Massively Parallel Sequencing of 43 Arrhythmia Genes in a Selected SUDI Cohort from Cape Town

2021 ◽  
Author(s):  
Laura Jane Heathfield ◽  
Hugh Watkins ◽  
Lorna Jean Martin ◽  
Raj Ramesar
Keyword(s):  
Age Of Onset ◽  
Massively Parallel Sequencing ◽  
African Ancestry ◽  
Male Infant ◽  
Added Value ◽  
Unexpected Death ◽  
Molecular Autopsy ◽  
Pathogenic Variants ◽  
Variant Of Unknown Significance ◽  
Unknown Significance

AbstractSudden unexpected death in infants (SUDI) is a devastating event, and unfortunately occurs frequently in developing countries. The emerging molecular autopsy has added value to post-mortem investigations, where genetic variants were able to explain the unexpected demise. Many of these variants have been found in genes involved in arrythmia pathways. The aim of this study was to sequence 43 genes previously associated with cardiac arrhythmia in a selected cohort of SUDI cases (n = 19) in South Africa. A total of 335 variants were found among the 19 infants, of which four were novel. The variants were classified as “likely pathogenic” (n = 1), “variant of unknown significance” (n = 54), “likely benign” (n = 56) or “benign” (n = 224). The likely pathogenic variant was LMNA NM_170707.2:c.1279C > T (p.Arg427Cys) and was found in a 3-week-old male infant of African ancestry. Variants in LMNA have previously been associated with dilated cardiomyopathy, with a typical age of onset in adulthood; therefore, this may be the first report in an infant. The yield of pathogenic or likely pathogenic variants in the classic genes typically associated with channelopathies and sudden death, was less in this study compared with other settings. This finding highlights the importance of population-specific research to develop a molecular autopsy which is locally relevant.

P1785Whole exome sequencing unravels new genes associated with mitral valve prolapse

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
A Van Wijngaarden ◽  
Y L Hiemstra ◽  
T T Koopmann ◽  
C A L Ruivenkamp ◽  
E Aten ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Mitral Valve ◽  
Exome Sequencing ◽  
Mitral Valve Prolapse ◽  
Pathogenic Variant ◽  
Pathogenic Variants ◽  
Cardiac Phenotype ◽  
Variant Of Unknown Significance ◽  
Unknown Significance ◽  
Population Databases

Abstract Background Several studies have suggested a familial clustering of mitral valve prolapse (MVP), especially for Barlow disease (BD), which is regarded as the effect of genetic or developmental errors. However, the genetic etiology of MVP, in particular BD, is largely unknown. So far only three genes have been identified: FLNA, DCHS1 and PLD1. Purpose The aim of this study was to identify genes associated with MVP using whole exome sequencing (WES). Methods Patients with MVP, who were classified as BD and/or had a positive family history for MVP, were referred for genetic counseling and WES. In total, 106 unrelated probands were included to identify potentially pathogenic variants in a set of 551 genes associated with cardiovascular development and/or diseases. The population databases Genome Aggregation and WES data from 110 parents of children with mental retardation were used as controls. Variants were analyzed using prediction programs, frequency in the population database and literature search. Variants were divided into the following categories: likely benign, variant of unknown significance or likely pathogenic. Results Thirteen percent (14/106) of the probands had a likely pathogenic variant in seven different genes: DCHS1 (1x), DSP (1x), HCN4 (2x), MYH6 (1x), TMEM67 (1x), TRPS1 (1x) and TTN (7x); the DSP, MYH6 and HCN4 variants cosegregated in affected relatives. None of the 110 parents of children with mental retardation had a likely pathogenic variant in these seven genes. In addition, 31% (33/106) of the probands harbored a variant of unknown significance in 23 different genes, including the genes DSP, FLNA, MYH6 and TTN (Fig). Remarkable, one variant of unknown significance in the FBN2 gene was shared among three unrelated probands and did not occur in population databases. Conclusion WES analysis conducted in probands with MVP using a large panel of genes associated with cardiac development and/or disease confirmed previously known causative genes (DCHS1) and expanded the cardiac phenotype of genes originally associated with cardiomyopathy (DSP, HCN4, MYH6 and TTN). This study is the first study that described the association between MVP and the genes DSP, MYH6 and TTN although the pathogenesis is still unknown. This high yield of likely pathogenic variants emphasizes the importance of genetic screening in MVP patients.

scholarly journals Molecular Autopsy of Sudden Cardiac Death in the Genomics Era

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1378
Author(s):  
Vincenzo Castiglione ◽  
Martina Modena ◽  
Alberto Aimo ◽  
Enrica Chiti ◽  
Nicoletta Botto ◽  
...  
Keyword(s):  
Diagnostic Features ◽  
Molecular Autopsy ◽  
Variants Of Unknown Significance ◽  
Pathogenic Variants ◽  
Genome Wide ◽  
Unknown Significance ◽  
New Challenges ◽  
Next Generation Sequencing Ngs ◽  
Cascade Genetic Screening ◽  
Generation Sequencing

Molecular autopsy is the process of investigating sudden death through genetic analysis. It is particularly useful in cases where traditional autopsy is negative or only shows non-diagnostic features, i.e., in sudden unexplained deaths (SUDs), which are often due to an underlying inherited arrhythmogenic cardiac disease. The final goal of molecular autopsy in SUD cases is to aid medico-legal inquiries and to guide cascade genetic screening of the victim’s relatives. Early attempts of molecular autopsy relied on Sanger sequencing, which, despite being accurate and easy to use, has a low throughput and can only be employed to analyse a small panel of genes. Conversely, the recent adoption of next-generation sequencing (NGS) technologies has allowed exome/genome wide examination, providing an increase in detection of pathogenic variants and the discovery of newer genotype-phenotype associations. NGS has nonetheless brought new challenges to molecular autopsy, especially regarding the clinical interpretation of the large number of variants of unknown significance detected in each individual.

scholarly journals Structural and biophysical characterization of HNF-1A as a tool to study MODY3 diabetes variants

2021 ◽  
Author(s):  
Laura Kind ◽  
Arne Raasakka ◽  
Janne Molnes ◽  
Ingvild Aukrust ◽  
Lise Bjørkhaug ◽  
...  
Keyword(s):  
Dna Binding ◽  
Target Genes ◽  
Age Of Onset ◽  
Binding Capacity ◽  
Dimerization Domain ◽  
Pathogenic Variants ◽  
Novel Approach ◽  
Unknown Significance ◽  
Precise Diagnosis

Hepatocyte nuclear factor 1A (HNF-1A) is a transcription factor expressed in several embryonic and adult tissues, modulating expression of numerous target genes. Pathogenic variants in the HNF1A gene cause maturity-onset diabetes of the young 3 (MODY3 or HNF1A MODY), characterized by dominant inheritance, age of onset before 25-35 years of age, and pancreatic β-cell dysfunction. A precise diagnosis alters management as insulin can be exchanged with sulfonylurea tablets and genetic counselling differs from polygenic forms of diabetes. More knowledge on mechanisms of HNF-1A function and the level of pathogenicity of the numerous HNF1A variants identified by exome sequencing is required for precise diagnostics. Here, we have structurally and biophysically characterized an HNF-1A protein containing both the DNA binding domain and the dimerization domain. We also present a novel approach to characterize HNF-1A variants. The folding and DNA binding capacity of two established MODY3 HNF-1A variant proteins (P112L, R263C) and one variant of unknown significance (N266S) were determined. All three variants showed reduced functionality compared to the wild-type protein. While the R263C and N266S variants displayed reduced binding to an HNF-1A target promoter, the P112L variant was unstable in vitro and in cells. Our results support and mechanistically explain disease causality for all investigated variants and allow for the dissection of structurally unstable and DNA binding defective variants. This points towards structural and biochemical investigation of HNF-1A being a valuable aid in reliable variant classification needed for precision diagnostics and management.

scholarly journals Diagnostic Yield of Genetic Testing in Sudden Cardiac Death with Autopsy Findings of Uncertain Significance

2021 ◽  
Vol 10 (9) ◽  
pp. 1806
Author(s):  
Mercedes Iglesias ◽  
Tomas Ripoll-Vera ◽  
Consuelo Perez-Luengo ◽  
Ana Belen García ◽  
Susana Moyano ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Ventricular Hypertrophy ◽  
Diagnostic Yield ◽  
Left Ventricular ◽  
Molecular Autopsy ◽  
Variants Of Unknown Significance ◽  
Pathogenic Variants ◽  
Unknown Significance ◽  
Uncertain Significance ◽  
Frequent Variant

Background: Sudden death (SD) in the young usually has an underlying genetic cause. In many cases, autopsy reveals unspecific and inconclusive results, like idiopathic left ventricular hypertrophy (LVH), nonsignificant coronary atherosclerosis (CA), and primary myocardial fibrosis (PMF). Their pathogenicity and their relation to SD cause is unknown. This study aims to evaluate the diagnostic yield of genetic testing in these cases. Methods: SD cases, between 1 and 50 years old, with findings of uncertain significance (idiopathic LVH, nonsignificant CA and PMF) on autopsy were evaluated prospectively, including information about medical and family history and circumstances of death. Genetic testing was performed. Results: In a series of 195 SD cases, we selected 31 cases presenting idiopathic LVH (n = 16, 51.61%), nonsignificant CA (n = 17, 54.84%), and/or PMF (n = 24, 77.42%) in the autopsy. Mean age was 41 ± 7.2 years. Diagnostic yield of genetic test was 67.74%, considering variants of unknown significance (VUS), pathogenic variants (PV) and likely pathogenic variants (LPV); 6.45% including only PV and LPV. Structural genes represented 41,93% (n = 13) of cases, while 38,7% (n = 12) were related to channelopathies. Conclusion: Molecular autopsy in SD cases between 1 and 50 years old, with findings of uncertain significance, has a low diagnostic yield, being VUS the most frequent variant observed.

Frequency and characterization of mutations in genes in a large cohort of patients referred to MODY registry

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Emily Breidbart ◽  
Liyong Deng ◽  
Patricia Lanzano ◽  
Xiao Fan ◽  
Jiancheng Guo ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Exome Sequencing ◽  
Large Scale ◽  
Age Of Onset ◽  
Family Members ◽  
Ethnically Diverse ◽  
Monogenic Diabetes ◽  
Diabetes Diagnosis ◽  
Pathogenic Variants ◽  
Atypical Diabetes

Abstract Objectives There have been few large-scale studies utilizing exome sequencing for genetically undiagnosed maturity onset diabetes of the young (MODY), a monogenic form of diabetes that is under-recognized. We describe a cohort of 160 individuals with suspected monogenic diabetes who were genetically assessed for mutations in genes known to cause MODY. Methods We used a tiered testing approach focusing initially on GCK and HNF1A and then expanding to exome sequencing for those individuals without identified mutations in GCK or HNF1A. The average age of onset of hyperglycemia or diabetes diagnosis was 19 years (median 14 years) with an average HbA1C of 7.1%. Results Sixty (37.5%) probands had heterozygous likely pathogenic/pathogenic variants in one of the MODY genes, 90% of which were in GCK or HNF1A. Less frequently, mutations were identified in PDX1, HNF4A, HNF1B, and KCNJ11. For those probands with available family members, 100% of the variants segregated with diabetes in the family. Cascade genetic testing in families identified 75 additional family members with a familial MODY mutation. Conclusions Our study is one of the largest and most ethnically diverse studies using exome sequencing to assess MODY genes. Tiered testing is an effective strategy to genetically diagnose atypical diabetes, and familial cascade genetic testing identified on average one additional family member with monogenic diabetes for each mutation identified in a proband.

scholarly journals Genetic Neonatal-Onset Epilepsies and Developmental/Epileptic Encephalopathies with Movement Disorders: A Systematic Review

2021 ◽  
Vol 22 (8) ◽  
pp. 4202
Author(s):  
Carlotta Spagnoli ◽  
Carlo Fusco ◽  
Antonio Percesepe ◽  
Vincenzo Leuzzi ◽  
Francesco Pisani
Keyword(s):  
Movement Disorders ◽  
Time Course ◽  
Neonatal Period ◽  
Age Of Onset ◽  
Brain Mri ◽  
Neonatal Seizure ◽  
Mri Findings ◽  
Epileptic Encephalopathies ◽  
Pathogenic Variants ◽  
Neonatal Onset

Despite expanding next generation sequencing technologies and increasing clinical interest into complex neurologic phenotypes associating epilepsies and developmental/epileptic encephalopathies (DE/EE) with movement disorders (MD), these monogenic conditions have been less extensively investigated in the neonatal period compared to infancy. We reviewed the medical literature in the study period 2000–2020 to report on monogenic conditions characterized by neonatal onset epilepsy and/or DE/EE and development of an MD, and described their electroclinical, genetic and neuroimaging spectra. In accordance with a PRISMA statement, we created a data collection sheet and a protocol specifying inclusion and exclusion criteria. A total of 28 different genes (from 49 papers) leading to neonatal-onset DE/EE with multiple seizure types, mainly featuring tonic and myoclonic, but also focal motor seizures and a hyperkinetic MD in 89% of conditions, with neonatal onset in 22%, were identified. Neonatal seizure semiology, or MD age of onset, were not always available. The rate of hypokinetic MD was low, and was described from the neonatal period only, with WW domain containing oxidoreductase (WWOX) pathogenic variants. The outcome is characterized by high rates of associated neurodevelopmental disorders and microcephaly. Brain MRI findings are either normal or nonspecific in most conditions, but serial imaging can be necessary in order to detect progressive abnormalities. We found high genetic heterogeneity and low numbers of described patients. Neurological phenotypes are complex, reflecting the involvement of genes necessary for early brain development. Future studies should focus on accurate neonatal epileptic phenotyping, and detailed description of semiology and time-course, of the associated MD, especially for the rarest conditions.

scholarly journals Genetic diagnosis of congenital hypopituitarism by a target gene panel: novel pathogenic variants in GLI2, OTX2 and GHRHR

2019 ◽  
Vol 8 (5) ◽  
pp. 590-595 ◽  
Author(s):  
Marilena Nakaguma ◽  
Fernanda A Correa ◽  
Lucas S Santana ◽  
Anna F F Benedetti ◽  
Ricardo V Perez ◽  
...  
Keyword(s):  
Target Gene ◽  
Gh Deficiency ◽  
Massively Parallel Sequencing ◽  
Genetic Diagnosis ◽  
Pituitary Hormones ◽  
Gene Panel ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Pathogenic Variants ◽  
Congenital Hypopituitarism

Aim Congenital hypopituitarism has an incidence of 1:3500–10,000 births and is defined by the impaired production of pituitary hormones. Early diagnosis has an impact on management and genetic counselling. The clinical and genetic heterogeneity of hypopituitarism poses difficulties to select the order of genes to analyse. The objective of our study is to screen hypopituitarism genes (candidate and previously related genes) simultaneously using a target gene panel in patients with congenital hypopituitarism. Methods Screening of 117 subjects with congenital hypopituitarism for pathogenic variants in 26 genes associated with congenital hypopituitarism by massively parallel sequencing using a customized target gene panel. Results We found three novel pathogenic variants in OTX2 c.295C>T:p.Gln99*, GLI2 c.1681G>T:p.Glu561* and GHRHR c.820_821insC:p.Asp274Alafs*113, and the previously reported variants in GHRHR c.57+1G>A and PROP1 [c.301_302delAG];[c.109+1G>A]. Conclusions Our results indicate that a custom-designed panel is an efficient method to screen simultaneously variants of biological and clinical relevance for congenital GH deficiency. A genetic diagnosis was possible in 5 out of 117 (4%) patients of our cohort. We identified three novel pathogenic variants in GHRHR, OTX2 and GLI2 expanding the spectrum of variants associated with congenital hypopituitarism.

scholarly journals MOLECULAR AUTOPSY: EVALUATION OF SUDDEN UNEXPECTED DEATH CASES IN TERMS OF “KCNQ1” GENETIC VARIATION

2019 ◽  
Vol 3 (6) ◽  
Author(s):  
Kenan Kaya ◽  
Mete Korkut Gülmen ◽  
Ayşe Serin ◽  
Necmi Çekin ◽  
Ahmet Hilal
Keyword(s):  
Genetic Variation ◽  
Genetic Analysis ◽  
Cause Of Death ◽  
Conduction System ◽  
Sudden Unexpected Death ◽  
Age Group ◽  
Unexpected Death ◽  
Molecular Autopsy ◽  
Sequence Variations ◽  
Death Cases

Background: Deaths occuring without a known disease and/or a known cause, deaths with non-lethal diseases are interpretated as sudden-unexpected-suspected deaths. Autopsy should always required to evaluate the cause of death. Some of the cases can be termed as negative autopsy since the cause of death can not be determined. This is one of the main interests of the future forensics. Molecular autopsies are one of the main practices of to reduce the negative autopsy ratios. Thus, post-mortem KCNQ1 genetic variation tests are done in sudden unexpected death cases. Material and methods: In this study 0 – 50 years old sudden-unexpected deaths autopsy cases were handled. Samples taken from cases were evaluated and “KCNQ1” genetic variation tests were done in our Department. Results: This study included 47 cases of 42 sudden unexpected death cases (0 – 50 age group) and 5 control group. 15 cases were between 40 – 50 age group and number of cases were increasing with age. 29 of cases (% 69) were male. Evaluation of body-mass index of cases were done and normal weighted cases were the most common with 21 cases (% 50). According to death locations; 17 cases had died (% 45,9) at home. Death location records of 5 cases couldn’t be found. Pathological examinations of all cases were done. We had identified fibrosis and fatty change appearances in SA node of 9 cases (% 21,4) and AV node of 13 cases (% 30,9) especially in conduction tissue examinations. As the result of KCNQ1 genetic analysis of cases, we identified sequence variations in 1638th nucleotid of exon 13 and 1986th nucleotid of exon 16. Conclusion: Cases with conduction system pathology and sequence variations of KCNQ1 genetic analysis shows that we are in need of these tests among routine practice to reduce negative autopsy ratios. Key words: KCNQ1, molecular autopsy, sudden unexpected death, conduction system, negative autopsy.

Correlates of Age at Natural Menopause in the Cohorts of Epic-Italy

2003 ◽  
Vol 89 (6) ◽  
pp. 608-614 ◽  
Author(s):  
Egidio Celentano ◽  
Rocco Galasso ◽  
Franco Berrino ◽  
Elisabetta Fusconi ◽  
Maria Concetta Giurdanella ◽  
...  
Keyword(s):  
Cigarette Smoking ◽  
Life Style ◽  
Ovarian Function ◽  
Age Of Onset ◽  
Large Population ◽  
Population Based ◽  
Added Value ◽  
Scientific Interest ◽  
Related Factors ◽  
Natural Menopause

A large number of studies have investigated the factors correlated to age at natural menopause in several populations. However, information on genetics and life-style factors influencing the age of onset of menopause in different populations is of current scientific interest. Specifically, for Italian women there are no large population-based data. The EPIC-Italy collaboration is a source of data of this kind; moreover, the geographical distribution of the cohorts (recruited in northern, central and southern Italy) is an added value as regards the scientific interest of these data. A number of biological and life-style-related factors have been analyzed to evaluate their association to the age at natural menopause in 14,454 menopausal women of the EPIC-Italy collaboration. As regards life-style and environmental factors, the main results are: a) women living in different areas of the country have different ages of onset of natural menopause; b) educational level is significantly associated to this age and may explain part of the between-center difference; c) cigarette smoking appears as a major correlate and probably determinant of the age at natural menopause across all the Italian cohorts; d) alcohol consumption does not have any relationship with the age at natural menopause; e) the use of oral contraceptives may influence age at natural menopause. As regards biological factors, short cycles and low parity have been found associated with earlier menopause. Overall, the results concerning menstrual cycles, parity, and cigarette smoking are consistent with the hypothesis that the number of oocytes in the ovary is pre-determined and any acceleration or impairment of the ovarian function leads to reduce the duration of the reproductive life.

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