The utility of next-generation sequencing technologies in diagnosis of Mendelian mitochondrial diseases and reflections on clinical spectrum

2021 ◽  
Vol 34 (4) ◽  
pp. 417-430
Author(s):  
Melis Kose ◽  
Esra Isik ◽  
Ayça Aykut ◽  
Asude Durmaz ◽  
Engin Kose ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Diagnostic Process ◽  
Unknown Etiology ◽  
Next Generation ◽  
Related Gene ◽  
Targeted Exome Sequencing ◽  
Novel Variants ◽  
Gene Defects ◽  
Generation Sequencing

Abstract Objectives Diagnostic process of mitochondrial disorders (MD) is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next-Generation Sequencing (NGS) technology offers a high-throughput platform for nuclear MD. Methods We included 59 of 72 patients that undergone WES and targeted exome sequencing panel suspected to have potential PMDs. Patients who were included in the analysis considering the possible PMD were reviewed retrospectively and scored according to the Mitochondrial Disease Criteria Scale. Results Sixty-one percent of the patients were diagnosed with whole-exome sequencing (WES) (36/59) and 15% with targeted exome sequencing (TES) (9/59). Patients with MD-related gene defects were included in the mito group, patients without MD-related gene defects were included in the nonmito group, and patients in whom no etiological cause could be identified were included in the unknown etiology group. In 11 out of 36 patients diagnosed with WES, a TES panel was applied prior to WES. In 47 probands in 39 genes (SURF1, SDHAF1, MTO1, FBXL4, SLC25A12, GLRX5, C19oRF12, NDUFAF6, DARS2, BOLA3, SLC19A3, SCO1, HIBCH, PDHA1, PDHAX, PC, ETFA, TRMU, TUFM, NDUFS6, WWOX, UBCD TREX1, ATL1, VAC14, GFAP, PLA2G6, TPRKB, ATP8A2, PEX13, IGHMBP2, LAMB2, LPIN1, GFPT1, CLN5, DOLK) (20 mito group, 19 nonmito group) 59 variants (31 mito group, 18 nonmito group) were detected. Seven novel variants in the mito group (SLC25A12, GLRX5, DARS2, SCO1, PC, ETFA, NDUFS6), nine novel variants in the nonmito group (IVD, GCDH, COG4, VAC14, GFAP, PLA2G6, ATP8A2, PEX13, LPIN1) were detected. Conclusions We explored the feasibility of identifying pathogenic alleles using WES and TES in MD. Our results show that WES is the primary method of choice in the diagnosis of MD until at least all genes responsible for PMD are found and are highly effective in facilitating the diagnosis process.

Ethnic Difference in Genomic Profiles of Chronic Lymphocytic Leukemia in Korea: Targeted Exome Sequencing and Molecular Cytogenetics

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1726-1726
Author(s):  
Jung-Ah Kim ◽  
Byungjin Hwang ◽  
Si Nae Park ◽  
Sunghoon Huh ◽  
Kyongok Im ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Chronic Lymphocytic Leukemia ◽  
Exome Sequencing ◽  
Ethnic Difference ◽  
Lymphocytic Leukemia ◽  
Next Generation ◽  
Prognostic Implication ◽  
Targeted Exome Sequencing ◽  
Cytogenetic Aberrations ◽  
Generation Sequencing

Abstract Background: Chronic lymphocytic leukemia (CLL) is considered as typical malignancy with ethnic difference, which is one of the common leukemia in western countries, while extremely rare in Asian countries. In addition to incidence rates, mean age of CLL in Asian is younger than that of Caucasian. Recently, many report using next generation sequencing revealed predictive mutations with prognostic implication and treatment response in Caucasian. Yet, genetic profiles of CLL and its prognostic significance have rarely been reported in Asian. To investigate whether genomic profile of CLL in Korea and prognostic impact of adverse mutation shows ethnic difference from Caucasian, we performed target capture sequencing of 87 hematologic malignancy related genes and fluorescent in situ hybridization for prognostic cytogenetic aberrations. Methods: A total of 71 CLL patients were enrolled (median age at diagnosis 61 years, range 23-81 years). Conventional cytogenetic study (n=60) and FISH for chromosome 12 enumeration, 13q14.3 deletions, and 17p13 deletions (n=51) were performed. Target exome sequencing for an 87-gene panel was performed using IlluminaHiSeq 2500 (n=48). Mutations were selected by running algorithms including SIFT, Polyphen2, and CADD, and normal variant was filtered by by 1000Gp, ESP6500, and the in-house Korean database (n=250). Candidate mutations were confirmed by Sanger sequencing. We assessed disease progression, survival and response to treatment. Results: Overall, 37 of 48 patients (77.1%) had at least one mutation; the mean number of mutations per patient was 2.1 (range 0-6). The average coverage of target regions was 200-fold. Targeted exome-sequencing analysis revealed 78 substitutions and insertion/deletions. The most common recurrent mutation (>5% frequency) was ATM (20.8%), followed by TP53 (14.6%), SF3B1 (10.4%), KLHL6 (8.3%), LAMB4 (6.25%), BCOR (6.25%) and NOTCH1 (6.25%). Compared to Caucasian, the ATM, KLHL6 and BCOR mutationsshowed higher frequency in Korean, while NOTCH1, LRP1B, CHD2, POT1 and TGM7 mutations were more frequent in Caucasian. Of note, the ATM mutation exhibited a 2-fold higher incidence (20.8% vs. 9%) in Koreans compared to Caucasians. Frequencies of TP53, SF3B1, MYD88, FAT4, SAMHD, DDX3X, ITPKB, and MED12 mutations were similar between Korean and Caucasian. The LAMB4, SH2B3, RUNX1, SCRIB, KIT, GATA2, CEBPA, TCF12, STAG2, ZRSR2, SETBP1, CSF1R, and SETBP1 mutations have not been reported in Caucasians. Mutations with adverse prognostic implication in Korean CLL was different from those of Caucasian. The TP53, MYD88, SF3B1, ITPKB, SAMHD1, and EGR2 mutations were associated with poor prognosis (P =0.023, P =0.005, P =0.032, P =0.011, P =0.049 and P =0.032, respectively, conventional Cox regression model, P <0.05). Aberrant karyotypes were observed in 28.3% (17/60) of patients by G-banding and in 66.7% (34/51) of patients by FISH. Compared to the reports of western countries, frequency of cytogenetic aberrations by FISH is similar and 13q14 deletion (45.8%, 22/48) was the most frequent chromosomal aberration, follow by trisomy 12 (30.0%, 15/50) and 17p deletion (23.5%, 12/51). Conclusions: The somatic mutation profiles and adverse prognostic genes of Korean CLL differed from that of Caucasian CLL patients, while cytogenetic profiles were similar. Novel mutations discovered in this study must be validated through large cohort studies and may offer clues to the mechanisms underlying the ethnic difference in CLL incidence. In the future, therapeutic strategies targeting these genes should be evaluated and considered. To our knowledge, this is the first comprehensive mutation analysis of CLL patients in Asians using next generation sequencing. Figure 1. Comparison of mutation frequencies (%) between Caucasian and Korean populations Figure 1. Comparison of mutation frequencies (%) between Caucasian and Korean populations Disclosures No relevant conflicts of interest to declare.

SAT0531 NEXT GENERATION SEQUENCING AND AUTOINFLAMMATORY SYNDROMES: CLINICAL AND GENETICAL CORRELATION ON AN ADULT POPULATION FROM A REFERRAL THIRD-CARE CENTRE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1223-1223
Author(s):  
J. R. Marques Soares ◽  
M. Antolin Mate ◽  
E. Garcia Arumi ◽  
E. Tizzano Ferrari ◽  
S. Bujan Rivas
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Data ◽  
Clinical Suspicion ◽  
Gene Panel ◽  
Adult Patients ◽  
Next Generation ◽  
Related Gene ◽  
Unknown Significance ◽  
Level Hospital ◽  
Generation Sequencing

Background:Systemic autoinflammatory diseases (sAID) are a group of conditions with recurrent episodes of inflammation in absence of infection or autoimmune response. Its physiopathology mainly lies on mono/poligenic mutations involving genes related to the innate immune system response. Next Generation Sequencing (NGS) platformss have been a big step forward on sAID diagnosis, although a clinical and genetic correlation is still needed.Objectives:To review the sAID related gene panel variants identified using NGS sAID gene panel on a cohort of adult patients screened for sAID from a referral third-level hospital.To correlate genetic and clinical findings for sAID related variants identified in order to the clinical suspicion diagnosis of sAID.Methods:A retrospective review of a cohort of adult (≥ 16 yo) patients with available NGS sAID related gene panel (MiSeq Illumina sequencing platform including intron and exon variants from up to 17 sAID genes, with coverage depth > x100) among 2014 and 2019 was performed.Demographic, clinical and genetic data were collected in a database.Genetic variants were classified according to the American College of Medical Genetics/Association for Molecular Pathology classification as benign/likely benign/variable of unknown significance (VUS)/likely pathogenic/pathogenic. In case of polymorphisms or lack of genetic data, the variants were named as unclassified.A description of the cohort and an analysis of the correlation assessment between clinical data and genetic findings were performed.Results:246 out of 299 (82%) patients with NGS sAID gene panel had clinical data available. 170/246 (69%) were adult patients. The medium age was 48 yo, and the M/F ratio was 2.46. 87/170 (51%) adult patients presented 122 variants involving sAID genes (60/87 patients with a single variant). All the variants out of 7 seven were heterozygous variants.Variants were classified according to ACMG/AMP as follow: pathogenic/probably pathogenic: 22/122 (18%), unknown significance: 74/122 (60.6%), benign/probably benign: 6/122 (4.91%). 20/122 (16.4%) were unclassified variants or polymorphisms.The most frequent variants identified involved MEFV (54/122), NOD2/CARD15 (18/122) and TNFRSF1A (17/122 including 12 p.Arg121Gln variants) genes.37/122 (30%) variants correlated with the clinical picture in 33 patients, allowing to confirm the suspected diagnosis. Among the 122 variants, 7 not previously communicated variants were identified.No somatic variants were found.Conclusion:NGS sAID related gene panel is a useful tool for sAID diagnosis. In this cohort of 170 adult patients from a referral third-level hospital, genetic tests identified sAID related variants in almost half of them.20% of patients who underwent genetic NGS sAID related gene panel studies were finally diagnosed with sAID.The identification of a genetic variant (even pathogenic / likely pathogenic variant) is not diagnostic for sAID if there is not a suggestive clinical picture.Despite genetic findings, a careful evaluation of clinical – genetic correlation is needed to confirm the suspicion diagnosis, especially for low penetrance variants like TNFRSF1A p. Arg121Gln.References:Diagnostic utility of a targeted next-generation sequencing gene panel in the clinical suspicion of systemic autoinflammatory diseases: a multi-center study. Karacan I, Balamir A, Uğurlu S, et al. . Rheumatol Int. 2019 May;39(5):911-919. doi: 10.1007/s00296-019-04252-5. Epub 2019 Feb 19.Disclosure of Interests:None declared

scholarly journals No Metagenomic Evidence of Causative Viral Pathogens in Postencephalitic Parkinsonism Following Encephalitis Lethargica

2021 ◽  
Vol 9 (8) ◽  
pp. 1716
Author(s):  
Dániel Cadar ◽  
Kurt A. Jellinger ◽  
Peter Riederer ◽  
Sabrina Strobel ◽  
Camelia-Maria Monoranu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Neuronal Loss ◽  
Unknown Etiology ◽  
Next Generation ◽  
Encephalitis Lethargica ◽  
Tissue Samples ◽  
Viral Pathogen ◽  
Postencephalitic Parkinsonism ◽  
Generation Sequencing ◽  
Post Infectious

Postencephalitic parkinsonism (PEP) is a disease of unknown etiology and pathophysiology following encephalitis lethargica (EL), an acute-onset polioencephalitis of cryptic cause in the 1920s. PEP is a tauopathy with multisystem neuronal loss and gliosis, clinically characterized by bradykinesia, rigidity, rest tremor, and oculogyric crises. Though a viral cause of EL is likely, past polymerase chain reaction-based investigations in the etiology of both PEP and EL were negative. PEP might be caused directly by an unknown viral pathogen or the consequence of a post-infectious immunopathology. The development of metagenomic next-generation sequencing in conjunction with bioinformatic techniques has generated a broad-range tool for the detection of unknown pathogens in the recent past. Retrospective identification and characterization of pathogens responsible for past infectious diseases can be successfully performed with formalin-fixed paraffin-embedded (FFPE) tissue samples. In this study, we analyzed 24 FFPE brain samples from six patients with PEP by unbiased metagenomic next-generation sequencing. Our results show that no evidence for the presence of a specific or putative (novel) viral pathogen was found, suggesting a likely post-infectious immune-mediated etiology of PEP.

scholarly journals Next-Generation Sequencing Gene Panels and “Solo” Clinical Exome Sequencing Applied in Structurally Abnormal Fetuses

2021 ◽  
pp. 1-11
Author(s):  
Montse Pauta ◽  
Berta Campos ◽  
Maria Segura-Puimedon ◽  
Gemma Arca ◽  
Alfons Nadal ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Diagnostic Yield ◽  
Monogenic Disease ◽  
Chromosomal Microarray Analysis ◽  
Next Generation ◽  
Clinical Exome Sequencing ◽  
Gene Panels ◽  
Generation Sequencing ◽  
Structural Anomalies

<b><i>Objective:</i></b> The aim of the study was to assess the diagnostic yield of 2 different next-generation sequencing (NGS) approaches: gene panel and “solo” clinical exome sequencing (solo-CES), in fetuses with structural anomalies and normal chromosomal microarray analysis (CMA), in the absence of a known familial mutation. <b><i>Methodology:</i></b> Gene panels encompassing from 2 to 140 genes, were applied mainly in persistent nuchal fold/fetal hydrops and in large hyperechogenic kidneys. Solo-CES, which entails sequencing the fetus alone and only interpreting the Online Mendelian Inheritance in Man genes, was performed in multisystem or recurrent structural anomalies. <b><i>Results:</i></b> During the study period (2015–2020), 153 NGS studies were performed in 148 structurally abnormal fetuses with a normal CMA. The overall diagnostic yield accounted for 35% (53/153) of samples and 36% (53/148) of the fetuses. Diagnostic yield with the gene panels was 31% (15/49), similar to 37% (38/104) in solo-CES. <b><i>Conclusions:</i></b> A monogenic disease was established as the underlying cause in 35% of selected fetal structural anomalies by gene panels and solo-CES.

scholarly journals Exome sequencing covers >98% of mutations identified on targeted next generation sequencing panels

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0170843 ◽  
Author(s):  
Holly LaDuca ◽  
Kelly D. Farwell ◽  
Huy Vuong ◽  
Hsiao-Mei Lu ◽  
Wenbo Mu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

scholarly journals Next-generation sequencing reveals three novel variants in Polish patients with Usher syndrome

Klinika Oczna ◽  
2018 ◽  
Vol 2018 (4) ◽  
pp. 189-194
Author(s):  
Anna Wawrocka ◽  
Joanna Walczak-Sztulpa ◽  
Anna Skorczyk-Werner ◽  
Łukasz Kuszel ◽  
Magdalena Socha ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Usher Syndrome ◽  
Next Generation ◽  
Novel Variants ◽  
Generation Sequencing

scholarly journals A teljesexom-szekvenálás jelentősége a ritka neurológiai betegségek diagnosztikájában – saját tapasztalatok egy ataxiás eset kapcsán

2018 ◽  
Vol 159 (28) ◽  
pp. 1163-1169 ◽  
Author(s):  
Péter Balicza ◽  
Zoltán Grosz ◽  
Renáta Bencsik ◽  
Anett Illés ◽  
Anikó Gál ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Cerebellar Ataxia ◽  
Clinical Symptoms ◽  
Spastic Paraparesis ◽  
Gene Panel ◽  
Next Generation ◽  
Hereditary Spastic Paraparesis ◽  
Disease Stratification ◽  
Generation Sequencing

Abstract: Next generation sequencing (NGS) technologies reshape the diagnostics of rare neurological diseases. In the background of certain neurological symptoms, such as ataxia, many acquired and genetic causes may be present. Variations in a given gene can present with variable phenotypes, too. Because of this phenomenon, the conventional one gene sequencing approach often fails to identify the genetic background of a disease. Next generation sequencing panels allow to sequence 50–100 genes simultaneously, and if the disease stratification is not possible based on the clinical symptoms, whole exome sequencing can help in the diagnostic of genetic disorders with atypical presentation. This case study is about the exome sequencing of a patient with cerebellar ataxia. Genetic investigations identified rare variants in the SPG11 gene in association with the clinical phenotype, which gene was originally described in the background of hereditary spastic paraparesis. Our article highlights that in certain cases the variability of the leading presenting symptom makes it hard to select the correct gene panel. In our case the variants in the gene, formerly associated to hereditary spastic paraparesis, resulted in cerebellar ataxia initially, so even an ataxia NGS gene panel would not detect those. Orv Hetil. 2018; 159(28): 1163–1169.

Sign in / Sign up

Export Citation Format

Share Document