PSEN1 p.Met233Val in a Complex Neurodegenerative Movement and Neuropsychiatric Disorder

Silke Appel-Cresswell,Ilaria Guella,Anna Lehman,Dean Foti,Matthew J. Farrer 대한파킨슨병및이상운동질환학회 2018 Journal Of Movement Disorders Vol.11 No.1

Mutations in presenilin 1 (PSEN1) are the most common cause of autosomal dominant Alzheimer’s disease. Here, we report a Canadian-Vietnamese family carrying a PSEN1 p.Met233Val mutation with an exceptionally early and severe presentation that includes a wide range of atypical symptoms, including prominent ataxia, Parkinsonism, spasticity, dystonia, action tremor, myoclonus, bulbar symptoms, seizures, hallucinations and behavioral changes. Whole-exome sequencing (WES) was performed on the affected proband after many assessments over several years proved diagnostically inconclusive. The results were analyzed using the AnnEx “Annotated Exomes” browser (http://annex.can.ubc.ca), a web-based platform that facilitates WES variant annotation and interpretation. High-throughput sequencing can be especially informative for complex neurological disorders, and WES warrants consideration as a first-line clinical test. Data analyses facilitated by web-based bioinformatics tools have great potential for novel insight, although confirmatory, diagnostically accredited Sanger sequencing is recommended prior to reporting.

차세대 염기서열분석을 이용한 유전성 대사질환의 유전진단

기창석,Chang-Seok Ki 대한유전성대사질환학회 2023 대한유전성대사질환학회지 Vol.23 No.2

Inherited metabolic disorders (IMD) are a group of disorders involving various metabolic pathways. Genetic diagnosis of IMD has been challenging because of extremely heterogeneous nature and extensive laboratory and/or phenotype overlap. Conventional genetic diagnosis was a gene-by-gene approach that needs a priori information on the causative genes that might underlie the IMD. Recent implementation of next-generation sequencing (NGS) technologies has changed the process of genetic diagnosis from a gene-by-gene approach to simultaneous analysis of targeted genes possibly associated with the IMD using gene panels or using whole exome/genome sequencing (WES/WGS) covering entire human genes. Clinical NGS tests can be a cost-effective approach for the rapid diagnosis of IMD with genetic heterogeneity and are becoming standard diagnostic procedures.

질병 원인 유전자 발견을 위한 엑솜 데이터 분석 파이프라인

전준범,신재문,공진화,윤지희,김윤중 한국정보과학회 2015 데이타베이스 연구 Vol.31 No.2

Most diseases are caused by mutations in more than one gene. Whole exome sequencing (WES)— the targeted sequencing of the subset of the human genome that is protein coding — provides a powerful, cost-effective and time-efficient tool for the study of the genetic variations. However, because the small size, sparseness and non-contiguous nature of exon regions makes the WES data more prone to noise, discovering and genotyping variants from WES data is more challenging than from whole genome sequencing (WGS) data. In this research, we propose a pipeline system to identify disease-causal genes in whole exome sequencing data, and provide a detailed method for implementing an exome data analyzer which is one of the main modules of the system. The analysis pipeline automates the execution of the following steps: 1) intial read data control and cleaning; 2) alignment to a reference genome; 3) post alignment analysis; 4) variation calling. The exome data analyzer, a downstream processor for the pipeline, drives the user allowing to browse the genomic variations (SNP, Indel, CNV) in the multi-scale of genetic (exonic) regions and easily access to OMIM, dbSNP, DGV, RefSeq databases for discovering variants-related informations. Furthermore, our exome data analyzer is a disease-specific PhenoToGeno knowledge-base system to integrate carefully curated and annotated phenotypic and genetic data sets, allows researchers to browse, search, check, filter out the identified variants for discovering variants-gene-phenotype relationships. By using the top-down approach for information browsing based on PhenoToGeno knowledge base, our system provides an efficient and easy-to-use solution for WES data analysis. Through our system non-IT mastered users can access to efficient public open softwares and biological databases, and quickly perform the experiments and analysis for identifying disease-causing gene. 대부분의 질병은 하나 이상의 유전자의 변이 발생에 그 발병 원인이 있다. 엑솜 시퀀싱 (whole exome sequencing, WES)은 전체 유전체 영역의 일부분인 단백질 코딩 영역만을 타겟 시퀀싱 하는 방식으로서, 유전자 변이를 발견하기 위한 시간, 비용 효율적인 강력한 도구가 된다. 그러나 WES 데이터는 엑손 영역이 갖는 작은 크기, 희소성, 비연속성의 특성으로 인하여 잡음의 영향을 많이 받기 때문에, 일반적으로 게놈 시퀀싱 (whole genome sequencing, WGS) 데이터에 비하여 변이 분석이 까다롭다. 본 연구에서는 질병 원인 유전자 발견을 위한 WES 데이터 분석 파이프라인 시스템을 제안하고, 주요모듈인 엑솜 데이터 분석기의 개발 방법론에 대하여 기술한다. 분석 파이프라인 시스템은 다음과 같은단계별 작업을 자동으로 수행한다: 1) 리드 데이터 제어 및 정제, 2) 리드 정렬, 3) 정렬 결과 후처리, 4) 유전 변이 추출. 파이프라인의 후반 처리 시스템인 엑솜 데이터 분석기는 추출된 유전 변이 (SNP, Indel, CNV) 정보를 다양한 유전체 영역 단위로 브라우징 가능하도록 지원하며, 또한 OMIM, dbSNP, DGV, RefSeq 등의 데이터베이스와 연동하여 변이 관련 정보의 검색 및 검증을 간단히 수행할 수 있도록 지원한다. 특히, 엑솜 분석기는 해당 분야 전문가에 의하여 개발된 질병 특이적 PhenoToGeno 지식베이스를 기반으로 구동되므로, 연구자로 하여금 변이-유전자-표현형 정보의 연관성을 밝히는 작업을 간편히 수행할 수 있도록 지원한다. 이와 같은 PhenoToGeno 지식베이스를 기반으로 하는 탑-다운 방식의정보 브라우징 기능은 보다 직관적이고 편리한 정보 검색/검증 환경을 사용자에게 제공하게 되며, 컴퓨팅 스킬을 충분히 갖추지 않은 연구자도 이 시스템을 통하여 효율적인 공용 소프트웨어 및 생물 데이터베이스를 간단히 사용 가능하며, 결과적으로 질병 원인 유전자 발견을 위한 실험 및 분석을 빠르게 진행시킬 수 있게 된다.

엑솜 염기서열 분석 방법을 이용한 단일유전자질환의 원인 유전자 발굴

이종극(Jong-Keuk Lee) 대한의학유전학회 2010 대한의학유전학회지 Vol.7 No.2

약 7,000 여개의 단일유전자질환이 보고되어 있지만 보고된 질환의 절반도 아직 원인 유전자가 밝혀지지 못한 상황이다. 그리고 기존에 밝혀진 원인 유전자의 돌연변이형들은 대부분 단백질을 코딩하는 부위의 돌연변이에 의하여 발생하고 있어서 인간 유전체에서 단백질을 코딩하는 엑손 부위만을 선별적으로 분리하여 염기서열을 분석하는 엑솜 염기서열 분석 방법은 희귀한 유전질환의 신규 원인 유전자 발굴을 위한 매우 효과적인 유전 분석법이 될 것이다. 엑솜은 전체 유전체의 약 1.5% 정도를 차지하고 있어서 매우 경제적으로 분석이 가능하다. 그리고 엑솜 염기서열 분석 방법은 엑솜 부위를 선별하는 기술과 대용량 염기서열 분석기술로 수행된다. Freeman-Sheldon 증후군의 원인 유전자를 엑솜 염기서열 분석 방법으로 발굴한 이후로 단일유전자질환의 원인 유전자 발굴을 위한 표준 분석법으로 엑솜 염기서열 분석 방법이사용되고 있다. 향후에는 엑솜 염기서열 분석 방법이 다양한 복합질병의 유전분석에도 활용되어 개인 맞춤의학의 실현을 앞당기는데 크게 기여할 것으로 기대된다. More than 7,000 rare Mendelian diseases have been reported, but less than half of all rare monogenic disorders has been discovered. In addition, the majority of mutations that are known to cause Mendelian disorders are located in protein-coding regions. Therefore, exome sequencing is an efficient strategy to selectively sequence the coding regions of the human genome to identify novel genes associated with rare genetic disorders. The “exome” represents all of the exons in the human genome, constituting about 1.5% of the human genome. Exome sequencing is carried out by targeted capture and intense parallel sequencing. After the first report of successful exome sequencing for the identification of causal genes and mutations in Freeman Sheldon syndrome, exome sequencing has become a standard approach to identify genes in rare Mendelian disorders. Exome sequencing is also used to search the causal genes and variants in complex diseases. The successful use of exome sequencing in Mendelian disorders and complex diseases will facilitate the development of personalized genomic medicine.

Identification of Two Cases of Ciliopathy-Associated Diabetes and Their Mutation Analysis Using Whole Exome Sequencing

Kim, Min Kyeong,Kwak, Soo Heon,Kang, Shinae,Jung, Hye Seung,Cho, Young Min,Kim, Seong Yeon,Park, Kyong Soo Korean Diabetes Association 2015 Diabetes and Metabolism Journal Vol.39 No.5

<P><B>Background</B></P><P>Alström syndrome and Bardet-Biedl syndrome are autosomal recessively inherited ciliopathies with common characteristics of obesity, diabetes, and blindness. Alström syndrome is caused by a mutation in the <I>ALMS1</I> gene, and Bardet-Biedl syndrome is caused by mutations in <I>BBS1-16</I> genes. Herein we report genetically confirmed cases of Alström syndrome and Bardet-Biedl syndrome in Korea using whole exome sequencing.</P><P><B>Methods</B></P><P>Exome capture was done using SureSelect Human All Exon Kit V4+UTRs (Agilent Technologies). HiSeq2000 system (Illumina) was used for massive parallel sequencing. Sanger sequencing was used for genotype confirmation and familial cosegregation analysis.</P><P><B>Results</B></P><P>A 21-year old Korean woman was clinically diagnosed with Alström syndrome. She had diabetes, blindness, obesity, severe insulin resistance, and hearing loss. Whole exome sequencing revealed a nonsense mutation in exon 10 of <I>ALMS1</I> (c.8776C>T, p.R2926X) and a seven base-pair deletion resulting in frameshift mutation in exon 8 (c.6410_6416del, p.2137_2139del). A 24-year-old Korean man had Bardet-Biedl syndrome with diabetes, blindness, obesity, and a history of polydactyly. Whole exome sequencing revealed a nonsynonymous mutation in exon 11 of the <I>BBS1</I> gene (c.1061A>G, p.E354G) and mutation at the normal splicing recognition site of exon 7 of the <I>BBS1</I> gene (c.519-1G>T).</P><P><B>Conclusion</B></P><P>We found novel compound heterozygous mutations of Alström syndrome and Bardet-Biedl syndrome using whole exome sequencing. The whole exome sequencing successfully identified novel genetic variants of ciliopathy-associated diabetes.</P>

Diagnostic Odyssey and Application of Targeted Exome Sequencing in the Investigation of Recurrent Infant Deaths in a Syrian Consanguineous Family: a Case of Spinal Muscular Atrophy with Respiratory Distress Type 1

김영아,진혜영,김유미 대한의학회 2019 Journal of Korean medical science Vol.34 No.9

Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a rare autosomal recessive disorder caused by a defect in the immunoglobulin mu binding protein 2 (IGHMBP2) gene, leading to motor neuron degeneration. We identified an infant with SMARD1 by targeted exome sequencing from a consanguineous Syrian family having a history of recurrent infant deaths. The patient initially presented intrauterine growth retardation, poor sucking, failure to thrive, and respiratory failure at the age of two months, and an inborn error of metabolism was suspected at first. Over a period of one month, the infant showed rapid progression of distal muscular weakness with hand and foot contractures, which were suggestive of neuromuscular disease. Using targeted exome sequencing, the mutation in IGHMBP2 was confirmed, although the first report was normal. Targeted exome sequencing enabled identification of the genetic cause of recurrent mysterious deaths in the consanguineous family. Additionally, it is suggested that a detailed phenotypic description and communication between bioinformaticians and clinicians is important to reduce false negative results in exome sequencing.

Exome and genome sequencing for diagnosing patients with suspected rare genetic disease

Go Hun Seo,Hane Lee 대한의학유전학회 2023 대한의학유전학회지 Vol.20 No.2

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 nextgeneration 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.

Individual exome analysis in diagnosis and management of paediatric liver failure of indeterminate aetiology

Vilarinho, S.,Choi, M.,Jain, D.,Malhotra, A.,Kulkarni, S.,Pashankar, D.,Phatak, U.,Patel, M.,Bale, A.,Mane, S.,Lifton, R.P.,Mistry, P.K. Elsevier Science Publishers 2014 Journal of hepatology Vol.61 No.5

Background & Aims: In children with liver failure, as many as half remain of indeterminate aetiology. This hinders timely consideration of optimal treatment options. We posit that a significant subset of these children harbour known inherited metabolic liver diseases with atypical presentation or novel inborn errors of metabolism. We investigated the utility of whole-exome sequencing in three children with advanced liver disease of indeterminate aetiology. Methods: Patient 1 was a 10year-old female diagnosed with Wilson disease but no detectable ATP7B mutations, and decompensated liver cirrhosis who underwent liver transplant and subsequently developed onset of neurodegenerative disease. Patient 2 was a full-term 2day-old male with fatal acute liver failure of indeterminate aetiology. Patient 3 was an 8year-old female with progressive syndromic cholestasis of unknown aetiology since age 3months. Results: Unbiased whole-exome sequencing of germline DNA revealed homozygous mutations in MPV17 and SERAC1 as the disease causing genes in patient 1 and 2, respectively. This is the first demonstration of SERAC1 loss-of-function associated fatal acute liver failure. Patient 1 expands the phenotypic spectrum of the MPV17-related hepatocerebral mitochondrial DNA depletion syndrome. Patient 3 was found to have syndromic cholestasis due to bi-allelic NOTCH2 mutations. Conclusions: Our findings validate the application of whole-exome sequencing in the diagnosis and management of children with advanced liver disease of indeterminate aetiology, with the potential to enhance optimal selection of treatment options and adequate counselling of families. Moreover, whole-exome sequencing revealed a hitherto unrecognized phenotypic spectrum of inherited metabolic liver diseases.

Whole Exome Sequencing Identifies Novel Genetic Alterations in Patients with Pheochromocytoma/Paraganglioma

서수현,김정희,김만진,조성임,김수진,강혜인,신찬수,박성섭,이규은,성문우 대한내분비학회 2020 Endocrinology and metabolism Vol.35 No.4

Background: Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort. Methods: Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAM tools. Results: Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected. Conclusion: Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.

Familial Glycogen Storage Disease Type IXa Diagnosed by Targeted Exome Sequencing

손영배,장주영,이다근,장자현,Sohn, Young Bae,Jang, Ju Young,Lee, Dakeun,Jang, Ja-Hyun The Korean Society of Inherited Metabolic Disease 2017 대한유전성대사질환학회지 Vol.17 No.3

당원병 IX형은 phosphorylase kinase 효소 결핍으로 분해되지 않은 당원이 간 또는 근육에 축적되는 유전성대사이상질환이다. 당원병 IXa형은 당원병 IX형 중 가장 흔한 형태로 PHKA2 유전자 변이로 발생한다. 당원병 IXa형의 임상증상은 간 비대, 간 효소 수치 상승, 성장 지연, 저혈당 등이 있다. 그러나, 이러한 임상 증상은 다른 타입의 당원병의 증상과 비슷하거나 겹쳐서 임상적으로는 구분하기가 어렵다. 저자들은 표적 엑솜 시퀀싱으로 진단된 가족성 당원병 IXa형 증례를 보고하고자 한다. 4세 남아가 간 비대와 간 효소 수치 상승을 주소로 내원하였다. 간 조직검사결과 간세포에 당원이 축적되어 있어 당원병을 의심하였으나 G6PC 유전자 검사는 음성이었다. 이에 당원병 타입을 감별진단 하기 위해 표적 엑솜시퀀싱을 시행하였으며, PHKA2 유전자에서 질환과의 연관성이 이미 보고된 바 있는 c.3632C>T (p.Thr121Met) 변이가 반접합체(hemizygote)로 발견되어 당원병 IXa로 진단하였다. 가족 유전자 검사를 통해 어머니가 이형접합체 보인자임을 확인하였으며, 남동생이 같은 변이를 가진 반접합체임을 확인하였다. 28개월 된 환자의 남동생 역시 신체 검진 상 간 비대가 있었으며, 혈액검사상 간 효소 수치가 상승되어 있어 같은 질환으로 확진하였다. 이환된 형제 모두 생 옥수수 전분 섭취와 복합 탄수화물을 섭취하도록 식이 조절을 하였으며 2년 추적관찰 동안 정상 성장 발달을 보이고 있다. 당원병과 같이 임상적으로 구분이 어려우며 유전학적으로 다양한 유전자 변이를 보이는 당원병과 같은 질환의 분자 유전학적 감별진단에 표적 엑솜 시퀀싱이 유용한 진단법이 될 수 있다. 신속하고 정확한 분자 유전학적 감별진단을 통해 환자와 보호자에게 질병의 적절한 치료법, 질병의 예후에 관한 정확한 정보를 제공할 수 있을 뿐 아니라, 적절한 유전상담을 제공할 수 있다. Glycogen storage disease type IX (GSD IX) is caused by deficiency of phosphorylase kinase which plays a role in breakdown of glycogen. Mutations in PHKA2 are the most common cause of GSD IX (GSD IXa). Clinical manifestations of GSD IXa include hepatomegaly, elevation of liver enzyme, growth retardation, fasting hypoglycemia, and fasting ketosis. However, the symptoms overlap with those of other types of GSDs. Here, we report Korean familial cases with GSD IXa whose diagnosis was confirmed by targeted exome sequencing. A 4-year old male patient was presented with hepatomegaly and persistently elevated liver enzyme. Liver biopsy revealed swollen hepatocyte filled with glycogen storage, suggesting GSDs. Targeted exome sequencing was performed for the differential molecular diagnosis of various types of GSDs. A hemizygous mutation in PHKA2 were detected by targeted exome sequencing and confirmed by Sanger sequencing: c.3632C>T (p.Thr121Met), which was previously reported. The familial genetic analysis revealed that his mother was heterozygous carrier of c.3632C>T mutation and his 28-month old brother had hemizygous mutation. His brother also had hepatomegaly and elevated liver enzyme. The hypoglycemia was prevented by frequent meals with complex carbohydrate, as well as cornstarch supplements. Their growth and development is in normal range. We suggest that targeted exome sequencing could be a useful diagnostic tool for the genetically heterogeneous and clinically indistinguishable GSDs. A precise molecular diagnosis of GSD can provide appropriate therapy and genetic counseling for the family.