Comprehensive Analysis of a Large-Scale Screen for MEFV Gene Mutations: Do They Truly Provide a “Heterozygote Advantage” in Turkey?

Ankylosing spondylitis (AS) is a common inflammatory rheumatic disease. Mediterranean fever (MEFV) gene, which has already been identified as being responsible for familial Mediterranean fever (FMF), is also a suspicious gene for AS because of the clinical association of these two diseases. The aim of this study was to explore the frequency and clinical significance ofMEFVgene mutations (M694V, M680I, V726A, E148Q and P369S) in a cohort of Turkish patients with AS. Genomic DNAs of 103 AS patients and 120 controls were isolated and genotyped using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods. There was a statistically significant difference of theMEFVgene mutation carrier rates between AS patients and healthy controls (p= 0.004, OR: 2.5, 95% CI: 1.32–4.76). This association was also observed in allele frequencies (p= 0.005, OR: 2.3, 95% CI: 1.27–4.2). A relatively higher frequency was observed for M694V mutation in AS patients than controls (10.7% versus 4.2% ,p= 0.060). There were no significant differences between MEFV mutation carriers and non-carriers with respect to the clinical and demographic characteristics. The results of this study suggest thatMEFVgene mutations are positively associated with a predisposition to develop AS.

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Frequency and Disease Severity of Familial Mediterranean Fever (FMF) Related MEFV Gene Mutations Among Ankylosing Spondylitis Patients

Turkiye Klinikleri Journal of Medical Sciences ◽

10.5336/medsci.2013-34490 ◽

2014 ◽

Vol 34 (2) ◽

pp. 223-230 ◽

Cited By ~ 2

Author(s):

Aslı TUFAN ◽

Sibel Zehra AYDIN ◽

Fatih EREN ◽

Pamir ATAGÜNDÜZ

Keyword(s):

Ankylosing Spondylitis ◽

Familial Mediterranean Fever ◽

Disease Severity ◽

Mefv Gene ◽

Gene Mutations ◽

Mediterranean Fever

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The Frequency of Familial Mediterranean Fever Gene Mutations and the Correlations between Phenotype and Genotype in Turkish Children

Asian Journal of Pediatric Research ◽

10.9734/ajpr/2020/v4i230145 ◽

2020 ◽

pp. 20-26

Author(s):

Hakan Erdogan ◽

Ayse Cavidan Sonkur ◽

Orhan Görükmez ◽

Ayse Erdogan ◽

Dilek Damla Saymazlar ◽

...

Keyword(s):

Familial Mediterranean Fever ◽

Mutation Screening ◽

Mefv Gene ◽

Gene Mutations ◽

Retrospective Case ◽

Turkish Children ◽

Pathogenic Variants ◽

Frequent Mutations ◽

Training And Research ◽

Mediterranean Fever

Aim: Familial Mediterranian Fever is an autosomal recessive disease characterized by recurrent inflammatory attacks of serosal membranes. The aim of the current study was to determine the frequency of the Mediterranean fever (MEFV) gene pathogenic variants in 158 children (78 male, 80 female) diagnosed with Familial Mediterranean Fever (FMF) and to compare the phenotype-genotype correlation. Methods: In our retrospective case-control study, 158 FMF patients (78 males, 80 females) who were diagnosed with MEFV gene mutation in Bursa Yuksek Ihtisas Training and Research Hospital, Department of Pediatrics between January 2018 and June 2019 were included in the study. Mutation screening of the MEFV gene was performed for 12 mutations and the 8 most common mutations were taken into the study. Results: Abdominal pain (77.8%), fever (74%) and arthralgia (46.2%) were the most prevalent clinical features in our patients. The most frequent mutations were M694V, E148Q, V726A, M680I and P369S. In cases with M694 mutation, it was noted that the incidence of arthritis was 2.5 times, appendectomy frequency 3.1 times higher, and early diagnosis probability 3.2 times higher. The frequency of chest pain was 2.9 times higher in the M680I mutation, and the frequency of arthralgia was 2.2 times higher in the P369S mutation. Conclusion: Patient’s mutations in FMF patients are important for clinical expectations, and some mutations such as P369S are not as innocent as expected. However, reevaluation of phenotypes of mutations that are rare with more patients will be significant.

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Analysis, identification and visualization of subgroups in genomics

Briefings in Bioinformatics ◽

10.1093/bib/bbaa217 ◽

2020 ◽

Author(s):

Gunnar Völkel ◽

Simon Laban ◽

Axel Fürstberger ◽

Silke D Kühlwein ◽

Nensi Ikonomi ◽

...

Keyword(s):

Large Scale ◽

Somatic Mutations ◽

Target Selection ◽

Gene Mutations ◽

Use Case ◽

The Past ◽

Wide Availability ◽

Approaches To Study ◽

User Friendly ◽

Personalized Intervention

Abstract Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact [email protected], phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502

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Analysis of CFTR Mutation Spectrum in Ethnic Russian Cystic Fibrosis Patients

Genes ◽

10.3390/genes11050554 ◽

2020 ◽

Vol 11 (5) ◽

pp. 554

Author(s):

Nika V. Petrova ◽

Nataliya Y. Kashirskaya ◽

Tatyana A. Vasilyeva ◽

Elena I. Kondratyeva ◽

Elena K. Zhekaite ◽

...

Keyword(s):

Ethnic Groups ◽

Mutant Allele ◽

Gene Mutations ◽

Copy Number Variations ◽

Comprehensive Analysis ◽

Mutation Spectrum ◽

Cftr Mutations ◽

The Russian Federation ◽

Numerous People ◽

Dependent Probe

The distribution and frequency of the CFTR gene mutations vary considerably between countries and ethnic groups. Russians are an East Slavic ethnic groups are native to Eastern Europe. Russians, the most numerous people of the Russian Federation (RF), make about 80% of the population. The aim is to reveal the molecular causes of CF in ethnic Russian patients as comprehensively as possible. The analysis of most common CFTR mutations utilized for CF diagnosis in multiethnic RF population accounts for about 83% of all CF-causing mutations in 1384 ethnic Russian patients. Variants c.1521_1523delCTT (F508del), c.54-5940_273+10250del21kb (CFTRdele2,3), c.2012delT (2143delT), c.2052_2053insA (2184insA), and c.3691delT (3821delT) are most typical for CF patients of Russian origin. DNA of 154 CF patients, Russian by origin, in whom at least one mutant allele was not previously identified (164 CF alleles), was analyzed by Sanger sequencing followed by the multiplex ligase-dependent probe amplification (MLPA) method. In addition to the 29 variants identified during the previous test for common mutations, 91 pathogenic CFTR variants were also revealed: 29 missense, 19 nonsense, 14 frame shift in/del, 17 splicing, 1 in frame ins, and 11 copy number variations (CNV). Each of the 61 variants was revealed once, and 17 twice. Each of the variants c.1209G>C (E403D), c.2128A>T (K710X), c.3883delA (4015delA), and c.3884_3885insT (4016insT) were detected for three, c.1766+1G>A (1898+1G>A) and c.2834C>T (S945L) for four, c.1766+1G>C (1898+1G>C) and c.(743+1_744-1)_(1584+1_1585-1)dup (CFTRdup6b-10) for five, c.2353C>T (R785X) and c.4004T>C (L1335P) for six, c.3929G>A (W1310X) for seven, c.580-1G>T (712-1G>T for eight, and c.1240_1244delCAAAA (1365del5) for 11 unrelated patients. A comprehensive analysis of CFTR mutant alleles with sequencing followed by MLPA, allowed not only the identification of 163 of 164 unknown alleles in our patient sample, but also expansion of the mutation spectrum with novel and additional frequent variants for ethnic Russians.

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The Genetic Control of Stoichiometry Underlying Autism

Annual Review of Neuroscience ◽

10.1146/annurev-neuro-100119-024851 ◽

2020 ◽

Vol 43 (1) ◽

pp. 509-533 ◽

Cited By ~ 1

Author(s):

Robert B. Darnell

Keyword(s):

Large Scale ◽

Biochemical Analysis ◽

Critical Role ◽

Gene Mutations ◽

Loss Of Function ◽

Case Control Studies ◽

Neurologic Disorder ◽

Regulatory Variants ◽

Whole Exome ◽

Number Variation

Autism is a common and complex neurologic disorder whose scientific underpinnings have begun to be established in the past decade. The essence of this breakthrough has been a focus on families, where genetic analyses are strongest, versus large-scale, case-control studies. Autism genetics has progressed in parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Gene mutations causing complete loss of function account for perhaps one-third of cases, largely detected through WES. This limitation has increased interest in understanding the regulatory variants of genes that contribute in more subtle ways to the disorder. Strategies combining biochemical analysis of gene regulation, WGS analysis of the noncoding genome, and machine learning have begun to succeed. The emerging picture is that careful control of the amounts of transcription, mRNA, and proteins made by key brain genes—stoichiometry—plays a critical role in defining the clinical features of autism.

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Large-Scale Whole-Genome Sequencing Reveals the Genetic Architecture of Primary Membranoproliferative GN and C3 Glomerulopathy

Journal of the American Society of Nephrology ◽

10.1681/asn.2019040433 ◽

2020 ◽

Vol 31 (2) ◽

pp. 365-373 ◽

Cited By ~ 7

Author(s):

Adam P. Levine ◽

Melanie M.Y. Chan ◽

Omid Sadeghi-Alavijeh ◽

Edwin K.S. Wong ◽

H. Terence Cook ◽

...

Keyword(s):

Large Scale ◽

Rare Variants ◽

Alternative Pathway ◽

Atypical Hemolytic Uremic Syndrome ◽

Gene Mutations ◽

Whole Genome Sequence ◽

European Ancestry ◽

Whole Genome ◽

C3 Glomerulopathy ◽

Complement Gene

BackgroundPrimary membranoproliferative GN, including complement 3 (C3) glomerulopathy, is a rare, untreatable kidney disease characterized by glomerular complement deposition. Complement gene mutations can cause familial C3 glomerulopathy, and studies have reported rare variants in complement genes in nonfamilial primary membranoproliferative GN.MethodsWe analyzed whole-genome sequence data from 165 primary membranoproliferative GN cases and 10,250 individuals without the condition (controls) as part of the National Institutes of Health Research BioResource–Rare Diseases Study. We examined copy number, rare, and common variants.ResultsOur analysis included 146 primary membranoproliferative GN cases and 6442 controls who were unrelated and of European ancestry. We observed no significant enrichment of rare variants in candidate genes (genes encoding components of the complement alternative pathway and other genes associated with the related disease atypical hemolytic uremic syndrome; 6.8% in cases versus 5.9% in controls) or exome-wide. However, a significant common variant locus was identified at 6p21.32 (rs35406322) (P=3.29×10−8; odds ratio [OR], 1.93; 95% confidence interval [95% CI], 1.53 to 2.44), overlapping the HLA locus. Imputation of HLA types mapped this signal to a haplotype incorporating DQA1*05:01, DQB1*02:01, and DRB1*03:01 (P=1.21×10−8; OR, 2.19; 95% CI, 1.66 to 2.89). This finding was replicated by analysis of HLA serotypes in 338 individuals with membranoproliferative GN and 15,614 individuals with nonimmune renal failure.ConclusionsWe found that HLA type, but not rare complement gene variation, is associated with primary membranoproliferative GN. These findings challenge the paradigm of complement gene mutations typically causing primary membranoproliferative GN and implicate an underlying autoimmune mechanism in most cases.

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A case with febrile attacks and vasculopathy associated with ADA2 and MEFV gene mutations

Pediatric Rheumatology ◽

10.1186/1546-0096-13-s1-p9 ◽

2015 ◽

Vol 13 (S1) ◽

Author(s):

H Ozdogan ◽

S Ugurlu ◽

A Hacioglu ◽

E Tahir Turanli ◽

A Kirectepe Aydin

Keyword(s):

Mefv Gene ◽

Gene Mutations

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