Pathogenic NOTCH3 Variants Are Frequent Among the Korean General Population

Abstract

Objective

This study aimed to determine the frequency of pathogenic NOTCH3 variants among Koreans.

Methods

In this cross-sectional study, we queried for pathogenic NOTCH3 variants in 2 Korean public genome databases: the Korean Reference Genome Database (KRGDB) and the Korean Genome Project (Korea1K). In addition, we screened the 3 most common pathogenic NOTCH3 variants (p.Arg75Pro, p.Arg544Cys, and p.Arg578Cys) for 1,000 individuals on Jeju Island, where the largest number of patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) have been reported in Korea.

Results

The pathogenic NOTCH3 variant (p.Arg544Cys) was found in 0.12% of sequences in the KRGDB, and 3 pathogenic variants (p.Arg75Pro, p.Arg182Cys, and p.Arg544Cys) were present in 0.44% of the Korea1K database. Of the 1,000 individuals on Jeju Island, we found 2 cysteine-altering NOTCH3 variants (p.Arg544Cys variant in 9 and p.Arg578Cys in 1 individual) in 1.00% of the participants (95% confidence interval: 0.48%–1.83%). The presence of cysteine-altering NOTCH3 variants was significantly associated with a history of stroke (p < 0.001).

Discussion

Pathogenic NOTCH3 variants are frequently found in the general Korean population. Such a high prevalence of pathogenic variants could threaten the brain health of tens of thousands to hundreds of thousands of older adults in Korea.

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) was known as a rare genetic disorder with an estimated prevalence of 2–5/100,000.^1,2 However, recent genomic database research clearly indicates an estimated global mutation prevalence of 3.4/1,000, much higher than that estimated previously.³ In particular, the East or South Asian regions showed the highest frequency of cysteine-altering NOTCH3 mutations with a prevalence of 9.0–11.7/1,000 individuals. This study aimed to determine the frequency of pathogenic NOTCH3 variants among Koreans.

Methods

Korean Public Genome Database Query

We queried for pathogenic NOTCH3 variants associated with CADASIL in 2 publicly available Korean genome databases: the Korean Reference Genome Database (KRGDB) and the Korean Genome Project (Korea1K).^4,5 The KRGDB was established by the Korean National Institute of Health and contains whole-genome data for 1,722 participants from various cohorts. The Korea1K data set included whole-genome data of 1,094 healthy individuals, mostly from the Ulsan metropolitan region located in the southern part of the Korean peninsula. ANNOVAR bioinformatics software was used for annotating any rare nonsynonymous variants, including missense, inframe insertion/deletion, frameshift, start gain/loss, stop gain/loss, and splice site variants in the NOTCH3 gene.⁶ In this study, a minor allele frequency <0.01 was defined as a rare variant. Among the rare variants retrieved from the database, we defined the variant as pathogenic if it was associated with CADASIL and classified as pathogenic or likely pathogenic in ClinVar (ncbi.nlm.nih.gov/clinvar/).

Screening for NOTCH3 Variants Among 1,000 Individuals Living on Jeju Island

Of the 4,350 anonymized genomic DNA samples, a randomly selected 1,000 samples with their health information were provided by the Biobank of Jeju National University Hospital, a member of the Korea Biobank Network. This study was approved by the Institutional Review Board of Jeju National University Hospital (IRB File No. JEJUNUH 2020-09-006). Informed consent was obtained at the time of DNA donation to the Biobank. We screened the 3 most frequently found NOTCH3 mutations on Jeju Island: p.Arg75Pro (c.244G>C), p.Arg544Cys (c.1630>T), and p.Arg578Cys (c.1732C>T). Other detailed information for the PCR, sequencing, and statistical analysis was provided as Supplemental Material, links.lww.com/NXG/A495.

Results

Pathogenic NOTCH3 Variants in 2 Korean Public Genome Databases

Three pathogenic NOTCH3 variants associated with CADASIL, p.Arg75Pro (c.224G>C), p.Arg182Cys (c.544C>T), and p.Arg544Cys (c.1630C>T), were found in 2 Korean public genome databases. In the KRGDB with 1,722 participants, only the p.Arg544Cys variant was identified with a carrier frequency of 0.12%. Three pathogenic variants (p.Arg75Pro, p.Arg182Cys, and p.Arg544Cys) were present in the Korea1K database with 1,094 individuals, and the carrier frequencies were 0.22, 0.11, and 0.11%, respectively. Only the p.Arg544Cys variant was discovered in common (Table 1).

Table 1.

Prevalence of Pathogenic NOTCH3 Variants in 2 Korean Public Genome Databases and 1,000 Individuals Living on Jeju Island

Screening Pathogenic NOTCH3 Variants in 1,000 Individuals on Jeju Island

Of 1,000 individuals on Jeju Island, 3 had a history of stroke, and 6.6% had a family history of stroke. We found 2 cysteine-altering NOTCH3 variants in 1.00% of the participants with a 95% confidence interval of 0.48–1.83% (p.Arg544Cys mutation in 9 individuals and p.Arg578Cys in 1). Compared with individuals without pathogenic NOTCH3 variants, those with the variants were more likely to have a history of stroke (p < 0.001) (Table 2). Of the 10 individuals with pathogenic variants, 2 participants underwent a brain MRI examination (eTable 3, links.lww.com/NXG/A495 and Figure).

Table 2.

Baseline Characteristics of the Jeju Participants

Figure. Brain MRI of the 2 Individuals With p.Arg544Cys Variants.

Patient 2 is a 58-year-old man who had had an abrupt onset of mild dysarthria at age 54 years. Diffusion MRI at that time showed a small subacute infarction on the left frontal white matter (arrow) and multiple small white matter hyperintensity lesions on fluid attenuated inversion recovery images. Patient 3 is a 50-year-old man and received a brain MRI examination as a screening health checkup and had a few small subcortical white matter hyperintensity lesions and periventricular white matter lesions.

Discussion

A recent study from Taiwan reported a very high prevalence of cysteine-altering NOTCH3 variants among Taiwanese (9/1,000), and the study also suggested that the cysteine-altering variant resulted in a 3.40-fold increased risk for stroke and even an 11.05-fold increased risk for small-vessel stroke.⁷ In line with the Taiwanese study, this study suggested a high prevalence of pathogenic NOTCH3 variants among the general Korean population, with an estimated number of carriers ranging from 1.2/1,000 to 4.4/1,000. On Jeju Island, located off the southern coast of the Korean peninsula with a current population of 670,000, the number of mutation carriers could reach 67,000, and they could be at increased risk of stroke or develop other symptoms reported in CADASIL. Long-term impact of harboring pathogenic NOTCH3 variants in seemingly healthy young individuals needs to be investigated further.

This study has several limitations. First, because of the limited sample size of the Korean public genome database and the Jeju screening study, this study was underpowered to prove whether the Korean general population has a high prevalence of pathogenic NOTCH3 variants reported in the previous literature. Second, we screened only the 3 most frequently found pathogenic variants in the Jeju screening study. Therefore, we might miss other rare pathogenic variant associated with CADASIL in these 1,000 individuals.

Appendix. Authors

Study Funding

This work was supported by a research grant from Jeju National University Hospital in 2020.

Disclosure

Go to Neurology.org/NG for full disclsoures.