• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제24권1호
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• pp.1-6
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• 2021

Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.

• Genomics & Informatics
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• 제13권2호
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• pp.31-39
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• 2015

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

• Journal of Genetic Medicine
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• 제20권2호
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• pp.31-38
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• 2023

Rare diseases, even though defined as fewer than 20,000 in South Korea, with over 8,000 rare Mendelian disorders having been identified, they collectively impact 6-8% of the global population. Many of the rare diseases pose significant challenges to patients, patients' families, and the healthcare system. The diagnostic journey for rare disease patients is often lengthy and arduous, hampered by the genetic diversity and phenotypic complexity of these conditions. With the advent of next-generation sequencing technology and clinical implementation of exome sequencing (ES) and genome sequencing (GS), the diagnostic rate for rare diseases is 25-50% depending on the disease category. It is also allowing more rapid new gene-disease association discovery and equipping us to practice precision medicine by offering tailored medical management plans, early intervention, family planning options. However, a substantial number of patients remain undiagnosed, and it could be due to several factors. Some may not have genetic disorders. Some may have disease-causing variants that are not detectable or interpretable by ES and GS. It's also possible that some patient might have a disease-causing variant in a gene that hasn't yet been linked to a disease. For patients who remain undiagnosed, reanalysis of existing data has shown promises in providing new molecular diagnoses achieved by new gene-disease associations, new variant discovery, and variant reclassification, leading to a 5-10% increase in the diagnostic rate. More advanced approach such as long-read sequencing, transcriptome sequencing and integration of multi-omics data may provide potential values in uncovering elusive genetic causes.

• 대한소아신경학회지
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• 제26권4호
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• pp.272-275
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• 2018

KBG 증후군은 특징적인 얼굴 기형 및 발달 장애, 저 신장 등을 보이는 희귀한 질환이며, ANKRD11유전자의 변이가 KBG 증후군을 일으킨다고 알려져 있다. 그 임상 양상의 스펙트럼은 넓은 편이며, 발달 장애와 신경학적 이상의 경우 개인마다 다양한 정도로 보고되고 있다. 본 증례의 환자들 역시 서로 다른 정도의 발달 장애를 보였으며, 그 중 더 심한 정도의 발달 장애를 가진 환자에서는 뇌전증이 동반되었다. 기존의 KBG증후군의 진단 기준에서 macrodontia는 매우 중요한 요소였으며, 대부분의 KBG 증후군 환자에서 나타난다고 보고되었다. 본 증례의 환자들은 발달장애를 보여 시행한 diagnostic exome sequencing을 통해 ANKRD11 유전자 이상을 확인하였지만 macrodontia는 관찰되지 않았다. 이는 KBG 증후군이 현재까지 밝혀진 것 보다 더 흔할 수 있으며, 특징적인 얼굴 기형이 없는 경우에도 발달장애가 있는 환자들에서는 더욱 적극적인 유전자 검사를 시행하여 KBG 증후군을 진단 할 필요가 있음을 시사한다.

• Journal of Interdisciplinary Genomics
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• 제2권1호
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• pp.10-12
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• 2020

Coffin-Lowry syndrome (CLS) is a genetic disorder characterized by intellectual disability, typical facial features, and skeletal abnormalities. But this syndrome shows highly variable clinical manifestations, and can't be diagnosed with conventional chromosome analysis or comparative genomic hybridization, leading to delayed diagnosis. Here we report an 18-year-old boy with CLS diagnosed by whole exome sequencing. Our patient initially presented with developmental delay, facial dysmorphism at the age of 1. At the age of 18, he developed orthopnea due to mitral regurgitation. At the 22 years of age, he was diagnosed as CLS diagnosed by whole exome sequencing. Our case implies that clinical suspicion is important for early diagnosis, and advanced diagnostic tools such as WES should be considered in suspected cases.

• Journal of Genetic Medicine
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• 제20권1호
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• 대한유전성대사질환학회지
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• 제20권2호
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• pp.50-54
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• 2020

Vici 증후군은 18q12.3 염색체에 위치하는 EPG5 유전자의 돌연변이로 인해 발생하는 상 염색체 열성 증후군이다. EPG5 유전자는 리소좀 형성에 관여하는 자가 포식 경로의 중요한 조절자를 암호화하므로 이에 대한 돌연변이로 인해 다양한 임상증상을 나타나게 된다. 주요한 임상증상으로는 뇌량 무형성, 백색증, 백내장, 심근 병증, 중증 정신 운동 지체, 발작, 면역 결핍 등이 있으며 다양한 임상증상을 나타내는 만큼 다른 질환들과 임상적으로 구분하기가 어렵다. 저자들은 Vici 증후군으로 진단된 3세 남자 환아의 증례를 보고하고자 한다. 환아는 생후 2개월 경 근긴장 저하와 수유 곤란을 주소로 내원하였으며 이후 Vici 증후군에서 나타나는 특징적인 임상 증상들을 나타내었다. 임상증상들의 감별 진단을 위해 시행한 Whole-exome sequencing (WES) 결과, EPG5 유전자에서 c.2254 C>T (p.Gln752Ter)와 c.5511-5518+2 del TATGCAAAGT 새로운 변이가 이형접합체로 확인되었다. Vici 증후군과 같이 임상적으로 구분이 어려우며 다양한 신체기관에 걸쳐 영향을 미치는 질환의 진단 시에는 Whole-exome sequencing (WES)가 유용하게 사용될 수 있다. 이 증례는 한국에서 확인된 첫 Vici 증후군 case로써 의의가 있다.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제22권6호
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• pp.581-587
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• 2019

Arthrogryposis-renal dysfunction-cholestasis (ARC) syndrome is a rare autosomal recessive multisystemic disease that is associated with the liver, kidney, skin, and central nervous and musculoskeletal systems. ARC occurs as a result of mutations in the VPS33B (Vacuolar protein sorting 33 homolog B) or VIPAR (VPS33B interacting protein, apical-basolateral polarity regulator) genes. A female infant presented with neonatal cholestasis with a severe clinical outcome. She was diagnosed with ARC syndrome using targeted exome sequencing (TES). Exome sequencing revealed compound heterozygous mutations, c.707A>T and c.239+5G>A, in VPS33B, where c.707A>T was a novel variant; the resultant functional protein defects were predicted via in silico analysis. c.239+5G>A, a pathogenic mutation that affects splicing, is found in less than 0.1% of the general population. Invasive techniques, such as liver biopsies, did not contribute to a differential diagnosis of ARC syndrome; thus, early TES together with clinical presentations constituted an apparently accurate diagnostic procedure.

• 대한유전성대사질환학회지
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• 제23권2호
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• pp.1-7
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• 2023

유전성 대사질환은 생화학적 대사 이상에 의해 발생하는 질환 군으로, 매우 다양할 뿐만 아니라 임상 양상이 서로 겹칠 수 있어 진단에 어려움을 겪을 수 있다. 과거에는 유전성 대사질환의 원인이 될 수 있는 유전자를 선정한 후 한 개씩 분석하는 방식으로 유전자 검사를 시행했다. 하지만, 최근에는 차세대 염기서열분석 기술이 발전함에 따라 유전성 대사질환과 관련된 수백-수천개의 유전자를 한꺼번에 분석하거나, 인간의 모든 유전자를 포함하는 엑솜/게놈 분석을 시행한 후 원인 유전자를 찾는 방식으로 유전 진단의 패러다임이 바뀌고 있다. 본 종설에서는 차세대 염기서열분석을 이용한 유전성 대사질환의 유전 진단 방법과 진단율 및 주의점 등을 살펴보고자 한다.

• Journal of Genetic Medicine
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• 제19권2호
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• pp.76-84
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• 2022

Purpose: Whole-exome sequencing (WES) has been a useful tool for novel gene discovery of various disease categories, further increasing the diagnostic yield. This study aimed to investigate the clinical utility of WES prospectively in undiagnosed genetic diseases. Materials and Methods: WES tests were performed on 110 patients (age range, 0-28 years) with suspected rare genetic diseases. WES tests were performed at a single reference laboratory and the variants reported were reviewed by clinical geneticists, pediatricians, neurologists, and laboratory physicians. Results: The patients' symptoms varied with abnormalities in the head or neck, including facial dysmorphism, being the most common, identified in 85.4% of patients, followed by abnormalities in the nervous system (83.6%). The average number of systems manifesting phenotypic abnormalities per patient was 3.9±1.7. The age at presentation was 2.1±2.7 years old (range, 0-15 years), and the age at WES testing was 6.7±5.3 years (range, 0-28 years). In total, WES test reported 100 pathogenic/likely pathogenic variants or variants of uncertain significance for 79 out of 110 probands (71.8%). Of the 79 patients with positive or inconclusive calls, 55 (50.0%) patients were determined to have good genotype-phenotype correlations after careful review. Further clinical reassessment and family member testing determined 45 (40.9%) patients to have been identified with a molecular diagnosis. Conclusion: This study showed a 40.9% diagnostic yield for WES test for a heterogeneous patient cohort with suspected rare genetic diseases. WES could be the feasible genetic test modality to overcome the diversity and complexity of rare disease diagnostics.