Comprehensive identification of pathogenic gene variants in patients with neuroendocrine disorders.

Author(s):  
Vishnopolska SA ◽  
Mercogliano MF ◽  
Camilletti MA ◽  
Mortensen AH ◽  
Braslavsky D ◽  
...  
2013 ◽  
Vol 50 (12) ◽  
pp. 802-811 ◽  
Author(s):  
Janneke H M Schuurs-Hoeijmakers ◽  
Anneke T Vulto-van Silfhout ◽  
Lisenka E L M Vissers ◽  
Ilse I G M van de Vondervoort ◽  
Bregje W M van Bon ◽  
...  

2021 ◽  
Author(s):  
Ravi Shah ◽  
Babken Asatryan ◽  
Ghaith Sharaf Dabbagh ◽  
Nay Aung ◽  
Mohammed Y Khanji ◽  
...  

Background: There is a paucity of data regarding the phenotype of dilated cardiomyopathy (DCM) gene variants in the general population. We aimed to determine the frequency and penetrance of DCM-associated putative pathogenic gene variants in a general, adult population, with a focus on the expression of clinical and subclinical phenotype, including structural, functional and arrhythmic disease features. Methods: UK Biobank participants who had undergone whole exome sequencing (WES), ECG and cardiovascular magnetic resonance (CMR) imaging were selected for study. Three different variant calling strategies (one primary and two secondary) were used to identify subjects with putative pathogenic variants in 44 DCM genes. The observed phenotype was graded to either 1) DCM (clinical or CMR diagnosis); 2) early DCM features, including arrhythmia and/or conduction disease, isolated ventricular dilation, and hypokinetic non-dilated cardiomyopathy; or 3) phenotype-negative. Results: Among 18,665 individuals included in the study, 1,463 (7.8%) subjects possessed ≥1 putative pathogenic variant in 44 DCM genes by the main variant calling strategy. A clinical diagnosis of DCM was present in 0.34% and early DCM features in 5.7% of individuals with putative pathogenic variants. ECG and CMR analysis revealed evidence of subclinical DCM in an additional 1.6% and early DCM features in 15.9% of individuals with putative pathogenic variants. Arrhythmias and/or conduction disease (15.2%) were the most common early DCM features, followed by hypokinetic non-dilated cardiomyopathy (4%). The combined clinical/subclinical penetrance was ≤30% with all three variant filtering strategies. Clinical DCM was slightly more prevalent among participants with putative pathogenic variants in definitive/strong evidence genes, as compared to those with variants in moderate/limited evidence genes. Conclusions: In the UK Biobank, approximately 1/6 of adults with putative pathogenic variants in DCM genes exhibited a subclinical phenotype based on ECG and/or CMR, most commonly manifesting with arrhythmias in the absence of substantial ventricular dilation/dysfunction.


2020 ◽  
Vol 2 (2) ◽  
pp. e99-e109 ◽  
Author(s):  
Alexandre Belot ◽  
Gillian I Rice ◽  
Sulliman Ommar Omarjee ◽  
Quentin Rouchon ◽  
Eve M D Smith ◽  
...  

2018 ◽  
Vol 28 (10-11) ◽  
pp. 2924-2936 ◽  
Author(s):  
Marianne A Jonker ◽  
Johannes A Rijken ◽  
Frederik J Hes ◽  
Hein Putter ◽  
Erik F Hensen

Accurate assessment of the age-dependent disease risk conferred by germline variants in disease susceptibility genes is often hampered by the way the data are collected. Cohort-based data sets frequently contain an overrepresentation of patients (i.e. carriers of the gene variant of interest affected with the associated disease), and an underrepresentation of disease-free carriers. In order to overcome this problem, penetrance estimates can be based on family-based study designs, through the evaluation of index patients and their family members. This approach facilitates the identification of asymptomatic germline variant carriers. By adjusting for the way these family data are ascertained, an estimate for the penetrance of the pathogenic gene variant can be obtained. However, the family structure is often incomplete or missing. This complicates the estimation of the penetrance, because full adjustment of the likelihood is not possible. We present a conditional likelihood for the estimation of the penetrance of pathogenic gene variants, based on a cohort of multiple families comprising index patients, disease-free and affected non-index carriers, but with missing information on pedigree structure. The proposed estimator corrects for the ascertainment in a robust way and is shown to be more accurate than the frequently used Kaplan–Meier estimator of the penetrance function.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 984-984 ◽  
Author(s):  
Lakshmi Srivaths ◽  
Jorge Di Paola ◽  
Charles Minard ◽  
Sarah H. O'Brien ◽  
Allison Wheeler ◽  
...  

Abstract Introduction: Low Von Willebrand factor (VWF) activity, considered a bleeding risk factor, is prevalent in some adolescents with heavy menstrual bleeding (HMB), wherein upfront hemostatic therapy may not be readily considered. There is a need to better define this patient subset phenotypically and genotypically, to stratify their risk to bleed, and to tailor their therapy in hopes of preventing complications. In adolescents with HMB and low VWF, we hypothesized that a significant proportion will have disease-causing sequence variations in the VWF gene and/or modifier genes that affect hemostasis, thrombosis or vascular biology, and these will correlate with their bleeding phenotype. Methods: The objectives of this multi-center, single arm, observational cohort study were to 1) study the genotype of adolescent females with HMB and low VWF (≥ 30 and ≤ 50 IU/dL), 2) correlate genotype with bleeding phenotype by Pictorial Blood Assessment Chart (PBAC) score and ISTH bleeding assessment tool (BAT) score. Post-menarchal females < 21 years, with HMB (defined as PBAC score >100) and low VWF were eligible for the study. Patients who did not meet these criteria or diagnosed with other bleeding disorders were ineligible. Members of the Foundation for Women and Girls with Blood Disorders are participating centers in the study. Clinical phenotype data including HMB characteristics, PBAC, BAT, response to desmopressin challenge, management details, clinical outcomes, and laboratory values were obtained. Blood samples were collected for analysis of a 142 gene array that includes VWF, genes involved in hemostasis, thrombosis and vascular biology. DNA sequencing of all exons and intron/exon boundaries was performed; variants were called presumably pathogenic if categorized as damaging by the pipeline with allele frequency <1% in databases of human genetic variation (1,000 genomes and ExAC). The prevalence of sequence variations in the VWF and other modifier genes were estimated with an exact, 95% Binomial confidence. PBAC and BAT scores were compared between groups (mutation vs. wild-type) using the Wilcoxon rank sum test. Results: 63 subjects were enrolled to date; 1 subject was later found to be ineligible due to detection of another bleeding disorder. The mean age was 16 years (range 11.5-20.2). The median BAT score was 5.0 (N=61; 2-20), median PBAC score was 481 (N=62; 114-8150). 11/48 (23%) had hemoglobin <12 gm/dl and 31/47 (66%) had ferritin <20 ng/ml at HMB diagnosis. 5/52 (10%) were hospitalized for HMB and 8/51 (16%) received PRBC transfusions. 57/62 (92%) underwent DDAVP challenge (intranasal, N=52; intravenous, N=5), with a mean rise of VWF activity at 1 hour of 3.0-fold (SD=1.3) and at 3-4 hours of 2.4-fold (SD=1.2), post-DDAVP. Genetic analysis in 51 subjects showed pathogenic gene variants: VWF - 9 in 7 subjects (14%; 95% CI: 6, 26), platelet (PLT) genes - 19 in 16 subjects (31%; 95% CI: 19, 46), coagulation factor (CF) genes - 10 in 7 subjects (14%; 95% CI: 6%, 26%). Two subjects had 2 VWF variants each, 3 had 2 PLT gene variants each and 1 had 4 CF gene variants; 1 had all 3 gene variants. Rest with VWF variants did not have co-existing PLT or CF gene variants. The median PBAC and BAT scores in subjects with/without VWF variants were 268/675 (P=0.06) and 4.5/5.5 (P=0.39), respectively. The median PBAC and BAT scores in subjects with/without PLT or CF genes and any variant were 561/525 (P=0.79) and 5.5/5.0 (P=0.77), and 380/777 (P=0.19) and 5/5 (P=0.94) respectively. Conclusion: Our study confirms the feasibility of a multi-center study in adolescent females with HMB and low VWF. All subjects had significant bleeding phenotype with elevated BAT and PBAC scores, with complications including anemia, iron deficiency, transfusion requirement, and hospitalization. Response to DDAVP challenge in subjects tested was good and sustained. Potential pathogenic gene variants, not only in VWF, but also in CF and PLT genes were found in 51% of the subjects, which may account for their bleeding phenotype. The separate or the combined presence of VWF, PLT and CF damaging gene variants does not appear to correlate with the subjects' bleeding severity in this interim analysis. A larger sample size and further analysis of gene variants may provide more information regarding the phenotype/genotype correlation in this patient population. Study supported by an investigator-initiated research grant from Baxalta US Inc., now part of Shire Disclosures Srivaths: Shire: Research Funding. Kulkarni:Bioverativ: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Bayer: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; NovoNordisk: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Shire: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Octa Pharma: Honoraria, Membership on an entity's Board of Directors or advisory committees; Kedrion: Honoraria, Membership on an entity's Board of Directors or advisory committees; Genetech: Honoraria, Membership on an entity's Board of Directors or advisory committees; BPL: Honoraria, Membership on an entity's Board of Directors or advisory committees. Mullins:Shire: Honoraria, Membership on an entity's Board of Directors or advisory committees. Ragni:Sangamo: Research Funding; Bioverativ: Consultancy, Research Funding; Shire: Research Funding; Alnylam: Membership on an entity's Board of Directors or advisory committees, Research Funding; SPARK: Consultancy, Research Funding; Biomarin: Membership on an entity's Board of Directors or advisory committees, Research Funding; MOGAM: Membership on an entity's Board of Directors or advisory committees; CSL Behring: Research Funding; Novo Nordisk: Research Funding. Kouides:Octapharma: Research Funding; UniQure: Other: DSMB.


2018 ◽  
Vol 90 (3) ◽  
pp. 268-271 ◽  
Author(s):  
Puja R Mehta ◽  
Ashley R Jones ◽  
Sarah Opie-Martin ◽  
Aleksey Shatunov ◽  
Alfredo Iacoangeli ◽  
...  

ObjectiveAmyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disease of motor neurons with a median survival of 2 years. Familial ALS has a younger age of onset than apparently sporadic ALS. We sought to determine whether this younger age of onset is a result of ascertainment bias or has a genetic basis.MethodsSamples from people with ALS were sequenced for 13 ALS genes. To determine the effect of genetic variation, age of onset was compared in people with sporadic ALS carrying a pathogenic gene variant and those who do not; to determine the effect of family history, we compared those with genetic sporadic ALS and familial ALS.ResultsThere were 941 people with a diagnosis of ALS, 100 with familial ALS. Of 841 with apparently sporadic ALS, 95 carried a pathogenic gene variant. The mean age of onset in familial ALS was 5.3 years younger than for apparently sporadic ALS (p=6.0×10−5, 95% CI 2.8 to 7.8 years). The mean age of onset of genetic sporadic ALS was 2.9 years younger than non-genetic sporadic ALS (p=0.011, 95% CI 0.7 to 5.2 years). There was no difference between the mean age of onset in genetic sporadic ALS and familial ALS (p=0.097).ConclusionsPeople with familial ALS have an age of onset about 5 years younger than those with apparently sporadic ALS, and we have shown that this is a result of Mendelian gene variants lowering the age of onset, rather than ascertainment bias.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Tatjana Welzel ◽  
Anna L. Wildermuth ◽  
Norbert Deschner ◽  
Susanne M. Benseler ◽  
Jasmin B. Kuemmerle-Deschner

Abstract Background Autoinflammatory diseases (AID) are rare chronic conditions with high disease burden, affecting children and adults. Clinically and genetically confirmed, AID can be effectively treated with targeted cytokine inhibition. In contrast, for patients with clinical AID symptoms without pathogenic gene variants, no treatment recommendations are available. Colchicine is approved and established as effective, safe and low-cost first-line therapy in Familial Mediterranean Fever. Up to now, efficacy data for colchicine in children with a clinical AID diagnosis without pathogenic gene variants are rare. This pilot study was performed to evaluate the effectiveness of colchicine in children with a clinical diagnosis of AID without pathogenic gene variants. Methods A pilot cohort study of consecutive children with active clinical AID without pathogenic gene variants treated with colchicine monotherapy was performed between 01/2009 and 12/2018. Demographics, clinical and laboratory characteristics were determined serially. Colchicine dosing and safety were documented. Physician estimate of disease activity was captured on visual analogue scales (VAS). Primary outcome: Complete response (PGA ≤2 plus CRP ≤0.5 mg/dL and/or SAA ≤10 mg/L) at last follow-up. Secondary outcomes: partial/no response, flare characteristics and requirement for rescue therapies. Analysis: Nonparametric comparison of disease activity measures. Results A total of 33 children were included; 39% were female. Median age at colchicine start was 3.8 years, median follow-up was 14.1 months. Clinical AID diagnoses included CAPS (24%), FMF (27%), PFAPA (43%) and unclassified AID (6%). At baseline, overall disease activity was moderate (PGA 4), inflammatory markers were elevated (CRP 12.1 mg/dL; SAA 289.2 mg/L), and 97% reported febrile flares. Outcome: 55% achieved complete response, 35% showed partial response and 58% had no febrile flares at last follow-up. Inflammatory markers (SAA: p < 0.0001, CRP: p < 0.005) and disease activity (p < 0.0001) decreased significantly. Overall, 93% of children experienced improvement of flare characteristics. Conclusion Colchicine was found to be effective and safe in children with a clinical AID diagnosis in the absence of pathogenic gene variants. Colchicine is a low-cost treatment option for non-organ threatening AID.


2013 ◽  
Vol 110 (23) ◽  
pp. 9403-9408 ◽  
Author(s):  
Mark Drost ◽  
Anne Lützen ◽  
Sandrine van Hees ◽  
Daniel Ferreira ◽  
Fabienne Calléja ◽  
...  

2018 ◽  
Vol 55 (7) ◽  
pp. 442-448 ◽  
Author(s):  
D Gareth Evans ◽  
Emma Woodward ◽  
Elaine F Harkness ◽  
Anthony Howell ◽  
Inga Plaskocinska ◽  
...  

PurposeThe identification of BRCA1, BRCA2 or mismatch repair (MMR) pathogenic gene variants in familial breast/ovarian/colorectal cancer families facilitates predictive genetic testing of at-risk relatives. However, controversy still exists regarding overall lifetime risks of cancer in individuals testing positive.MethodsWe assessed the penetrance of BRCA1, BRCA2, MLH1 and MSH2 mutations in men and women using Bayesian calculations based on ratios of positive to negative presymptomatic testing by 10-year age cohorts. Mutation position was also assessed for BRCA1/BRCA2.ResultsUsing results from 2264 presymptomatic tests in first-degree relatives (FDRs) of mutation carriers in BRCA1 and BRCA2 and 646 FDRs of patients with MMR mutations, we assessed overall associated cancer penetrance to age of 68 years as 73% (95% CI 61% to 82%) for BRCA1, 60% (95% CI 49% to 71%) for BRCA2, 95% (95% CI 76% to 99%) for MLH1% and 61% (95% CI 49% to 76%) for MSH2. There was no evidence for significant penetrance for males in BRCA1 or BRCA2 families and males had equivalent penetrance to females with Lynch syndrome. Mutation position and degree of family history influenced penetrance in BRCA2 but not BRCA1.ConclusionWe describe a new method for assessing penetrance in cancer-prone syndromes. Results are in keeping with published prospective series and present modern-day estimates for overall disease penetrance that bypasses retrospective series biases.


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