scholarly journals FSHD1 Diagnosis in a Russian Population Using a qPCR-Based Approach

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 982
Author(s):  
Nikolay Vladimirovich Zernov ◽  
Anna Alekseevna Guskova ◽  
Mikhail Yurevich Skoblov
Keyword(s):  
Southern Blotting ◽  
Tandem Repeats ◽  
Inverse Correlation ◽  
Russian Population ◽  
Diagnostic Methods ◽  
Partial Deletion ◽  
Allele Size ◽  
Allele Distribution ◽  
Molecular Combing ◽  
Disease Penetrance

Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant myodystrophy. Approximately 95% of cases of FSHD are caused by partial deletion of the D4Z4 macrosatellite tandem repeats on chromosome 4q35. The existing FSHD1 diagnostic methods are laborious and not widely used. Here, we present a comprehensive analysis of the currently used diagnostic methods (Southern blotting and molecular combing) against a new qPCR-based approach for FSHD1 diagnosis. We observed 93% concordance between the results obtained by the new qPCR-based approach, reference Southern blotting and molecular combing methods. Applying the qPCR-based approach in the studied population, we observed a prevalence (64.9%) of the permissive alleles in the range of 3–6 D4Z4 units for a group of patients, while in a group of carriers, the permissive alleles were mostly (84.6%) present in the range of 6–9 D4Z4 units. No prevalence of disease penetrance depending on gender was observed. The results confirmed the earlier established inverse correlation between permissive allele size and disease severity, disease penetrance. The results suggest the applicability of the qPCR-based approach for FSHD1 diagnosis and its robustness in a basic molecular genetics laboratory. To our knowledge, this is the first study of FSHD1 permissive allele distribution in a Russian population.

Molecular-genetic characteristics of Facioscapulohumeral muscular dystrophy in the Russian population

2020 ◽  
pp. 57-58
Author(s):  
Н.В. Зернов ◽  
А.А. Гуськова ◽  
М.Ю. Скоблов
Keyword(s):  
Genetic Factors ◽  
Autosomal Dominant ◽  
Molecular Genetic ◽  
Inverse Correlation ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Russian Population ◽  
Partial Deletion ◽  
Allele Size ◽  
Genetic Characteristics ◽  
Disease Penetrance

Миодистрофия Ландузи-Дежерина (МЛД) в 95% случаев вызвана частичной делецией массива макросателлитных повторов D4Z4 на одном из аллелей 4-й хромосомы в сцеплении с пермиссивным гаплотипом. В данной работе мы провели молекулярно-генетическую диагностику МЛД в группе российских пациентов с клиническими проявлениями МЛД и их фенотипически здоровых родственников. Полученные данные распределения патогенных аллелей по длине соответствуют ранее описанным зарубежным популяционным исследованиям. Кроме того, наличие здоровых носителей патогенного аллеля подтверждает, что для проявления заболевания требуется сочетания генетических, эпигенетических и средовых факторов. Facioscapulohumeral dystrophy (FSHD) is an autosomal dominant myodystrophy. In approximately 95% of cases FSHD is caused by partial deletion of the D4Z4 macrosatellite tandem repeat on chromosome 4q35 (FSHD1). Here we present results FSHD1 diagnostic of patients and unaffected relatives from Russian population. We demonstrate that FSHD1 permissive alleles are bigger in size for unaffected carriers, which indicate previously reported phenomenon of inverse correlation between permissive allele size and disease penetrance and expressivity. In addition, presence of patients and unaffected carriers from one family with the same permissive allele size demonstrate importance of non-genetic factors for disease development.

scholarly journals Molecular genetic survey of five Japanese families with high-molecular- weight kininogen deficiency

Blood ◽  
1990 ◽  
Vol 75 (6) ◽  
pp. 1296-1304 ◽  
Author(s):  
H Hayashi ◽  
F Ishimaru ◽  
T Fujita ◽  
N Tsurumi ◽  
T Tsuda ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Rna Splicing ◽  
Southern Blotting ◽  
Molecular Genetic ◽  
Low Molecular Weight ◽  
Partial Deletion ◽  
Molecular Abnormality ◽  
Genetic Survey ◽  
Gene Status

Abstract Analyses of the kininogen (KGN) molecule and KGN gene status in five Japanese families with high-molecular-weight (HMW) KGN deficiency were performed by the immunoblotting method with monoclonal antibodies to HMW-KGN, and by the Southern blotting method with the cDNA for human low-molecular-weight prekininogen. No molecular abnormality of KGN was detected in the DNA from four patients with total KGN deficiency or one patient with isolated HMW-KGN deficiency. In the former, the KGN gene appeared to be grossly normal at the level of the whole genome on Southern blotting. In isolated HMW-KGN deficiency, a partial deletion in intron 7 was found by restriction analyses of EcoRI, BamHI, HindIII, Sca I, and Bgl II fragments. This partial deletion is assumed to be related to an abnormality of the alternative RNA splicing events for HMW-prekininogen mRNA.

scholarly journals Mungbean yellow mosaic virus-Vi Agroinfection by Codelivery of DNA A and DNA B From One Agrobacterium Strain

Plant Disease ◽  
2003 ◽  
Vol 87 (3) ◽  
pp. 247-251 ◽  
Author(s):  
S. S. Jacob ◽  
R. Vanitharani ◽  
A. S. Karthikeyan ◽  
Y. Chinchore ◽  
P. Thillaichidambaram ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Tandem Repeat ◽  
Southern Blotting ◽  
Tandem Repeats ◽  
Binary Vector ◽  
Yellow Mosaic Virus ◽  
Viral Dna ◽  
Agrobacterium Strain ◽  
Single Strain ◽  
Mungbean Yellow Mosaic Virus

Agroinfection of bipartite geminiviruses is routinely done by mixing two Agrobacterium strains that independently harbor partial tandem repeats of DNA A and DNA B. We report here an improved agroinfection method for bipartite geminiviruses that utilizes one strain of Agrobacterium that harbors DNA A and DNA B partial tandem repeats on two compatible replicons. A cointegrate vector, pGV2260∷pGV1.3A, with the partial tandem repeat of Mungbean yellow mosaic virus-Vi (MYMV-Vi) DNA A and a binary vector, pGA1.9B, with the partial tandem repeat of MYMV-Vi DNA B gave an agroinfection efficiency of 24% when harbored in two Agrobacterium strains and an efficiency of 61% when harbored in one Agrobacterium strain. A combination of binary vectors, pGA1.9A with MYMV-Vi DNA A partial tandem repeat and pGA1.9B with DNA B partial tandem repeat, gave an agroinfection efficiency of 74% when harbored in two strains. But pGA1.9A and pPZP1.9B (a partial tandem repeat of DNA B), when present in the same Agrobacterium strain, gave 100% agroinfection. Accumulation of viral DNA was shown by Southern blotting. The single-strain method using two compatible replicons consistently gave 100% agroinfection efficiency.

scholarly journals VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 983-993 ◽  
Author(s):  
M D Shriver ◽  
L Jin ◽  
R Chakraborty ◽  
E Boerwinkle
Keyword(s):  
Tandem Repeats ◽  
Repeat Unit ◽  
Allele Size ◽  
Frequency Distributions ◽  
Mutation Model ◽  
Stepwise Mutation ◽  
One Step ◽  
Simulation Results ◽  
Summary Measures ◽  
The One

Abstract Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

scholarly journals Mosaic chromosome 18 anomaly delineated in a child with dysmorphism using a three-pronged cytogenetic techniques approach: a case report

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Harsh Sheth ◽  
Sunil Trivedi ◽  
Thomas Liehr ◽  
Ketan Patel ◽  
Deepika Jain ◽  
...  
Keyword(s):  
Cell Line ◽  
Chromosomal Abnormalities ◽  
Ring Chromosome ◽  
Chromosome Analysis ◽  
Diagnostic Methods ◽  
Molecular Karyotyping ◽  
Facial Dysmorphism ◽  
Chromosome 18 ◽  
Partial Deletion ◽  
Case Presentation

Abstract Background A plethora of cases are reported in the literature with iso- and ring-chromosome 18. However, co-occurrence of these two abnormalities in an individual along with a third cell line and absence of numerical anomaly is extremely rare. Case presentation A 7-year-old female was referred for diagnosis due to gross facial dysmorphism and severe developmental delay. She presented with dysmorphic features, hypo/hyper pigmentation of the skin, intellectual disability and craniosynostosis. G-banding chromosome analysis suggested mos 46,XX,psu idic(18)(p11.2)[25]/46,XX,r(?18)[30]. Additional analysis by molecular karyotyping suggested pure partial deletion of 15 Mb on 18p (18p11.32p11.21). Lastly, multiple rearrangements and detection of a third cell line (ring chr18 and interstitial deletion) of chr18 was observed by multi-color banding. Conclusion The current study presents a novel case of chromosomal abnormalities pertaining to chromosome 18 across 3 cell lines, which were delineated with a combinatorial approach of diagnostic methods.

scholarly journals Molecular genetic survey of five Japanese families with high-molecular- weight kininogen deficiency

Blood ◽  
1990 ◽  
Vol 75 (6) ◽  
pp. 1296-1304
Author(s):  
H Hayashi ◽  
F Ishimaru ◽  
T Fujita ◽  
N Tsurumi ◽  
T Tsuda ◽  
...  
Keyword(s):  
Molecular Weight ◽  
High Molecular Weight ◽  
Rna Splicing ◽  
Southern Blotting ◽  
Molecular Genetic ◽  
Low Molecular Weight ◽  
Partial Deletion ◽  
Molecular Abnormality ◽  
Genetic Survey ◽  
Gene Status

Analyses of the kininogen (KGN) molecule and KGN gene status in five Japanese families with high-molecular-weight (HMW) KGN deficiency were performed by the immunoblotting method with monoclonal antibodies to HMW-KGN, and by the Southern blotting method with the cDNA for human low-molecular-weight prekininogen. No molecular abnormality of KGN was detected in the DNA from four patients with total KGN deficiency or one patient with isolated HMW-KGN deficiency. In the former, the KGN gene appeared to be grossly normal at the level of the whole genome on Southern blotting. In isolated HMW-KGN deficiency, a partial deletion in intron 7 was found by restriction analyses of EcoRI, BamHI, HindIII, Sca I, and Bgl II fragments. This partial deletion is assumed to be related to an abnormality of the alternative RNA splicing events for HMW-prekininogen mRNA.

scholarly journals Plasma Homocysteine and Polymorphisms of Genes Involved in Folate Metabolism Correlate with DNMT1 Gene Methylation Levels

Metabolites ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 298
Author(s):  
Fabio Coppedè ◽  
Andrea Stoccoro ◽  
Pierpaola Tannorella ◽  
Lucia Migliore
Keyword(s):  
Dna Methylation ◽  
Vitamin B12 ◽  
Promoter Methylation ◽  
Dna Methyltransferase ◽  
Tandem Repeats ◽  
Inverse Correlation ◽  
Plasma Homocysteine ◽  
Gene Methylation ◽  
Folate And Vitamin B12 ◽  
Methylation Patterns

DNA methyltransferase 1 (DNMT1) is responsible for the maintenance of DNA methylation patterns during cell division. Several human diseases are characterized by impaired DNMT1 gene methylation, but less is known about the factors that regulate DNMT1 promoter methylation levels. Dietary folates and related B-vitamins are essential micronutrients for DNA methylation processes, and we performed the present study to investigate the contribution of circulating folate, vitamin B12, homocysteine, and common polymorphisms in folate pathway genes to the DNMT1 gene methylation levels. We investigated DNMT1 gene methylation levels in peripheral blood DNA samples from 215 healthy individuals. All the DNA samples were genotyped for MTHFR 677C > T (rs1801133) and 1298A > C (rs1801131), MTRR 66A > G (rs1801394), MTR 2756A > G (rs1805087), SLC19A1 (RFC1) 80G > A (rs1051266), TYMS 28-bp tandem repeats (rs34743033) and 1494 6-bp insertion/deletion (indel) (rs34489327), DNMT3A -448A > G (rs1550117), and DNMT3B -149C > T (rs2424913) polymorphisms. Circulating homocysteine, folate, and vitamin B12 levels were available from 158 of the recruited individuals. We observed an inverse correlation between plasma homocysteine and DNMT1 methylation levels. Furthermore, both MTR rs1805087 and TYMS rs34743033 polymorphisms showed a statistically significant effect on DNMT1 methylation levels. The present study revealed several correlations between the folate metabolic pathway and DNMT1 promoter methylation that could be of relevance for those disorders characterized by altered DNA methylation.

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