scholarly journals Identification of potential genetic causal variants for rheumatoid arthritis by whole-exome sequencing

Oncotarget ◽  
2017 ◽  
Vol 8 (67) ◽  
pp. 111119-111129 ◽  
Author(s):  
Ying Li ◽  
Elaine Lai-Han Leung ◽  
Hudan Pan ◽  
Xiaojun Yao ◽  
Qingchun Huang ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Causal Variants

scholarly journals Brief Report: Whole-Exome Sequencing for Identification of Potential Causal Variants for Diffuse Cutaneous Systemic Sclerosis

2016 ◽  
Vol 68 (9) ◽  
pp. 2257-2262 ◽  
Author(s):  
Angel C. Y. Mak ◽  
Paul L. F. Tang ◽  
Clare Cleveland ◽  
Melanie H. Smith ◽  
M. Kari Connolly ◽  
...  
Keyword(s):  
Systemic Sclerosis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Causal Variants ◽  
Diffuse Cutaneous Systemic Sclerosis

scholarly journals A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families

2018 ◽  
Author(s):  
Maëva Veyssiere ◽  
Javier Perea ◽  
Laetitia Michou ◽  
Anne Boland ◽  
Christophe Caloustian ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Rare Variants ◽  
P Value ◽  
Macrophage Differentiation ◽  
Extended Pedigrees ◽  
Whole Exome ◽  
New Variant ◽  
Multiplex Families

AbstractThe triggering and development of Rheumatoid Arthritis (RA) is conditioned by environmental and genetic factors. Despite the identification of more than one hundred genetic variants associated with the disease, not all the cases can be explained. Here, we performed Whole Exome Sequencing in 9 multiplex families (N=30) to identify rare variants susceptible to play a role in the disease pathogenesis. We pre-selected 73 genes which carried rare variants with a complete segregation with RA in the studied families. Follow-up linkage and association analyses with pVAAST highlighted significant RA association of 24 genes (p-value < 0.05 after 106 permutations) and pinpointed their most likely causal variant. We re-sequenced the 10 most significant likely causal variants (p-value ≤ 0.019 after 106 permutations) in the extended pedigrees and 9 additional multiplex families (N=110). Only one SNV in SUPT20H, c.73T>A (p.Lys25*), presented a complete segregation with RA in an extended pedigree with early-onset cases. In summary, we identified in this study a new variant associated with RA in SUPT20H gene. This gene belongs to several biological pathways like macro-autophagy and monocyte/macrophage differentiation, which contribute to RA pathogenesis. In addition, these results showed that analyzing rare variants using a family-based approach is a strategy that allows to identify RA risk loci, even with a small dataset.Author summaryRheumatoid arthritis (RA) is one of the most frequent auto-immune disease in the world. It causes joint swellings and pains which can lead to mobility impairment. To date, the scientific community has identified a hundred genes carrying variants predisposing to RA, in addition to the major gene HLA-DRB1. However, they do not explain all cases of RA. By examining nine families with multiple RA cases, we identified a new rare nonsense variant in SUPT20H gene, c.73T>A (p.Lys25*). This finding is supported by the literature as the SUPT20H gene regulates several biological functions, such as macro-autophagy or monocyte/macrophage differentiation, that contribute to RA pathogenesis.

scholarly journals A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families

PLoS ONE ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. e0213387 ◽  
Author(s):  
Maëva Veyssiere ◽  
Javier Perea ◽  
Laetitia Michou ◽  
Anne Boland ◽  
Christophe Caloustian ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Multiplex Families

scholarly journals Identification of potential causal variants for premature ovarian failure by whole exome sequencing

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Haengun Jin ◽  
JuWon Ahn ◽  
YoungJoon Park ◽  
JeongMin Sim ◽  
Han Sung Park ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Premature Ovarian Failure ◽  
Ovarian Failure ◽  
Reproductive Age ◽  
Bioinformatics Analyses ◽  
Korean Patients ◽  
Pathogenic Variants ◽  
Whole Exome ◽  
Causal Variants

Abstract Background Premature ovarian failure (POF) is a highly heterogeneous disorder that occurs in 1% of women of reproductive age. Very few causative genes and variants contributing to POF have been detected, and the disease remains incompletely understood. In this study, we used whole exome sequencing (WES) to identify potential causal variants leading to POF. Methods WES was conducted to identify variants in 34 Korean patients with POF, alongside 10 normal controls. Detected variants were filtered using a range of characterized bioinformatics analyses, and the machine learning tools, CADD and VEST, were used to predict pathogenic variants that could cause disease. VarSome was used for a comprehensive interpretation of the variants. Potential causal variants finally screened by these analyses were confirmed using Sanger sequencing. Results We identified nine potential causative variants in genes previously associated with POF in 8 of 34 (24%) Korean patients by WES variant analysis. These potentially pathogenic variants included mutations in the MCM8, MCM9, and HFM1 genes, which are involved in homologous recombination, DNA repair, and meiosis, and are established as causing POF. Using a combination of CADD and VEST, 72 coding variants were also identified in 72 genes, including ADAMTSL1 and FER1L6, which have plausible functional links to POF. Conclusions WES is a useful tool to detect genetic variants that cause POF. Accumulation and systematic management of data from a number of WES studies in specialized groups of patients with POF (family data, severe case populations) are needed to better comprehend the genetic landscape underlying POF.

Whole Exome Sequencing (WES) in Familien mit linksventrikulärer Ausfluβtraktobstruktion (LVOTO)

2014 ◽  
Vol 62 (S 02) ◽  
Author(s):  
M. Hitz ◽  
S. Al-Turki ◽  
A. Schalinski ◽  
U. Bauer ◽  
T. Pickardt ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome

FV 1031. Whole Exome Sequencing for Children with Dyskinetic Movement Disorder

2018 ◽  
Author(s):  
Yasemin Dincer ◽  
Michael Zech ◽  
Matias Wagner ◽  
Nikolai Jung ◽  
Volker Mall ◽  
...  
Keyword(s):  
Movement Disorder ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Whole Exome ◽  
Dyskinetic Movement
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