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Original Article
한국인 신경섬유종증 1형 환자에서 관찰된 NF1 유전자 변이 분포
NF1 Variant Spectrum in Korean Patients with Neurofibromatosis Type 1 Disorder
가톨릭대학교 의과대학 진단검사의학교실1
가톨릭대학교 의과대학 서울성모병원 가톨릭유전진단검사센터2
Department of Laboratory Medicine1, College of Medicine, The Catholic University of Korea
Catholic Genetic Laboratory Center2, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Lab Med Online 2021; 11(1): 17-24
Published January 1, 2021 https://doi.org/10.47429/lmo.2021.11.1.17
Copyright © The Korean Society for Laboratory Medicine.
방법: 본 연구에는 서울성모병원에 의뢰된 NF1 유전자 검사 462 건이 포함되었다. NF1 유전자 변이는 messenger RNA (mRNA) 및 일부 genomic DNA 직접염기서열분석법과 multiplex ligation-dependent probe amplification (MLPA) 방법으로 분석하였다.
결과: 전체 462명 중 303명(65.6%)의 환자에서 231종류의 변이를 검출하였다. 217종류의 변이를 질병연관변이로 보고하였고, 이 중 106개(48.4%)의 변이는 이전 보고가 없는 새로운 변이였다. 가장 많은 환자들에게서 검출된 변이는 절단형 돌연변이로, 177명의 환 자에서 135종류의 변이를 검출하였다. 짜깁기 변이는 42명의 환자 에서 39종류, 과오변이는 44명의 환자에서 36종류가 검출되었다. MLPA에서만 확인되었던 엑손 단위 이상의 큰 결실은 25명의 환자 에서 8종류가 관찰되었다. mRNA 분석에서 4건의 aberrant transcript를 발견하였다. NF1 유전자의 변이 검출 률은 NIH 진단기준 충족 수에 따라 유의하게 높았다.
결론: 본 연구에서는 한국인 NF1 환자가 지닌 다양한 종류의 변이 를 검출하였다. 이러한 다양한 스펙트럼의 변이를 검출하기 위해 서 mRNA 및 gDNA에 대한 염기서열분석과 MLPA 검사를 통합적 으로 수행하여야 하며 새로 검출한 변이를 규명하기 위해 추가적 평가가 필요할 것으로 생각된다.
Methods: A total of 462 cases were enrolled for NF1 analysis at Seoul St. Mary’s Hospital. NF1 was analyzed through Sanger sequencing of messenger RNA (mRNA) and genomic DNA (gDNA), and/or multiplex ligation-dependent probe amplification (MLPA) analysis.
Results: We identified 231 types of NF1 variants in 303 out of the 462 patients (65.6%). Of these, 217 variants were classified as pathogenic or likely pathogenic, and 48.4% (N=106) of these were novel changes. Truncating variants encompassing frameshift and nonsense variants were most commonly observed (135 types of variants in 177 patients), followed by splicing defect variants (39 types in 42 patients) and missense variants (36 types in 44 patients). There were 8 distinctive large deletions in 25 patients, detected via MLPA analysis. Interestingly, 4 cases showed aberrant transcripts that were identified through mRNA Sanger sequencing. The frequency of NF1 mutation detected was significantly higher according to the number of satisfying National Institutes of Health (NIH) diagnostic criteria.
Conclusions: This study revealed a wide spectrum of NF1 variants in Korean NF1 patients. A comprehensive analytical strategy that combines mRNA and gDNA analyses and MLPA is required to detect sequence variants. Additionally, it is important to define the effect of newly detected variants on the clinical course.
Keywords
신경섬유종증 1형(neurofibromatosis type 1, NF1)은 2,500-3,000명당 1명 정도의 빈도로 발병하는 상염색체 우성 유전질환이다. 환자의 절반 정도는 가족성으로 발생하고 나머지는 가족력 없이 산발성으로 발생하며[1, 2], 17번 염색체 장완에 위치한
현재까지 국내에서 진행된
1. 대상 환자
2010년 2월부터 2019년 5월까지 서울성모병원에
2. NF1 유전자 변이 검출 방법
1) mRNA 직접염기서열분석(Sanger sequencing)
환자의 말초혈액에서 High Pure RNA Isolation Kit (Roche, Mann-heim, Germany)를 이용하여 RNA를 분리하고 Transcriptor First Strand cDNA Synthesis Kit (Roche)로 cDNA를 합성하였다. 염기서열분석을 위한 시발체(primer)는 Primer 3 (http://bioinfo.ut.ee/primer3)를 이용하여 제작하였다. 중합효소연쇄반응(polymerase chain reaction, PCR)은 Thermal Cycler C1000 또는 S1000 (Bio-Rad, Foster City, CA, USA)에서 96°C 5분 반응시킨 후 95°C 30초, 58°C 30초, 72°C 60초 조건을 34회 반복하고 72°C에서 5분간 반응시켜 이후 4°C에서 유지하였다. PCR 산물을 전기영동으로 확인하고 3500xL Genetic Analyzer (Thermo Fisher Scientific, Foster City, CA, USA)으로 염기서열을 분석하였다. mRNA 분석 시 양호한 염기서열분석 결과를 얻기 어려운 부위인 엑손 19, 38, 39, 49, 52는 gDNA를 추가로 분석하였다. mRNA 염기서열분석에서 변이가 검출된 경우 해당 부위에 대한 gDNA 염기서열분석을 시행하여 확인하였다.
3. 통계
1. NF1 유전자 변이 빈도 및 분포
분석된 462명 중 303명(65.6%)에서
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Table 1 . Detected variants of the
NF1 genePathogenic/LP VUS Total Patient Variant Patient Variant Patient Variant Truncating 177 (61.2%) 135 (62.2%) 0 (0%) 0 (0%) 177 (58.4%) 135 (58.4%) Splicing 42 (14.5%) 39 (18.0%) 0 (0%) 0 (0%) 42 (13.9%) 39 (16.9%) Missense 34 (11.8%) 26 (12.0%) 10 (71.4%) 10 (71.4%) 44 (14.5%) 36 (15.6%) Large del 25 (8.7%) 8 (3.7%) 0 (0%) 0 (0%) 25 (8.3%) 8 (3.5%) In-frame del 7 (2.4%) 5 (2.3%) 0 (0%) 0 (0%) 7 (2.3%) 5 (2.2%) In-frame dup 0 (0%) 0 (0%) 1 (7.1%) 1 (7.1%) 1 (0.3%) 1 (0.4%) Aberrant transcript 4 (1.4%) 4 (1.8%) 2 (14.3%) 2 (14.3%) 6 (2.0%) 6 (2.6%) Synonymous 0 (0%) 0 (0%) 1 (7.1%) 1 (7.1%) 1 (0.3%) 1 (0.4%) Total 289 217 14 14 303 231 Abbreviations: LP, likely pathogenic; VUS, variant of unknown significance; del, deletion; dup, duplication.
변이의 위치는
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Figure 1. Identified
NF1 variant spectrum and location. At the midline of the figure, the involved exons and/or introns of theNF1 gene are listed. Each block upward the midline represents one variation. Different kinds of variations are shown in different colors as indicated in the category above the chart. Large deletions are indicated by the green rectangle at the bottom of the midline. Here, each variant is displayed in the vertical direction. The different horizontal length of each rectangle indicates the deleted scope of each individual variant.
변이의 유형별로 보면, 무의미 변이(nonsense mutation) 및 틀이동 변이(frameshift mutation)를 포함한 절단형 돌연변이(truncating mutation)가 177명(58.4%)에서 관찰되었고, in-frame deletion은 7명(2.3%)의 환자에서 관찰되었다. 짜깁기(splicing)변이는 42명(13.9%)에서 관찰되었고, 이중 기존에 질병연관변이로 보고된 24개, 그리고 짜깁기 공여자 및 수여자부위에 발생한 15개의 변이가 있었다. mRNA 분석에서 aberrant transcript가 관찰된 경우, deep intronic mutation 가능성이 높을 것으로 예측되는 4예의 경우 likely pathogenic으로 보고하였다. 미량의 aberrant transcript가 검출된 2예의 경우, RNA 분리 지연에 의해 이러한 산물이 비정상적으로 발생하였을 가능성을 배제할 수 없어[3, 8] 재채혈 검체에서 확인하고자 하였으나 추적이 되지 않아 VUS로 분류하였다(Table 2). 44명(14.5%)의 환자에서 36개(15.6%)의 과오변이가 검출되었으며 여기에는 질병연관변이로 보고되었던 pathogenic 변이(21/36, 58.3%), likely pathogenic 변이(5/36, 13.9%), 그리고 VUS (10/36, 27.8%)가 포함되었다. 그 외에도 in-silico에서 짜깁기 과정에 영향을 줄 수 있다고 예측된 동의미(synonymous) 변이 1개(c.6033A>G)와 in-frame duplication 1개(c.5036_5041dup, p.Ile1679_Tyr1680dup)가 VUS로 분류되었다.
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Table 2 .
NF1 variants causing aberrant transcriptsNo ID Class variant AA change Location Test methods 1 L003 LP r.100_204del p.Val34_Met68del Exon 2 Sanger 2 L004 LP c.205-13T > G p.Arg69_Gly96del Intron 2 Sanger 3 L018 LP r.1063_1185del Splicing defect Intron 9 Sanger, MLPA 4 L067 LP r.4725_4835del p.His1576_Arg1612del Exon 36 Sanger, MLPA 5 V002 VUS r.1642_1845del204 Splicing defect Exon 15-16 Sanger, MLPA 6 V013 VUS c.6642+31T > G Splicing defect Intron 43 Sanger, MLPA Abbreviations: AA, amino acid; LP, likely pathogenic; VUS, variant of unknown significance; Sanger, Sanger sequencing; MLPA, multiplex ligation-dependent probe amplification.
검사가 의뢰된 환자 중 임상정보를 수집할 수 있었던 61명 중 70.5% (42/61)에서
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Table 3 . Comparison of clinical characteristics of neurofibromatosis 1 patients with detected
NF1 variants and those devoid ofNF1 variantsMutation Detected Not detected P OR (95% CI) Number of patients 43 18 Age, yr* 13 (1-60) 22 (4-74) 0.014 Sex (N, %) 0.678 0.792 (0.263-2.385) Male 24 (55.8%) 9 (50%) Female 19 (44.2%) 9 (50%) Number of satisfying NIH criteria (1988) 2 or more 23 (92.0%) 2 (8%) 0.002 9.200 (1.881-44.998) One 20 (66.7%) 10 (33.3%) < 0.001 4.583 (2.779-7.559) None 0 (0.0%) 6 (100%) Clinical presentation (N, %) 1st degree family history 7 (16.3%) 1 (5.6%) 0.258 3.306 (0.376-29.045) Café-au-lait spots 39 (90.7%) 9 (50.0%) < 0.001 9.750 (2.446-38.869) Neurofibroma 18 (41.9%) 1 (5.6%) 0.005 12.240 (1.490-100.538) Axillary/groin freckling 4 (9.3%) 1 (5.6%) 0.627 1.744 (0.181-16.778) Lisch nodule 8 (18.6%) 2 (11.1%) 0.471 1.829 (0.348-9.603) Optic glioma 2 (4.7%) 0 (0%) 0.352 1.049 (0.982-1.120) Skeletal dysplasia 1 (2.3%) 0 (0%) 0.514 1.024 (0.978-1.072) Brain hamartoma 14 (32.6%) 0 (0%) 0.006 1.483 (1.205-1.825) Seizure, mental retardation 1 (2.3%) 0 (0%) 0.514 1.024 (0.978-1.072) MPNST 1 (2.3%) 0 (0%) 0.514 1.024 (0.978-1.072) Other mass lesion 0 (0%) 6 (33.3%) < 0.001 0.667 (0.481-0.924) *Median (range).
Abbreviations: OR, odds ratio; CI, confidence interval; NIH, National Institutes of Health; MPNST, malignant peripheral nerve sheath tumors.
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Figure 2. Flow chart showing the
NF1 gene analysis according to the clinical findings of enrolled patients. NIH, National Institutes of Health; Sequencing, Sanger sequencing of mRNA and gDNA; MLPA, multiplex ligation-dependent probe amplification.
NF1은 질환의 표현형이 다양하게 나타날 수 있으며, 처음 검사한 시점에는 NIH에 제시된 기준을 충족시키지 않더라도 연령이 높아짐에 따라서 진단 기준에 합당한 임상 양상이 새롭게 나타날 수 있다. 질환을 조기에 진단하고 중대한 합병증을 예방할 수 있도록 질환이 의심되는 환자에서 검사를 시행하여 유전자 변이를 검출하고 빨리 치료를 시행하는 것이 중요하다[4]. 본 연구에서는 한국인 NF1 환자를 대상으로 단일 기관에서
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Table 4 . Review of previous reports on sequence variants of the
NF1 geneCountry Number of individuals Methods Detected numbers Types of variants Reference Korea 78 individuals from 60 families DNA sequencing mRNA sequencing MLPA FISH 52 variants in 78 individuals Missense 23.1% Nonsense 34.6% Splicing 21.2% Indel 13.5% Large del 7.7% [13] Spain 474 unrelated individuals DNA sequencing mRNA sequencing mRNA SSCP/HD 142 variants in 189 individuals Missense 8% Nonsense 9% Splicing 31% Frameshift 50% Others 2% [16] China 107 unrelated individuals DNA sequencing DHPLC microsatellite genotyping Q-PCR RT-PCR 68 individuals Missense 16.2% Nonsense 29.4% Splice site 13.2% Frameshift 33.8% Large del 7.4% [17] UK 169 unrelated individuals DNA sequencing DHPLC MLPA FISH 88 variants in 109 individuals Missense 15% Nonsense 27% Splicing 19% Frameshift 27% Large del 9% Others 3% [18] France 565 unrelated individuals DNA sequencing mRNA sequencing microsatellite genotyping MLPA 546 individuals Missense 7.7% Nonsense 21.6% Splicing 27.1% Frameshift 30.0% Large del 8.4% Others 5.1% [19] Japan 86 unrelated individuals NGS DNA sequencing MLPA 67 variants in 80 individuals Missense 16.3% Nonsense 37.5% Splicing 10% Frameshift 23.8% Large del 12.5% [20] Netherlands 1985 unrelated individuals DNA sequencing SSCP MLPA FISH 1178 individuals Missense 9.8% Nonsense 29.4% Splicing 19.7% Frameshift 31.7% Others 4.1% [21] China 109 individuals, 100 families DNA sequencing mRNA sequencing MLPA 89 variants in 100 families Missense 13.5% Nonsense 23.6% Splicing 16.9% Frameshift 29.2% Large del 12.4% Others 4.5% [22] Italy 79 unrelated individuals NGS MLPA 73 variants in 79 individuals Missense 30% Nonsense 34% Splicing 7% Small del 24.7% Insertion 1.4% Large del 2.7% [23] Abbreviations: MLPA, multiplex ligation-dependent probe amplification; FISH, Fluorescence in situ hybridization; SSCP, single-strand conformation polymorphism; DHPLC, denaturing high performance liquid chromatography; RT-PCR, reverse transcriptase polymerase chain reaction; NGS, next-generation sequencing; Indel, insertion/deletion; del, deletion.
이전 연구[21]와 같이, 본 연구에서도 NIH consensus criteria (1988)에서 제시하는 임상진단 기준을 2개 이상 충족하는 환자군에서 NF1 의증 환자들에 비해 유의하게
NIH 진단기준에 합당한 임상 양상 2개 이상을 충족할 경우 92%의 환자에서 변이가 검출되어
본 연구를 통하여 한국인 NF1 환자에서 다양한
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