scholarly journals New Insights on Genetic Diagnostics in Cardiomyopathy and Arrhythmia Patients Gained by Stepwise Exome Data Analysis

2020 ◽  
Vol 9 (7) ◽  
pp. 2168
Author(s):  
Konstantinos Kolokotronis ◽  
Natalie Pluta ◽  
Eva Klopocki ◽  
Erdmute Kunstmann ◽  
Daniel Messroghli ◽  
...  
Keyword(s):  
Data Analysis ◽  
Exome Sequencing ◽  
Candidate Genes ◽  
Genetic Heterogeneity ◽  
Diagnostic Yield ◽  
Genetic Diagnostics ◽  
Routine Diagnostics ◽  
Exome Data ◽  
Gene Panels ◽  
Diagnostic Benefit

Inherited cardiomyopathies are characterized by clinical and genetic heterogeneity that challenge genetic diagnostics. In this study, we examined the diagnostic benefit of exome data compared to targeted gene panel analyses, and we propose new candidate genes. We performed exome sequencing in a cohort of 61 consecutive patients with a diagnosis of cardiomyopathy or primary arrhythmia, and we analyzed the data following a stepwise approach. Overall, in 64% of patients, a variant of interest (VOI) was detected. The detection rate in the main sub-cohort consisting of patients with dilated cardiomyopathy (DCM) was much higher than previously reported (25/36; 69%). The majority of VOIs were found in disease-specific panels, while a further analysis of an extended panel and exome data led to an additional diagnostic yield of 13% and 5%, respectively. Exome data analysis also detected variants in candidate genes whose functional profile suggested a probable pathogenetic role, the strongest candidate being a truncating variant in STK38. In conclusion, although the diagnostic yield of gene panels is acceptable for routine diagnostics, the genetic heterogeneity of cardiomyopathies and the presence of still-unknown causes favor exome sequencing, which enables the detection of interesting phenotype–genotype correlations, as well as the identification of novel candidate genes.

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 The genetic landscape of intellectual disability and epilepsy in adults and the elderly: a systematic genetic work-up of 150 individuals

2021 ◽  
Author(s):  
Pia Zacher ◽  
Thomas Mayer ◽  
Frank Brandhoff ◽  
Tobias Bartolomaeus ◽  
Diana Le Duc ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Exome Sequencing ◽  
Diagnostic Yield ◽  
Fragile X ◽  
Genetic Diagnostics ◽  
High Yield ◽  
Chromosomal Microarray ◽  
Limited Information ◽  
Single Nucleotide Variants ◽  
Elderly Individuals

Abstract Purpose Genetic diagnostics of neurodevelopmental disorders with epilepsy (NDDE) are predominantly applied in children, thus limited information is available regarding adults or elderly. Methods We investigated 150 adult/elderly individuals with NDDE by conventional karyotyping, FMR1 testing, chromosomal microarray, panel sequencing, and for unresolved cases, also by exome sequencing (nsingle = 71, ntrios = 24). Results We identified (likely) pathogenic variants in 71 cases (47.3%) comprising fragile X syndrome (n = 1), disease-causing copy number (n = 23), and single-nucleotide variants (n = 49). Seven individuals displayed multiple independent genetic diagnoses. The diagnostic yield correlated with the severity of intellectual disability. Individuals with anecdotal evidence of exogenic early-life events (e.g., nuchal cord, complications at delivery) with alleged/unproven association to the disorder had a particularly high yield of 58.3%. Screening for disease-specific comorbidities was indicated in 45.1% and direct treatment consequences arose in 11.8% of diagnosed individuals. Conclusion Panel/exome sequencing displayed the highest yield and should be considered as first-tier diagnostics in NDDE. This high yield and the numerous indications for additional screening or treatment modifications arising from genetic diagnoses indicate a current medical undersupply of genetically undiagnosed adult/elderly individuals with NDDE. Moreover, knowledge of the course of elderly individuals will ultimately help in counseling newly diagnosed individuals with NDDE.

scholarly journals P.109 Diagnostic Yield of Targeted Exome Sequencing in West Syndrome

2021 ◽  
Vol 48 (s3) ◽  
pp. S50-S50
Author(s):  
M Parfyonov ◽  
I Guella ◽  
DM Evans ◽  
S Adam ◽  
C DeGuzman ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Genetic Heterogeneity ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Diagnostic Yield ◽  
Genetic Diagnosis ◽  
West Syndrome ◽  
Global Developmental Delay ◽  
Targeted Exome Sequencing ◽  
Ion Proton

Background: West syndrome (WS) is characterized by the onset of epileptic spasms usually within the first year of life. Global developmental delay with/without regression is common. Advances in high-throughput sequencing have supported the genetic heterogeneity of this condition. To better understand the genetic causes of this disorder, we investigated the results of targeted exome sequencing in 29 patients with WS. Methods: Whole exome sequencing (WES) was performed on an Ion ProtonTM and variant reporting was restricted to sequences of 620 known epilepsy genes. Diagnostic yield and treatment impact are described for 29 patients with WS. Results: A definitely/likely diagnosis was made in 10 patients (34%), which included 10 different genes (ALG13, PAFAH1B1, SLC35A2, DYNC1H1, ADSL, DEPDC5, ARX, CDKL5, SCN8A, STXBP1) known to be associated with epilepsy or WS. Most variants were de novo dominant (X-linked/autosomal) except for ARX (X-linked recessive) and ADSL (autosomal recessive). 4 out of 10 (40%) had a genetic diagnosis with potential treatment implications. Conclusions: These results emphasize the genetic heterogeneity of WS. The high diagnostic yield, along with the significant genetic variability, and the potential for treatment impact, supports the early use of this testing in patients with unexplained WS.

Diagnostic Yield and Novel Candidate Genes by Exome Sequencing in 152 Consanguineous Families With Neurodevelopmental Disorders

2017 ◽  
Vol 74 (3) ◽  
pp. 293 ◽  
Author(s):  
Miriam S. Reuter ◽  
Hasan Tawamie ◽  
Rebecca Buchert ◽  
Ola Hosny Gebril ◽  
Tawfiq Froukh ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Neurodevelopmental Disorders ◽  
Diagnostic Yield

scholarly journals Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders

2019 ◽  
Author(s):  
Benjamin Büttner ◽  
Sonja Martin ◽  
Anja Finck ◽  
Maria Arelin ◽  
Carolin Baade-Büttner ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Neurodevelopmental Disorders ◽  
Scientific Community ◽  
Scientific Evaluation ◽  
Research Setting ◽  
Routine Diagnostics ◽  
Personalized Care ◽  
Speed Up ◽  
Important Milestone

AbstractBackgroundDeciphering the monogenetic causes of neurodevelopmental disorders (NDD) is an important milestone to offer personalized care. But the plausibility of reported candidate genes in exome studies often remains unclear, which slows down progress in the field.MethodsWe performed exome sequencing (ES) in 198 cases of NDD. Cases that remained unresolved (n=135) were re-investigated in a research setting. We established a candidate scoring system (CaSc) based on 12 different parameters reflecting variant and gene attributes as well as current literature to rank and prioritize candidate genes.ResultsIn this cohort, we identified 158 candidate variants in 148 genes with CaSc ranging from 2 to 11.7. Only considering the top 15% of candidates, 14 genes were already published or funneled into promising validation studies.ConclusionsWe promote that in an approach of case by case re-evaluation of primarily negative ES, systematic and standardized scoring of candidate genes can and should be applied. This simple framework enables better comparison, prioritization, and communication of candidate genes within the scientific community. This would represent an enormous benefit if applied to the tens of thousands of negative ES performed in routine diagnostics worldwide and speed up deciphering the monogenetic causes of NDD.

scholarly journals CNV Detection from Exome Sequencing Data in Routine Diagnostics of Rare Genetic Disorders: Opportunities and Limitations

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1427
Author(s):  
Beryl Royer-Bertrand ◽  
Katarina Cisarova ◽  
Florence Niel-Butschi ◽  
Laureane Mittaz-Crettol ◽  
Heidi Fodstad ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Genetic Disorders ◽  
Copy Number Variations ◽  
Gene Panel ◽  
Sequencing Data ◽  
Routine Diagnostics ◽  
Pathogenic Cnvs ◽  
Gene Panels ◽  
Good Coverage ◽  
Cnv Detection

To assess the potential of detecting copy number variations (CNVs) directly from exome sequencing (ES) data in diagnostic settings, we developed a CNV-detection pipeline based on ExomeDepth software and applied it to ES data of 450 individuals. Initially, only CNVs affecting genes in the requested diagnostic gene panels were scored and tested against arrayCGH results. Pathogenic CNVs were detected in 18 individuals. Most detected CNVs were larger than 400 kb (11/18), but three individuals had small CNVs impacting one or a few exons only and were thus not detectable by arrayCGH. Conversely, two pathogenic CNVs were initially missed, as they impacted genes not included in the original gene panel analysed, and a third one was missed as it was in a poorly covered region. The overall combined diagnostic rate (SNVs + CNVs) in our cohort was 36%, with wide differences between clinical domains. We conclude that (1) the ES-based CNV pipeline detects efficiently large and small pathogenic CNVs, (2) the detection of CNV relies on uniformity of sequencing and good coverage, and (3) in patients who remain unsolved by the gene panel analysis, CNV analysis should be extended to all captured genes, as diagnostically relevant CNVs may occur everywhere in the genome.

scholarly journals A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification

2020 ◽  
Vol 21 (24) ◽  
pp. 9355
Author(s):  
Marta Martín-Sánchez ◽  
Nereida Bravo-Gil ◽  
María González-del Pozo ◽  
Cristina Méndez-Vidal ◽  
Elena Fernández-Suárez ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Candidate Genes ◽  
Diagnostic Yield ◽  
Diagnostic Algorithm ◽  
Clinical Genetics ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Causal Variants ◽  
Simultaneous Study ◽  
Candidate Loci

The management of unsolved inherited retinal dystrophies (IRD) cases is challenging since no standard pipelines have been established. This study aimed to define a diagnostic algorithm useful for the diagnostic routine and to address unsolved cases. Here, we applied a Next-Generation Sequencing-based workflow, including a first step of panel sequencing (PS) followed by clinical-exome sequencing (CES) and whole-exome sequencing (WES), in 46 IRD patients belonging to 42 families. Twenty-six likely causal variants in retinal genes were found by PS and CES. CES and WES allowed proposing two novel candidate loci (WDFY3 and a X-linked region including CITED1), both abundantly expressed in human retina according to RT-PCR and immunohistochemistry. After comparison studies, PS showed the best quality and cost values, CES and WES involved similar analytical efforts and WES presented the highest diagnostic yield. These results reinforce the relevance of panels as a first step in the diagnostic routine and suggest WES as the next strategy for unsolved cases, reserving CES for the simultaneous study of multiple conditions. Standardizing this algorithm would enhance the efficiency and equity of clinical genetics practice. Furthermore, the identified candidate genes could contribute to increase the diagnostic yield and expand the mutational spectrum in these disorders.

scholarly journals Personalised virtual gene panels reduce interpretation workload and maintain diagnostic rates of proband-only clinical exome sequencing for rare disorders

2021 ◽  
pp. jmedgenet-2020-107303
Author(s):  
Leslie Patricia Molina-Ramírez ◽  
Claire Kyle ◽  
Jamie M Ellingford ◽  
Ronnie Wright ◽  
Algy Taylor ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Gene Selection ◽  
Diagnostic Yield ◽  
Cost Effective ◽  
Gene Panel ◽  
Monogenic Disorders ◽  
Use Of Resources ◽  
Clinical Exome Sequencing ◽  
Cost Effective Approach ◽  
Gene Panels

PurposeThe increased adoption of genomic strategies in the clinic makes it imperative for diagnostic laboratories to improve the efficiency of variant interpretation. Clinical exome sequencing (CES) is becoming a valuable diagnostic tool, capable of meeting the diagnostic demand imposed by the vast array of different rare monogenic disorders. We have assessed a clinician-led and phenotype-based approach for virtual gene panel generation for analysis of targeted CES in patients with rare disease in a single institution.MethodsRetrospective survey of 400 consecutive cases presumed by clinicians to have rare monogenic disorders, referred on singleton basis for targeted CES. We evaluated diagnostic yield and variant workload to characterise the usefulness of a clinician-led approach for generation of virtual gene panels that can incorporate up to three different phenotype-driven gene selection methods.ResultsAbnormalities of the nervous system (54.5%), including intellectual disability, head and neck (19%), skeletal system (16%), ear (15%) and eye (15%) were the most common clinical features reported in referrals. Combined phenotype-driven strategies for virtual gene panel generation were used in 57% of cases. On average, 7.3 variants (median=5) per case were retained for clinical interpretation. The overall diagnostic rate of proband-only CES using personalised phenotype-driven virtual gene panels was 24%.ConclusionsOur results show that personalised virtual gene panels are a cost-effective approach for variant analysis of CES, maintaining diagnostic yield and optimising the use of resources for clinical genomic sequencing in the clinic.

Abstract 15882: Gene-Panel Based Next Generation Sequencing (NGS) Greatly Improves Clinical Genetic Diagnostics in Inherited Cardiomyopathies

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Jan D Jongbloed ◽  
Anna Pósafalvi ◽  
Renée C Niessen ◽  
Yvonne M Hoedemaekers ◽  
Paul A van der Zwaag ◽  
...  
Keyword(s):  
Diagnostic Yield ◽  
Gene Panel ◽  
Genetic Diagnostics ◽  
Clinical Genetic ◽  
Routine Diagnostics ◽  
Clinical Criteria ◽  
Pathogenic Mutations ◽  
Inherited Cardiomyopathies ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

INTRODUCTION: NGS techniques can be successfully applied to find mutations underlying genetic cardiomyopathies. However, Exome Sequencing (ES) shows incomplete representation and coverage of exons, leading to clinically relevant mutations being missed. Thus, ES will, at least for now, coexist in clinical genetic diagnostics with other NGS-based strategies, such as gene-panel based resequencing. Therefore, we aimed at evaluating the yield of gene-panel based resequencing of 55 genes in cardiomyopathy patients referred to our department. METHODS: We constructed an enrichment kit targeting 55 cardiomyopathy genes and implemented this into routine diagnostics. We evaluated our first 162 patients: 47 fulfilled generally accepted clinical criteria for hypertrophic cardiomyopathy (HCM), 72 fulfilled the Mestroni criteria for dilated cardiomyopathy (DCM) and 3 were diagnosed with arrhythmogenic cardiomyopathy (ACM). In addition, 23, 11 and 6 cases showed signs of DCM, HCM and ACM, yet did not fulfill the formal criteria. Additional cosegregation analyses were performed to further support pathogenicity of potentially causal mutations. RESULTS: In the DCM cohort 40 pathogenic or likely pathogenic mutations were identified (55%; 40/72). Mutations in TTN were found in 14% of DCM patients (10/72). The yield in criteria positive HCM and ACM patients was 40% (17/43) and 33% (1/3). In patients not fully fulfilling criteria for DCM, HCM and ACM the yield was 52% (12/23), 36% (4/11) and 83% (5/6). In 13 % (21/162) of cases two or more (potentially) pathogenic mutations were identified. Results of cosegregation analyses supported pathogenicity of potentially causal mutations in 42 families. In 6 results argued against pathogenicity. CONCLUSIONS: Gene-panel based NGS results in a substantial increase in diagnostic yield for DCM patients compared to previous results of Sanger sequencing most prevalent genes (55% vs 20-25%). TTN mutations are most prevalent in DCM patients (14%). Higher diagnostic yields are achieved for patients fulfilling DCM and HCM criteria. Cosegregation analyses further support pathogenicity of potentially causal mutations. Together, our gene-panel based approach greatly improved genetic diagnostics in cardiomyopathies.

A Guideline for the Diagnosis of Pediatric Mitochondrial Disease: The Value of Muscle and Skin Biopsies in the Genetics Era

2017 ◽  
Vol 48 (04) ◽  
pp. 309-314 ◽  
Author(s):  
Johannes Mayr ◽  
Jean Nuoffer ◽  
Holger Prokisch ◽  
Wolfgang Sperl ◽  
Saskia Wortmann
Keyword(s):  
Candidate Genes ◽  
Diagnostic Yield ◽  
Mitochondrial Diseases ◽  
Genetic Diagnostics ◽  
First Line ◽  
The Past ◽  
Biochemical Diagnosis ◽  
Genetic Level ◽  
Skin Biopsies ◽  
Generation Sequencing

AbstractMitochondrial diseases are highly heterogeneous on the clinical, biochemical, and genetic level. In the traditional diagnostic approach (“biopsy first”) the evaluation of the affected individual and his body fluids, combined with the analysis of the respiratory chain enzymes in muscle based the subsequent Sanger sequencing of single candidate genes (“from function to gene”). Within the past few years, next-generation sequencing techniques of leucocyte-derived DNA (e.g., exome sequencing), with a diagnostic yield of more than 40%, have become the first line routine technology. This implicates that the invasive muscle biopsy is performed less often, especially in children. Furthermore, in this “genetics-first” approach the detection of new candidate genes precedes functional evaluations (“from gene to function”) leading to reverse phenotyping of affected individuals. Here, we line out the value of muscle and other tissue biopsies in this “genetics-first” era. We describe when and why it is still needed. We create awareness of pitfalls in the genetic diagnostics of mitochondrial diseases still necessitating tissue biopsies. Finally, we discuss why tissue biopsies are required for confirmatory diagnostics, or for getting a biochemical diagnosis in patients with hidden variants not detectable by standard genetics.

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