scholarly journals Two Variants in the NOTCH4 and HLA-C Genes Contribute to Familial Clustering of Psoriasis

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Minglong Cai ◽  
He Huang ◽  
Zhulin Hu ◽  
Tao Yuan ◽  
Weiran Li ◽  
...  
Keyword(s):  
Association Analysis ◽  
Genetic Predisposition ◽  
Genetic Architecture ◽  
Large Scale ◽  
Complex Phenotypes ◽  
Histocompatibility Complex ◽  
Immune Mediated ◽  
The Family ◽  
Familial Clustering ◽  
Family Aggregation

Psoriasis is a multifactorial immune-mediated skin disease with a strong genetic background. Previous studies reported that psoriasis with a family history (PFH) and sporadic psoriasis (SP) have a distinct manifestation and genetic predisposition. However, the genetic heterogeneity of PFH and SP in the major histocompatibility complex (MHC) region has not been fully elucidated. To explore genetic variants in the MHC region that drive family aggregation of psoriasis, we included a total of 8,127 psoriasis cases and 9,906 healthy controls from Han Chinese and divided psoriasis into two subtypes, PFH ( n = 1,538 ) and SP ( n = 5,262 ). Then, we calculated the heritability of PFH and SP and performed a large-scale stratified association analysis. We confirmed that variants in the MHC region collectively explained a higher heritability of PFH (16.8%) than SP (13.3%). Further stratified association analysis illustrated that HLA-C ∗ 06:02 and NOTCH4:G511S contribute to the family aggregation of psoriasis, and BTNL2:R281K specifically confers risk for SP. HLA-C ∗ 06:02 and NOTCH4:G511S could partially explain why patients with PFH have a stronger genetic predisposition, more complex phenotypes, and more frequent other autoimmune diseases. The identification of the SP-specific variant BTNL2:R281K revealed that the genetic architecture of SP is not just a subset of PFH.

scholarly journals Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases

2016 ◽  
Vol 99 (1) ◽  
pp. 22-39 ◽  
Author(s):  
Salman M. Tajuddin ◽  
Ursula M. Schick ◽  
John D. Eicher ◽  
Nathalie Chami ◽  
Ayush Giri ◽  
...  
Keyword(s):  
Blood Cell ◽  
Association Analysis ◽  
White Blood Cell ◽  
Large Scale ◽  
Immune Mediated

scholarly journals Exautomate: A user-friendly tool for region-based rare variant association analysis (RVAA)

2019 ◽  
Author(s):  
Brent D. Davis ◽  
Jacqueline S. Dron ◽  
John F. Robinson ◽  
Robert A. Hegele ◽  
Dan J. Lizotte
Keyword(s):  
Association Analysis ◽  
Rare Variant ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Rare Variants ◽  
Great Promise ◽  
Rare Variant Association ◽  
Complex Phenotypes ◽  
Rare Genetic Variation ◽  
User Friendly

AbstractRegion-based rare variant association analysis (RVAA) is a popular method to study rare genetic variation in large datasets, especially in the context of complex traits and diseases. Although this method shows great promise in increasing our understanding of the genetic architecture of complex phenotypes, performing a region-based RVAA can be challenging. The sequence kernel association test (SKAT) can be used to perform this analysis, but its inputs and modifiable parameters can be extremely overwhelming and may lead to results that are difficult to reproduce. We have developed a software package called “Exautomate” that contains the tools necessary to run a region-based RVAA using SKAT and is easy-to-use for any researcher, regardless of their previous bioinformatic experiences. In this report, we discuss the utilities of Exautomate and provide detailed examples of implementing our package. Importantly, we demonstrate a proof-of-principle analysis using a previously studied cohort of 313 familial hypercholesterolemia (FH) patients. Our results show an increased burden of rare variants in genes known to cause FH, thereby demonstrating a successful region-based RVAA using Exautomate. With our easy-to-use package, we hope researchers will be able to perform reproducible region-based RVAA to further our collective understanding behind the genetics of complex traits and diseases.

A Family With Autosomal-Dominant Progressive Sensorineural Hearing Loss

1996 ◽  
Vol 5 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Chris Halpin ◽  
Barbara Herrmann ◽  
Margaret Whearty
Keyword(s):  
Speech Production ◽  
Hearing Aids ◽  
Role Models ◽  
Speech Intelligibility ◽  
Large Scale ◽  
Speech Language Pathology ◽  
The Family ◽  
Patient Will ◽  
Language Pathology

The family described in this article provides an unusual opportunity to relate findings from genetic, histological, electrophysiological, psychophysical, and rehabilitative investigation. Although the total number evaluated is large (49), the known, living affected population is smaller (14), and these are spread from age 20 to age 59. As a result, the findings described above are those of a large-scale case study. Clearly, more data will be available through longitudinal study of the individuals documented in the course of this investigation but, given the slow nature of the progression in this disease, such studies will be undertaken after an interval of several years. The general picture presented to the audiologist who must rehabilitate these cases is that of a progressive cochlear degeneration that affects only thresholds at first, and then rapidly diminishes speech intelligibility. The expected result is that, after normal language development, the patient may accept hearing aids well, encouraged by the support of the family. Performance and satisfaction with the hearing aids is good, until the onset of the speech intelligibility loss, at which time the patient will encounter serious difficulties and may reject hearing aids as unhelpful. As the histological and electrophysiological results indicate, however, the eighth nerve remains viable, especially in the younger affected members, and success with cochlear implantation may be expected. Audiologic counseling efforts are aided by the presence of role models and support from the other affected members of the family. Speech-language pathology services were not considered important by the members of this family since their speech production developed normally and has remained very good. Self-correction of speech was supported by hearing aids and cochlear implants (Case 5’s speech production was documented in Perkell, Lane, Svirsky, & Webster, 1992). These patients received genetic counseling and, due to the high penetrance of the disease, exhibited serious concerns regarding future generations and the hope of a cure.

The Use of Medical Record Linkage for Population and Genetic Studies

1969 ◽  
Vol 08 (01) ◽  
pp. 07-11 ◽  
Author(s):  
H. B. Newcombe
Keyword(s):  
Record Linkage ◽  
Large Scale ◽  
Medical Record Linkage ◽  
Canadian Province ◽  
Genetic Studies ◽  
Parental Characteristics ◽  
Family Histories ◽  
The Family ◽  
Large Populations ◽  
Machine Readable

Methods are described for deriving personal and family histories of birth, marriage, procreation, ill health and death, for large populations, from existing civil registrations of vital events and the routine records of ill health. Computers have been used to group together and »link« the separately derived records pertaining to successive events in the lives of the same individuals and families, rapidly and on a large scale. Most of the records employed are already available as machine readable punchcards and magnetic tapes, for statistical and administrative purposes, and only minor modifications have been made to the manner in which these are produced.As applied to the population of the Canadian province of British Columbia (currently about 2 million people) these methods have already yielded substantial information on the risks of disease: a) in the population, b) in relation to various parental characteristics, and c) as correlated with previous occurrences in the family histories.

Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses

2021 ◽  
Author(s):  
Minxian Wang ◽  
Vivian S. Lee-Kim ◽  
Deepak S. Atri ◽  
Nadine H. Elowe ◽  
John Yu ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Coronary Artery ◽  
Association Analysis ◽  
Rare Variant ◽  
Odds Ratio ◽  
Large Scale ◽  
Missense Mutations ◽  
Rare Variant Association ◽  
Missense Variants ◽  
Artery Disease

Background: Corin is a protease expressed in cardiomyocytes that plays a key role in salt handling and intravascular volume homeostasis via activation of natriuretic peptides. It is unknown if Corin loss-of-function (LOF) is causally associated with risk of coronary artery disease (CAD). Methods: We analyzed all coding CORIN variants in an Italian case-control study of CAD. We functionally tested all 64 rare missense mutations in Western Blot and Mass Spectroscopy assays for proatrial natriuretic peptide cleavage. An expanded rare variant association analysis for Corin LOF mutations was conducted in whole exome sequencing data from 37 799 CAD cases and 212 184 controls. Results: We observed LOF variants in CORIN in 8 of 1803 (0.4%) CAD cases versus 0 of 1725 controls ( P , 0.007). Of 64 rare missense variants profiled, 21 (33%) demonstrated <30% of wild-type activity and were deemed damaging in the 2 functional assays for Corin activity. In a rare variant association study that aggregated rare LOF and functionally validated damaging missense variants from the Italian study, we observed no association with CAD—21 of 1803 CAD cases versus 12 of 1725 controls with adjusted odds ratio of 1.61 ([95% CI, 0.79–3.29]; P =0.17). In the expanded sequencing dataset, there was no relationship between rare LOF variants with CAD was also observed (odds ratio, 1.15 [95% CI, 0.89–1.49]; P =0.30). Consistent with the genetic analysis, we observed no relationship between circulating Corin concentrations with incident CAD events among 4744 participants of a prospective cohort study—sex-stratified hazard ratio per SD increment of 0.96 ([95% CI, 0.87–1.07], P =0.48). Conclusions: Functional testing of missense mutations improved the accuracy of rare variant association analysis. Despite compelling pathophysiology and a preliminary observation suggesting association, we observed no relationship between rare damaging variants in CORIN or circulating Corin concentrations with risk of CAD.

Coexistence of TDP-43 and C5b-9 staining of muscle in a patient with inclusion body myositis

2021 ◽  
Vol 14 (2) ◽  
pp. e238312
Author(s):  
Christina Law ◽  
Huili Li ◽  
Sankar Bandyopadhyay
Keyword(s):  
Inclusion Body ◽  
Transcriptional Repression ◽  
Inclusion Body Myositis ◽  
Inflammatory Myopathy ◽  
Membrane Attack Complex ◽  
Muscle Fibres ◽  
Rimmed Vacuoles ◽  
Histocompatibility Complex ◽  
Immune Mediated ◽  
Sporadic Inclusion Body Myositis

While sporadic inclusion body myositis (sIBM) is the most commonly acquired inflammatory myopathy above 50 years of age, its refractory response to conventional immunosuppressive treatments raises questions about its perplexing pathogenesis. Muscle biopsy typically reveals major histocompatibility complex I antigens and CD8+ T cell endomysial infiltrates invading non-necrotic muscle fibres early in the disease course with rimmed vacuoles, protein aggregates and amyloid inclusions later in the disease. Transactive response DNA-binding protein-43 (TDP-43), a protein implicated in transcriptional repression in neurodegenerative diseases, is also found in sIBM. C5b-9 membrane attack complex, an effector protein involved in the complement cascade of the immune response, is commonly found in dermatomyositis, but has rarely been reported in IBM. We describe a novel case of IBM with simultaneous C5b-9 and TDP-43 staining on quadriceps biopsy, raising the question of a possibility of concurrent immune-mediated inflammatory and myodegenerative pathogenesis.

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