered pathogenic and 8, 41, 44, and 5 patients were genetically solved in step 1, 2, 3, and 4, respectively. Totally, 44.5% (98/220) of the patients were genetically solved, and 50 (51.0%) were EYS-associated and 5 (5.1%) were Alu element-associated. Among the unsolved 122 patients, 22 had at least one possible pathogenic variant.

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

“…By incorporating the simplified grep program in our clinical diagnostic pipeline, we detected MEI in RP1 , which can provide a definitive molecular diagnosis that is typically missed by short-read sequencing. In our cohort with compatible phenotypes (n = 273), MEI was detected in 1.8% of patients, consistent with the frequencies reported in previous studies 24 . Numa et al suggested that tier-based approach is more efficient to detect pathogenic variants in Japanese RP as following orders: (1) Sanger sequencing of two major mutations in EYS , (2) targeted sequencing of all EYS coding exons, (3) WGS, and (4) Sanger sequencing of the Alu element in RP1 24 .…”

“…In our cohort with compatible phenotypes (n = 273), MEI was detected in 1.8% of patients, consistent with the frequencies reported in previous studies 24 . Numa et al suggested that tier-based approach is more efficient to detect pathogenic variants in Japanese RP as following orders: (1) Sanger sequencing of two major mutations in EYS , (2) targeted sequencing of all EYS coding exons, (3) WGS, and (4) Sanger sequencing of the Alu element in RP1 24 . However, our grep program detected the RP1-Alu insertion efficiently without further experiments or sequencing and yielded no false-positives.…”

“…Studies aimed at detecting pathogenic MEIs in Asian populations are relatively limited, despite the potential for population-specific founder MEIs. Recently, a founder Alu insertion in exon 4 of RP1 has been reported with autosomal recessive inheritance in Japanese patients with macular dystrophy 10 , 14 , 15 , 24 . Therefore, the founder MEI found in the Japanese population should be also investigated in the Korean population.…”

Genotype Profile of Global EYS-Associated Inherited Retinal Dystrophy and Clinical Findings in a Large Chinese Cohort

“…In the present study, the larger sample size identified these two mutations as additional hotspots in Chinese populations. Two Japanese hotspot mutations, c.4957_4958insA and c.8805C > A (Numa et al, 2020), were detected less frequently in the G1 cohort, indicating differences between the hotspots among patients in the Asian population.…”

Diverse Genetic Landscape of Suspected Retinitis Pigmentosa in a Large Korean Cohort

“…The overall diagnostic yield in our study was similar to those of previous studies [ 13 , 14 , 15 ], but the composition ratios of frequently found causative genes were slightly different: EYS (8.2%) and USH2A (6.8%). From previous studies, EYS variants account for the largest portion of causative genes in the East Asian region, especially in Korea and Japan; EYS variants account for 20 to 30% of RP cases, and USH2A variants cause less than 10% [ 16 , 17 , 18 ]. On the other hand, USH2A variants make up 20 to 40% and EYS variants account for less than 10% of RP cases, among the total RP population in Western or European ethnicities [ 8 , 19 , 20 ] as well as Chinese or Taiwanese populations [ 7 , 21 ].…”