The study of copy number variations in the regions of PRKAB2 and PPM1K among congenital heart defects patients

SUMMARY OBJECTIVE: This study was to assess the genetic association of copy number variations in two genes (PRKAB2 and PPM1K) located in two regions (tetralogy of Fallot and ventricular septal defect) in a Chinese Han population. METHODS: A total of 200 congenital heart disease patients (100 tetralogy of Fallot patients and 100 ventricular septal defect patients) and 100 congenital heart defect-free controls were recruited, and quantitative real-time PCR analysis was used to replicate the association of two copy number variations with congenital heart defects in a Chinese Han population. RESULTS: One deletion at PRKAB2 and one duplication at PPM1K were found in two of the tetralogy of Fallot patients, respectively; while all these regions were duplicated in both ventricular septal defect patients and in the 100 congenital heart defects-free controls. CONCLUSIONS: We replicated the copy number variations at the disease-candidate genes of PRKAB2 and PPM1K with tetralogy of Fallot in a Chinese Han population, and in patients with ventricular septal defect mutations in these two genes were not found. These results indicate the same molecular population genetics exist in these two genes with different ethnicity. This shows that these two genes are possibly specific pf tetralogy of Fallot candidates.

RESUMO OBJETIVO: Este estudo teve como objetivo avaliar a associação genética do número de cópias em dois genes (PRKAB2 e PPM1K) localizados em duas regiões (tetralogia de Fallot e comunicação interventricular) em uma população chinesa da etnia Han. METODOLOGIA: Um total de 200 pacientes com doença cardíaca congênita (100 pacientes com tetralogia de Fallot e 100 com comunicação interventricular) e 100 indivíduos livres de defeitos cardíacos congênitos foram recrutados, e uma análise quantitativa de PCR em tempo real foi utilizada para replicar a associação de duas variações de número de cópia de defeitos cardíacos congênitos, em uma população chinesa da etnia Han. RESULTADOS: Uma supressão em PRKAB2 e duplicação em PPM1K foram encontradas em dois pacientes com tetralogia de Fallot, respectivamente; todas essas regiões estavam duplicadas nos pacientes com comunicação interventricular e nos 100 indivíduos livres de defeitos cardíacos congênitos. CONCLUSÃO: Nós replicado a variações no número de cópias de genes candidatos de doença PRKAB2 e PPM1K com tetralogia de Fallot em uma população chinesa da etnia Han; em pacientes com comunicação interventricular, não foram encontradas mutações nesses dois genes. Estes resultados indicam que a mesma genética de população molecular existe nestes dois genes em diferentes etnias. Isso mostra que esses dois genes são possivelmente candidatos a genes específicos de tetralogia de Fallot.

The use of TCGA and GEO datasets to analyze clinical significance of glutathione reductase in gastric cancer / 中国医师杂志

Objective To explore the expressions of glutathione reductase in gastric cancer,to investigate the relationship between glutathione reductase (GSR) and clinical pathological characteristics of gastric cancers,to identify the role of GSR in evaluation of the prognosis of gastric cancer patients,and to investigate the role of GSR in the development of gastric cancer.Methods The gastric cancer datasets were searched and downloaded from The Cancer Genome Atlas (TCGA),and chip data were analyzed with clinical information.Gene set enrichment analysis (GSEA) was conducted to explore the gene sets enriched in samples with high GSR expression.Results The expression of GSR was down-regulated in high grade tumors (P ＜ 0.01).No significant difference was found between different age,Shortest tumor diameter,American Joint Committee on Cancer (AJCC) M stage,Barrett's esophagus,family history of gastric cancer,and Helicobacter pylori (H.pylori) infection.Higher expression of GSR indicated poor prognosis in gastric cancer.GSEA indicated that GSR regulates gene sets associated with oxidative phosphorylation,metabolism of nucleotides,mitochondrial protein import,and mitotic G1 S phases.Conclusions GSR can be used as an indicator to predict the prognosis of gastric cancer patients and a target for the treatment of gastric cancer.

Exclusive gene mapping on a Chinese familial IgA nephropathy family / 中华肾脏病杂志

Objective To initially map the gene responsible for autosomal dominant familial IgA nephropathy of a Chinese family by exclusive the five loci that had been reported with linkage analysis.Methods The genetic pattern of the familial IgA nephropathy was identified and the genomic DNA was extracted from the blood samples collected from the family members.Short tandem repeat (STR) inside the loci that had been reported was selected,such as 2q36,3p23-24,4q26-31,6q22-23,17q12-22,and the data with two-point linkage analysis were performed.Results Autosomal dominant inheritance pattern was demonstrated in phenotypes of the family and there was no linkage relationship in the above five loci of chromosomes because the maximum two-point LOD score was 0.39 at D17S1868.Conclusion Following exclusion of the loci which had been reported,there are other new pathopoiesis loci of FIgAN and it reveals that FIgAN has the genetic heterogeneity according to initial result at the same time.

Genetic mapping and mutation analysis in a family with paroxysmal kinesigenic dystonia / 中华神经科杂志

Objective To study the clinical characteristics and genetic cause of a Chinese family affected with paroxysmal kinesigenic dystonia(PKD).Methods The detailed clinical data and the blood samples of the affected patients with PKD and their relatives were collected.After genomic DNA was extracted from blood leukocytes,target linkage analysis Was performed using multiplex PCR by microsatellite marker's located in the reported critical region on chromosome 16.All exons and flanking regions of SCNN1G and ITGAL genes were amplified by PCR-sequence.Results In this three-generation 12 member family,5 individuals have been diagnosed as PKD.Target linkage analysis suggested the disease gene linked to chromosome 16.between D16S3396 and D16S3057 with two-point LOD score of 1.47 at recombination fraction(θ)=0.0.All affected individuals shared a common haplotype which co-segregated with the phenotype.Except for 8 reported SNPs,no pathologic sequence variants were found in candidate genes SCNN1G and ITGAL.Conclusions The studied family is genetically linked to the reported critical locus of PKD on chromosome 16.SCNN1G and ITGAL were ruled out as the causative genes for the studied pedigree.Further genetic analysis in this family may reveal new genetic cause responsible for PKD.

Advances in genes-related to moyamoya disease / 国际脑血管病杂志

Moyamoya disease is a rare cerebrovascular disease,its etiology remains unknown.The genetic factor may play an important role during the course of the disease,This article reviews the advances in genes-related to moyamoya disease in recent years,hoping to provide new ideas for future research.

Characterization analysis and polymorphism detection of the porcine Myd88 gene

The myeloid differentiation primary response protein 88 (Myd88) is an essential adaptor protein, which mediates in all Toll-like receptor (TLR) members signal transduction, except for TLR3. In this study, the 4464 bp genomic sequence of porcine Myd88 was first isolated, whereupon tissue distribution, chromosome mapping and single nucleotide polymorphism (SNP) were analyzed. Our results revealed that porcine Myd88 gene, which was located at chromosome 13 linked with marker S0288 (distance = 40 cR; LOD = 8.66), was widely expressed in all the examined tissues. There were 16 potential SNPs in the isolated genome fragment. SNP 797T/C in the first intron was studied, with no significant association being found between the genotype and immune traits in pigs (p > 0.05). The porcine Myd88 protein contained both the death domain (DD) and the Toll/IL-1 receptor domain (TIR). Leu residues, essential for its structure, were the most abundant encountered in the DD. The TIR contained two conserved motifs which may play important roles in the Myd88 function.

Linkage analysis in 2 pure familial paroxysmal kinesigenic dyskinesia families / 中华神经科杂志

Objective Linkage analysis were performed in 2 pure Chinese paroxysmal kinesigenic dyskinesia families to localize the locus of them. Method Microsatellites markers corresponding to pericentrometric region of chromosome 16 were used in parametric and nonparametrie linkage analysis for 27 members in the 2 pedigrees, haplotypes were constructed subsequently. Result The maximum LOD score and NPL score in the 2 families were all negative, P values were significantly larger than 0.05.No haplotype segregated with PKD phenotype was found. It showed no evidence of association with known PKD loci in both pedigrees, providing evidence for a novel PKD locus. Conclusion PKD is heterogeneous, a novel PKD locus may be in pure Chinese pedigrees.

Genetic linkage analysis of a Chinese family with freckle / 中华皮肤科杂志

Objective To report a three-generation Chinese family with freckle and to make a genetic linkage analysis in this family.MethodsGenetic linkage analysis was carried out in this family using microsatellite markers distributed over chromosome 4q and 1.Two-point logarithm of odds(LOD)scores were calculated using the Linkage program package(version 5.1),and haplotype was analyzed with Cyrillic version 2.01 software.Results Freckle was inherited in an autosomal dominant pattern with a penetrance of99.9% in this family;linkage to chromosome 4q was ruled out however,supportive evidence was obtained for linkage to microsatellite markers D1S2635 and D1S2844 in chromosome 1q with a maximum LOD score of 1.50.Haplotype analysis in this family localized the locus of freckle to a 12 Mb region flanked by D1S2624 and D1S2799.Conclusions Freckle is a genetically heterogeneous disorder.The causative gene may be located in a 21.2 cM region on chromosome 1q22-24.

Heritability and linkage study on heart rates in a Mongolian population

Elevated heart rate has been proposed as an independent risk factor for cardiovascular diseases, but their interrelationships are not well understood. In this study, we performed a genome-wide linkage scan in 1,026 individuals (mean age 30.6 years, 54.5% women) from 73 extended families of Mongolia and determined quantitative trait loci that influence heart rate. The DNA samples were genotyped using deCODE 1,039 microsatellite markers for 3 cM density genome-wide linkage scan. Correlation analysis was carried out to evaluate the correlation of the covariates and the heart rate. T-tests of the heart rate were also performed on sex, smoking and alcohol intake. Consequently, this model was used in a nonparametric genome-wide linkage analysis using variance component model to create a multipoint logarithm of odds (LOD) score and a corresponding P value. In the adjusted model, the heritability of heart rate was estimated as 0.32 (P<.0001) and a maximum multipoint LOD score of 2.03 was observed in 77 cM region at chromosome 18. The second largest LOD score of 1.52 was seen on chromosome 5 at 216 cM. Genes located on the specified locations in chromosomes 5 and 18 may be involved in the regulation of heart rate.

Gene Mapping of Disseminated Superficial Porokeratosis / 中华皮肤科杂志

Objective To target the disease gene of disseminated superficial form of porokeratosis (DSP) in a six-generation of a Chinese family including a total of 254 family members in Shandong province. Methods The clinical data and the peripheral blood samples were collected in the pedigree members. The genomic DNA was extracted from the blood samples. A genome-wide scan was performed using 382 pairs of primers labelled with fluorescent stain. The primers were designed for human autosomes. The sequencing results were analyzed by the software of Genescan and Genotype. Linkage analysis was processed by Linkage software package to define the region of disease gene. For fine targeting the disease gene, other 10 micro-satellite markers for the above region were set up for further fine sequencing. Results We obtained the maximum two-point LOD scores of 3.06 at micro-satellite marker D12S78 (recombination fraction ? = 0.00). After fine mapping, the DSP gene is located within a 38.5 cM region between markers D12S326 and D12S79. Conclusion The DSP gene is mapped to chromosome 12q21.2~24.2.

Gene Mapping and Mutation Identification in Patients with Primary Erythromelalgia / 中华皮肤科杂志

Objective To map the specific gene responsible for primary erythromelalgia and identify gene mutations in a Chinese family and one sporadic patient with primary erythromelalgia. Methods Geno-mic DNA was extracted from peripheral lymphocytes of the family members of the pedigree and the sporadic patient. Scanning the genes on chromosome 2q that had been identified was performed by using 6 microsatellite markers for the family members with primary erythromelalgia. Then linkage analysis and haplotype analysis were conducted. All exons of SCN9A gene were analyzed by PCR-DNA sequencing. The mutation identification was also confirmed by restriction fragment length polymorphism(RFLP). Results A maximum 2-point LOD score of 2.11 was found at a recombination fraction (? = 0.00) with markers D2S2370 and D2S2330. Recombination events were detected by markers D2S1353 and D2S2345 in this family by the haplotype analysis. There were two missense heterozygous point mutations in the 15th exon of SCN9A gene both in the family(T2573A) and the sporadic patient(T2543C), leading to the substitution of the amino acid leucine to histidine(L858H) and isoleucine to threonine(I848T), respectively. The above mutations were not found in 400 normal alleles. Conclusion It is proved that primary erythromelalgia is caused by mutations in SCN9A gene.

Identification of Hereditary Symmetrical Dyschromatosis Susceptibility Locus by Genome-wide Scan / 中华皮肤科杂志

Objective To identify a locus for hereditary symmetrical dyschromatosis(HSD).Methods A genome-wide scan was performed with402microsatellite markers in two large Chinese HSD families to map the chromosome location of the susceptible gene.The LINKAGE software(Version5.10)and CYRILLIC soft-ware(Version2.01)were used for linkage and haplotype analysis.Results A locus was identified at chro-mosome1q11-1q21with a cumulative maximum two-point LOD score of8.85at microsatellite marker D1S2343(?=0.00).Haplotype analysis indicated that the candidate gene was located within11.6cM region between markers D1S2696and D1S2635.This was the first locus identified for HSD.This study provided a map location for isolation of the candidate genes causing HSD.Conclusion Chromosome1q11-1q21contains the candidate gene susceptible for dyschromatosis symmetrica hereditaria.

Chromosomal localization of primary gout susceptibility gene in a Chinese pedigree / 中华内分泌代谢杂志

Objective To determine chromosomal localization of the primary gout susceptibility gene in a pedigree.Methods The clinical data and the peripheral blood samples were collected in the pedigree members and the genomic DNA was extracted from peripheral blood.A genome-wide screening was performed using 400 micro-satellite DNA markers in this family,and linkage analysis was used to determine the chromosomal location of the primary gout susceptibility gene.Results Linkage analysis showed that the maximum LOD score reached 1.50 at marker D4S1572 (at recombination fraction?=0.00).Conclusion Since D4S1572 is localized at 4q25,the primary gout susceptibility gene of this pedigree is localized at 4q25.

Genetic analysis in a Chinese family with autosomal dominant nonsyndromic deafness / 解放军医学杂志

Objective To analyze and determine the genetic characteristics of a large Chinese family with autosomal dominant nonsyndromic deafness(named pedigree Z029).Methods A hereditary deafness family was found from the profuse genetic resource established in the Otolaryngology Institute of PLA General Hospital.A sequence of bilateral sensorineural hearing impairment transmitted through five generations was found by investigating 47 individuals in the pedigree.The genetic forms of hearing loss in 18 members of the Z029 pedigree were diagnosed by otologic,audiologic,and physical examination,as well as by the study on their family history.Pedigree map was drawn by using Cyrillic2.1 software.Results The phynotype of Z029 family showed that most affected individuals had sensorineural hearing impairment with subsequent gradual progression covering all frequencies.The phynotype was transmitted from 1 to 5 generations.One of the parents of every patient was definitely a patient of the same disease.The affected ratio was same in both sexes,and the incidence of deafness declined through the first to fifth generation.Conclusion The phenotype characteristics of Z029 family were of autosomal dominant nonsyndromic hereditary deafness.In this pedigree,hearing impairment occurred in the majority of affected individuals after their twentieth year of age,and the penetrance of the impairment appeared to be age-correlated.No obvious vestibular dysfunction and other associated abnormalities were found.It may provide a foundation for the study of gene mapping and gene cloning of the pathogenic gene to analyze and determine the phenotype characteristics of this pedigree.This pedigree also provided an excellent model for the further study on the pathological and molecular mechanisms of hereditary hearing impairment related to age.