scholarly journals Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature

Open Heart ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. e000915 ◽  
Author(s):  
Gabriella Captur ◽  
Eloisa Arbustini ◽  
Petros Syrris ◽  
Dina Radenkovic ◽  
Ben O'Brien ◽  
...  
Keyword(s):  
Heart Disease ◽  
Cardiac Involvement ◽  
Hierarchical Cluster ◽  
Missense Mutations ◽  
Nuclear Localisation Signal ◽  
Contingency Analysis ◽  
Pathogenic Variants ◽  
Cardiac Phenotype ◽  
Genetics And Genomics ◽  
Malignant Ventricular Arrhythmia

ObjectiveTwo LMNA genotype–phenotype cardiac correlations are reported: first, that cardiac involvement in multisystem laminopathies prevails with mutations upstream of the nuclear localisation signal (NLS); second, that worse outcomes occur with non-missense (compared with missense) mutations. We tested whether LMNA mutation DNA location and mutation subtype can predict phenotype severity in patients with lamin heart disease.MethodsWe used a semantic workflow platform and manual electronic literature search to identify published LMNA mutations with cardiac-predominant phenotype. Hierarchical cluster analysis (HCA) assembled lamin heart disease into classes based on phenotype severity. 176 reported causative mutations were classified and any relationships to mutation location/subtype assessed by contingency analysis.ResultsMore adverse phenotype was associated with mutation location upstream of the NLS (p=0.014, OR 2.38, 95% CI 1.19 to 4.80) but not with non-missense mutations (p=0.337, OR 1.36, 95% CI 0.72 to 2.57), although an association with non-missense mutations was identified in a subcluster with malignant ventricular arrhythmia (p=0.005, OR 2.64, 95% CI 0.76 to 9.21). HCA limited to the 65 mutations described on ClinVar as pathogenic/likely pathogenic showed similar findings (upstream of NLS, p=0.030, OR 4.78, 95% CI 1.28 to 17.83; non-missense, p=0.121, OR 2.64, 95% CI 0.76 to 9.21) as did analysis limited to pathogenic/likely pathogenic variants according to the American College of Medical Genetics and Genomics standards.ConclusionCardiac patients with an LMNA mutation located upstream versus downstream of the NLS have a more adverse cardiac phenotype, and some missense mutations can be as harmful as non-missense ones.

scholarly journals Diagnostic exome-based preconception carrier testing in consanguineous couples: results from the first 100 couples in clinical practice

2021 ◽  
Author(s):  
Suzanne C. E. H. Sallevelt ◽  
Alexander P. A. Stegmann ◽  
Bart de Koning ◽  
Crool Velter ◽  
Anja Steyls ◽  
...  
Keyword(s):  
Autosomal Recessive ◽  
Rare Variants ◽  
Clinical Care ◽  
Carrier Testing ◽  
Carrier Status ◽  
Routine Diagnostics ◽  
Affected Offspring ◽  
Pathogenic Variants ◽  
Increased Risk ◽  
Genetics And Genomics

Abstract Purpose Consanguineous couples are at increased risk of being heterozygous for the same autosomal recessive (AR) disorder(s), with a 25% risk of affected offspring as a consequence. Until recently, comprehensive preconception carrier testing (PCT) for AR disorders was unavailable in routine diagnostics. Here we developed and implemented such a test in routine clinical care. Methods We performed exome sequencing (ES) for 100 consanguineous couples. For each couple, rare variants that could give rise to biallelic variants in offspring were selected. These variants were subsequently filtered against a gene panel consisting of ~2,000 genes associated with known AR disorders (OMIM-based). Remaining variants were classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, after which only likely pathogenic and pathogenic (class IV/V) variants, present in both partners, were reported. Results In 28 of 100 tested consanguineous couples (28%), likely pathogenic and pathogenic variants not previously known in the couple or their family were reported conferring 25% risk of affected offspring. Conclusion ES-based PCT provides a powerful diagnostic tool to identify AR disease carrier status in consanguineous couples. Outcomes provided significant reproductive choices for a higher proportion of these couples than previous tests.

scholarly journals BIOM-10. PREVALENCE OF NF1 MISSENSE MUTATIONS AND CANDIDATE MODIFIER GENES IN SPINAL NEUROFIBROMATOSIS PATIENTS

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii3-ii3
Author(s):  
Paola Riva ◽  
Donata Bianchessi ◽  
Eleonora Mangano ◽  
Claudia Cesaretti ◽  
Paola Bettinaglio ◽  
...  
Keyword(s):  
Rare Variants ◽  
Sporadic Case ◽  
Modifier Genes ◽  
Lower Percentage ◽  
Missense Mutations ◽  
Cutaneous Manifestations ◽  
Classical Form ◽  
Ras Pathway ◽  
Pathogenic Variants ◽  
Patients At Risk

Abstract INTRODUCTION Spinal Neurofibromatosis (SNF), a distinct clinical entity of NF1, characterized by bilateral neurofibromas involving all spinal roots and a few, if any, cutaneous manifestations, entails greater morbidity than the classical form of disease. Nevertheless, there are no reliable patterns to sort out patients at risk for developing SNF. MATERIALS AND METHODS We investigated 19 NF1 families with at least one SNF member, 37 sporadic SNF patient and 100 NF1 patients with classical form of disease. We applied Targeted NGS using a panel consisting of 139 genes encoding RAS pathway effectors, neurofibromin interactors and genes mapping at 17q11.2 region. RESULTS In SNF patients we found a higher percentage of missense (21% versus 8%, p=0 0.016, OR 3.13 (95% CI 01.1 -8.2) and a lower percentage of nonsense NF1 mutations (12.5% versus 28%,, p= 0.026, OR 0.36 (95% CI 0.14–0.9) than in classical NF1 cases. Furthermore, we evaluated rare variants with damaging potential predictors in genes of the RAS pathway and in neurofibromin interactors. In more than one sporadic case possible pathogenic variants were found in LIMK2 (neurofibromin interactor), RASAL1, RASAL3, SOS1, A2ML1, MAP3K1 (RAS pathway effectors), while in more than one SNF family were detected RASAL1, RASAL3, MAP3K1 genes variations. CONCLUSIONS Our results confirm the correlation between NF1 genotype and SNF phenotype as previously reported (Ruggieri, 2015), suggesting that neurofibromin gain-of-functions mutations are associated to SNF. In some patients, the co-occurrence of potential pathogenic variants in NF1 related genes with severe phenotypes was detected supporting their role as modifier genes and promising therapeutic targets.

scholarly journals Novel compound heterozygous EYS variants may be associated with arRP in a large Chinese pedigree

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Chunli Wei ◽  
Ting Xiao ◽  
Jingliang Cheng ◽  
Jiewen Fu ◽  
Qi Zhou ◽  
...  
Keyword(s):  
Novel Mutation ◽  
Gene Mutations ◽  
Chinese Family ◽  
Compound Heterozygous ◽  
Missense Mutations ◽  
The Novel ◽  
Pathogenic Variants ◽  
Pathogenic Genes ◽  
Compound Heterozygous Variants ◽  
Normal Controls

Abstract As a genetically heterogeneous ocular dystrophy, gene mutations with autosomal recessive retinitis pigmentosa (arRP) in patients have not been well described. We aimed to detect the disease-causing genes and variants in a Chinese arRP family. In the present study, a large Chinese pedigree consisting of 31 members including a proband and another two patients was recruited; clinical examinations were conducted; next-generation sequencing using a gene panel was used for identifying pathogenic genes, and Sanger sequencing was performed for verification of mutations. Novel compound heterozygous variants c.G2504A (p.C835Y) and c.G6557A (p.G2186E) for the EYS gene were identified, which co-segregated with the clinical RP phenotypes. Sequencing of 100 ethnically matched normal controls didn’t found these mutations in EYS. Therefore, our study identified pathogenic variants in EYS that may cause arRP in this Chinese family. This is the first study to reveal the novel mutation in the EYS gene (c.G2504A, p.C835Y), extending its mutation spectrum. Thus, the EYS c.G2504A (p.C835Y) and c.G6557A (p.G2186E) variants may be the disease-causing missense mutations for RP in this large arRP family. These findings should be helpful for molecular diagnosis, genetic counseling and clinical management of arRP disease.

scholarly journals Tumour risks and genotype–phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes SDHB, SDHC and SDHD

2018 ◽  
Vol 55 (6) ◽  
pp. 384-394 ◽  
Author(s):  
Katrina A Andrews ◽  
David B Ascher ◽  
Douglas Eduardo Valente Pires ◽  
Daniel R Barnes ◽  
Lindsey Vialard ◽  
...  
Keyword(s):  
Succinate Dehydrogenase ◽  
Phenotypic Variability ◽  
Cohort Analysis ◽  
Cumulative Risk ◽  
Clinical Information ◽  
Missense Mutations ◽  
Pathogenic Variants ◽  
Mutation Carriers ◽  
Kaplan Meier ◽  
Age Related

BackgroundGermline pathogenic variants in SDHB/SDHC/SDHD are the most frequent causes of inherited phaeochromocytomas/paragangliomas. Insufficient information regarding penetrance and phenotypic variability hinders optimum management of mutation carriers. We estimate penetrance for symptomatic tumours and elucidate genotype–phenotype correlations in a large cohort of SDHB/SDHC/SDHD mutation carriers.MethodsA retrospective survey of 1832 individuals referred for genetic testing due to a personal or family history of phaeochromocytoma/paraganglioma. 876 patients (401 previously reported) had a germline mutation in SDHB/SDHC/SDHD (n=673/43/160). Tumour risks were correlated with in silico structural prediction analyses.ResultsTumour risks analysis provided novel penetrance estimates and genotype–phenotype correlations. In addition to tumour type susceptibility differences for individual genes, we confirmed that the SDHD:p.Pro81Leu mutation has a distinct phenotype and identified increased age-related tumour risks with highly destabilising SDHB missense mutations. By Kaplan-Meier analysis, the penetrance (cumulative risk of clinically apparent tumours) in SDHB and (paternally inherited) SDHD mutation-positive non-probands (n=371/67 with detailed clinical information) by age 60 years was 21.8% (95% CI 15.2% to 27.9%) and 43.2% (95% CI 25.4% to 56.7%), respectively. Risk of malignant disease at age 60 years in non-proband SDHB mutation carriers was 4.2%(95% CI 1.1% to 7.2%). With retrospective cohort analysis to adjust for ascertainment, cumulative tumour risks for SDHB mutation carriers at ages 60 years and 80 years were 23.9% (95% CI 20.9% to 27.4%) and 30.6% (95% CI 26.8% to 34.7%).ConclusionsOverall risks of clinically apparent tumours for SDHB mutation carriers are substantially lower than initially estimated and will improve counselling of affected families. Specific genotype–tumour risk associations provides a basis for novel investigative strategies into succinate dehydrogenase-related mechanisms of tumourigenesis and the development of personalised management for SDHB/SDHC/SDHD mutation carriers.

Genetic Characterization of Hereditary Cancer Syndromes Based on Targeted Next-Generation Sequencing

2021 ◽  
pp. 1-9
Author(s):  
Pelin Ercoskun ◽  
Cigdem Yuce Kahraman ◽  
Guller Ozkan ◽  
Abdulgani Tatar
Keyword(s):  
Hereditary Cancer ◽  
Hereditary Cancer Syndrome ◽  
Cancer Syndrome ◽  
Targeted Next Generation Sequencing ◽  
Pathogenic Variants ◽  
Novel Variants ◽  
Genetics And Genomics ◽  
Cancer Syndromes ◽  
Generation Sequencing

A hereditary cancer syndrome is a genetic predisposition to cancer caused by a germline mutation in cancer-related genes. Identifying the disease-causing variant is important for both the patient and relatives at risk in cancer families because this could be a guide in treatment and secondary cancer prevention. In this study, hereditary cancer panel harboring cancer-related genes was performed on MiSeq Illumina NGS system from peripheral blood samples. Sequencing files were fed into a cloud-based data analysis pipeline. Reportable variants were classified according to the American College of Medical Genetics and Genomics guidelines. Three hundred five individuals were included in the study. Different pathogenic/likely pathogenic variants were detected in 75 individuals. The majority of these variants were in the <i>MUTYH</i>, <i>BRCA2</i>, and <i>CHEK2</i> genes. Nine novel pathogenic/likely pathogenic variants were identified in <i>BRCA1</i>, <i>BRCA2</i>, <i>GALNT12</i>, <i>ATM</i>, <i>MLH1</i>, <i>MSH2</i>, <i>APC</i>, and <i>KIT</i> genes. We obtained interesting and novel variants which could be related to hereditary cancer, and this study confirmed that NGS is an indispensable method for the risk assessment in cancer families.

Cardiac involvement in genetic disease

2010 ◽  
pp. 2834-2841
Author(s):  
Thomas A. Traill
Keyword(s):  
Congenital Heart Disease ◽  
Heart Disease ◽  
Family History ◽  
Genetic Disease ◽  
Congenital Heart ◽  
Cardiac Involvement ◽  
Atrioventricular Canal ◽  
Marfan's Syndrome ◽  
Atrioventricular Canal Defect ◽  
History Of

Many clinicians find themselves faced, from time to time, with a patient who has a family history of a known disorder, such as Marfan’s syndrome, or who has noncardiac features that suggest a syndrome. Down’s syndrome—25 to 50% have congenital heart disease, most characteristically atrioventricular canal defect....

scholarly journals Germline Pathogenic Variants in 7636 Japanese Patients With Prostate Cancer and 12 366 Controls

2019 ◽  
Vol 112 (4) ◽  
pp. 369-376 ◽  
Author(s):  
Yukihide Momozawa ◽  
Yusuke Iwasaki ◽  
Makoto Hirata ◽  
Xiaoxi Liu ◽  
Yoichiro Kamatani ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Genetic Testing ◽  
Clinical Characteristics ◽  
Statistical Tests ◽  
Japanese Patients ◽  
Pathogenic Variants ◽  
Liver Cancers ◽  
Genetics And Genomics ◽  
Genetic Testing Guidelines ◽  
And Control

AbstractBackgroundGenetic testing has been conducted in patients with prostate cancer (PCa) using multigene panels, but no centralized guidelines for genetic testing exist. To overcome this limitation, we investigated the demographic and clinical characteristics of patients with pathogenic variants.MethodsWe sequenced eight genes associated with hereditary PCa in 7636 unselected Japanese patients with PCa and 12 366 male, cancer-free control individuals. We assigned clinical significance for all 1456 variants using the American College of Medical Genetics and Genomics guidelines and ClinVar. We compared the frequency of carriers bearing pathogenic variants between cases and control participants with calculated PCa risk in each gene and documented the demographic and clinical characteristics of patients bearing pathogenic variants. All statistical tests were two-sided.ResultsWe identified 136 pathogenic variants, and 2.9% of patients and 0.8% of control individuals had a pathogenic variant. Association with PCa risk was statistically significant for variants in BRCA2 (P &lt; .001, odds ratio [OR] = 5.65, 95% confidence interval [CI] = 3.55 to 9.32), HOXB13 (P &lt; .001, OR = 4.73, 95% CI = 2.84 to 8.19), and ATM (P &lt; .001, OR = 2.86, 95% CI = 1.63 to 5.15). We detected recurrent new pathogenic variants such as p.Gly132Glu of HOXB13. Patients with pathogenic variants were 2.0 years younger at diagnosis and more often had smoking and alcohol drinking histories as well as family histories of breast, pancreatic, lung, and liver cancers.ConclusionsThis largest sequencing study of PCa heredity provides additional evidence supporting the latest consensus among clinicians for developing genetic testing guidelines for PCa.

Are there any novel markers in acute rheumatic fever: neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio, and monocyte-to-lymphocyte ratio

2020 ◽  
Vol 30 (5) ◽  
pp. 717-721
Author(s):  
Dilek Giray ◽  
Olgu Hallioglu
Keyword(s):  
Heart Disease ◽  
Rheumatic Fever ◽  
Sedimentation Rate ◽  
Acute Rheumatic Fever ◽  
Cardiac Involvement ◽  
C Reactive Protein ◽  
Lymphocyte Ratio ◽  
Reactive Protein ◽  
Erythrocyte Sedimentation ◽  
Rheumatic Heart

AbstractObjective:The aim of this study was to investigate the relationship between C-reactive protein and erythrocyte sedimentation rate and neutrophil-to-lymphocyte, platelet-to-lymphocyte, and monocyte-to-lymphocyte ratios in acute rheumatic fever in children.Method:In this retrospective study, 182 patients with acute rheumatic fever and 173 controls were included. Complete blood count parameters, and neutrophil-to-lymphocyte, monocyte-to-lymphocyte, and platelet-to-lymphocyte ratios were recorded for all the patients underwent transthoracic echocardiography.Results:Neutrophil-to-lymphocyte, monocyte-to-lymphocyte, and platelet-to-lymphocyte ratios were significantly higher in patients with rheumatic heart disease than patients without cardiac involvement (p < 0.05). C-reactive protein and erythrocyte sedimentation rate levels were found to have a positive correlation with neutrophil-to-lymphocyte (r = 0.228, p = 0.001; r = 0.355, p = 0.001), platelet-to-lymphocyte (r = 0.227, p = 0.01; r = 0.149, p = 0.005), and monocyte-to-lymphocyte ratios (r = 0.117, p = 0.005; r = 0.107, p = 0.044). Cardiac involvement was present in 152 (83.5%) of the patients. Neutrophil-to-lymphocyte, monocyte-to-lymphocyte, and platelet-to-lymphocyte ratios were significantly higher in patients with rheumatic heart disease than patients without cardiac involvement (p < 0.05). Patients with carditis were grouped according to mitral, aortic, or both valve involvement but there was no significant difference between the groups with respect to neutrophil-to-lymphocyte, monocyte-to-lymphocyte, and platelet-to-lymphocyte ratios. In addition, neutrophil-to-lymphocyte and monocyte-to-lymphocyte ratios were significantly higher in patients with Sydenham’s chorea than without chorea (p < 0.05).Conclusion:Neutrophil-to-lymphocyte, platelet-to-lymphocyte, and monocyte-to-lymphocyte ratios may help make the diagnosis of acute rheumatic fever and its prognosis by serial measurements in follow-up but none of them tell us the severity of carditis. Also, this is the first study showing the positive correlation between Sydenham’s chorea and neutrophil-to-lymphocyte and monocyte-to-lymphocyte ratios. Further studies are needed to confirm this hypothesis, as this is the first study in the literature on this topic.

Red cell adenylate kinase deficiency in India: identification of two novel missense mutations (c.71A>G and c.413G>A)

2019 ◽  
Vol 72 (6) ◽  
pp. 393-398 ◽  
Author(s):  
Rashmi Dongerdiye ◽  
Pranoti Kamat ◽  
Punit Jain ◽  
Prashant Warang ◽  
Rati Devendra ◽  
...  
Keyword(s):  
Enzyme Activity ◽  
Adenylate Kinase ◽  
Structural Changes ◽  
Psychomotor Retardation ◽  
Red Cell ◽  
Missense Mutations ◽  
Rare Disorders ◽  
Pathogenic Variants ◽  
Cell Enzyme ◽  
Next Generation Sequencing Ngs

Adenylate kinase (AK) deficiency is a rare erythroenzymopathy associated with hereditary nonspherocytic haemolytic anaemia along with mental/psychomotor retardation in few cases. Diagnosis of AK deficiency depends on the decreased level of enzyme activity in red cell and identification of a mutation in the AK1 gene. Until, only eight mutations causing AK deficiency have been reported in the literature. We are reporting two novel missense mutation (c.71A > G and c.413G > A) detected in the AK1 gene by next-generation sequencing (NGS) in a 6-year-old male child from India. Red cell AK enzyme activity was found to be 30% normal. We have screened a total of 32 family members of the patient and showed reduced red cell enzyme activity and confirm mutations by Sanger’s sequencing. On the basis of Sanger sequencing, we suggest that the proband has inherited a mutation in AK1 gene exon 4 c.71A > G (p.Gln24Arg) from paternal family and exon 6 c.413G > A (p.Arg138His) from maternal family. Bioinformatics tools, such as SIFT, Polymorphism Phenotyping v.2, Mutation Taster, MutPred, also confirmed the deleterious effect of both the mutations. Molecular modelling suggests that the structural changes induced by p.Gln24Arg and p.Arg138His are pathogenic variants having a direct impact on the structural arrangement of the region close to the active site of the enzyme. In conclusion, NGS will be the best solution for diagnosis of very rare disorders leading to better management of the disease. This is the first report of the red cell AK deficiency from the Indian population.

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