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1.
Article in Chinese | WPRIM | ID: wpr-928701

ABSTRACT

OBJECTIVE@#To explore the genotype mutation characteristics of patients with glucose-6-phosphate dehydrogenase(G6PD) deficiency in Wuhan.@*METHODS@#A total of 1 321 neonates with positive screening and outpatients were received G6PD mutation detection, 12 kinds of common G6PD mutation in Chinese people was detected by using multicolor melting curve analysis (MMCA) method, for those with negative results, the enzyme activity and clinical information were analyzed, sequencing was recommended after informed consent when it is necessary.@*RESULTS@#Among 1321 patients, a total of 768 mutations were detected out, with a detection rate of 58.1%. A total of 18 types of G6PD genotypes were identified, including c.1388G>A, c.1376G>T, c.95G>A, c.1024C>T, c.871G>A, c.392G>T, c.487G>A, c.1360C>T, c.1004C>A, c.517T>C, c.592C>T, c.94C>G, c.152C>T, c.320A>G, c.1028A>G, c.1316G>A, c.1327G>C and c.1376G>C, including 683 male hemizygotes, 3 female homozygotes, 80 female heterozygotes and 2 female compound heterozygous.@*CONCLUSION@#A total of 18 types of G6PD mutations are identified in the reaserch, and c.94C>G, c.1028A>G and c.1327G>C are first reported in Chinese population. The most common G6PD mutation types in Wuhan are c.1388G>A, c.1376G>T, c.95G>A.


Subject(s)
Asians/genetics , Female , Genotype , Glucosephosphate Dehydrogenase/genetics , Glucosephosphate Dehydrogenase Deficiency/genetics , Heterozygote , Humans , Infant, Newborn , Male , Mutation
2.
Article in Chinese | WPRIM | ID: wpr-928454

ABSTRACT

OBJECTIVE@#To explore the genotype-phenotype correlation of a case with GM1-gangliosidosis caused by compound heterogenic variants in GLB1.@*METHODS@#Genomic DNA was extracted from peripheral blood samples from the patient and her parents. Trio-based whole-exome sequencing (WES) was performed for the family and suspected mutation was verified by Sanger sequencing.@*RESULTS@#The proband, a 2-year-3-month old Chinese girl, presented with psychomotor deterioration, absent speech, intellectual disabilities and behavior problem. Trio-based WES has identified compound heterozygosity for 2 variants in the GLB1 gene: NM_000404.2:c.1343A>T, p.Asp448Val and c.1064A>C, p.Gln355Pro (GRCh37/hg19),which was inherited from the mother and father, respectively. Homozygous or compound heterozygous pathogenic variants in GLB1, encoding β-galactosidase, are responsible for GM1-gangliosidosis,an autosomal recessive lysosomal storage disorder characterized by variable degrees of neurodegeneration and skeletal abnormalities. The p.Asp448Val variant has been classified as pathogenic for GM1 gangliosidosis in medical literatures for the reason that functional studies demonstrated that expression of the p.Asp448Val variant in COS-1 cells resulted in no detectable β-galactosidase activity compared to wild type GLB1. The p.Gln355Pro variant has not been reported in literatures or database. The variant is highly conserved residue (PM1), and was not found in either the Genome Aggregation Database or the 1000 Genomes Project (PM2) and was predicted to have a deleterious effect on the gene product by multiple in silico prediction tools (PP3). Next, the β-galactosidase activity of the patient's peripheral blood leukocytes was determined by fluorescent method. The result was 0.0 nmol/mg. It showed that the p.Gln355Pro variant also resulted in loss of β-galactosidase activity, thus the variant was classified into clinical pathogenic variant.@*CONCLUSION@#Our study expands the mutational spectrum of the GLB1 gene and provides genetic counseling for the family.


Subject(s)
Asians/genetics , China , Female , G(M1) Ganglioside , Gangliosidosis, GM1/genetics , Humans , Mutation , beta-Galactosidase/genetics
3.
Article in Chinese | WPRIM | ID: wpr-928451

ABSTRACT

OBJECTIVE@#To detect the genetic variant of a child with cleidocranial dysplasia (CCD) and to find out the causation of the illness.@*METHODS@#Gene variant was identified by the second generation targeted sequencing and Sanger sequencing.@*RESULTS@#The gene sequencing revealed that the RUNX2 gene had c.196C>T(p.Glu66*) nonsense variant, which was predicted to be a pathogenic variant according to the ACMG guidelines(PVS1+PS2).@*CONCLUSION@#The variant of c.196C > T in the RUNX2 gene may be the cause of the child with CCD, and the novel variant enriches the RUNX2 gene variant spectrum.


Subject(s)
Asians/genetics , Child , China , Cleidocranial Dysplasia/genetics , Core Binding Factor Alpha 1 Subunit/genetics , Humans , Mutation
4.
Article in Chinese | WPRIM | ID: wpr-928409

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a child featuring complex cortical dysplasia and other brain malformations (CDCBM3).@*METHODS@#Genomic DNA was extracted from peripheral blood samples from the patient and his parents. Whole exome sequencing (WES) was carried out for the family trio. Suspected variant was verified by Sanger sequencing.@*RESULTS@#The proband, a 1-year-and-2-month old Chinese boy, had presented with motor developmental delay, lissencephaly, severe cognitive impairments, absent speech and congenital laryngomalacia. WES revealed that he has harbored a heterozygous missense variant of the KIF2A gene, namely NM_001098511.2: c.952G>A, p.Gly318Arg (GRCh37/hg19). The highly conserved residue is located around the ATP nucleotide-binding pocket in the kinesin motor domain (PM1). The variant was not found in the Genome Aggregation Database and the 1000 Genomes Project (PM2), and was predicted to be deleterious on the gene product by multiple in silico prediction tools (PP3). This variant was unreported previously and was de novo in origin (PS2). Based on the ACMG guidelines, it was categorized as likely pathogenic (PS2+PM1+PM2+PP3). Furthermore, the congenital laryngomalacia found in our patient was absent in previously reported CDCBM3 cases.@*CONCLUSION@#The novel variant of the KIF2A gene probably underlay the disorders in the proband. Above finding has expanded the phenotypic and mutational spectrum of CDCBM3.


Subject(s)
Asians/genetics , Brain , China , Humans , Infant , Kinesins/genetics , Male , Malformations of Cortical Development/genetics , Whole Exome Sequencing
5.
Article in Chinese | WPRIM | ID: wpr-928400

ABSTRACT

OBJECTIVE@#To determine the carrier rate for 21 inherited metabolic diseases among a Chinese population of childbearing age.@*METHODS@#A total of 897 unrelated healthy individuals (including 143 couples) were recruited, and DNA was extracted from their peripheral blood samples. Whole exome sequencing (WES) was carried out to screen potential variants among 54 genes associated with 21 inherited metabolic diseases. Pathogenic and likely pathogenic variants and unreported loss-of-function variants were analyzed.@*RESULTS@#One hundred fourty types of pathogenic/likely pathogenic variants (with an overall number of 183) and unreported loss-of-function variants were detected, which yield a frequency of 0.20 per capita. A husband and wife were both found to carry pathogenic variants of the SLC25A13 gene and have given birth to a healthy baby with the aid of preimplantation genetic diagnosis. The detected variants have involved 40 genes, with the most common ones including ATP7B, SLC25A13, PAH, CBS and MMACHC. Based on the Hardy-Weinberg equilibrium, the incidence of the 21 inherited metabolic diseases in the population was approximately 1/1100, with the five diseases with higher incidence including citrullinemia, methylmalonic acidemia, Wilson disease, glycogen storage disease, and phenylketonuria.@*CONCLUSION@#This study has preliminarily determined the carrier rate and incidence of 21 inherited metabolic diseases among a Chinese population of childbearing age, which has provided valuable information for the design of neonatal screening program for inherited metabolic diseases. Pre-conception carrier screening can provide an important measure for the prevention of transmission of Mendelian disorders in the population.


Subject(s)
Asians/genetics , China , Exome , Female , Humans , Infant, Newborn , Metabolic Diseases/genetics , Mitochondrial Membrane Transport Proteins/genetics , Oxidoreductases/genetics , Whole Exome Sequencing
6.
Article in Chinese | WPRIM | ID: wpr-928396

ABSTRACT

OBJECTIVE@#To study the polymorphism of human platelet antigen (HPA) system 10 among ethnic Han Chinese from Shandong, China so as to supplement the data of platelet donor bank in the region.@*METHODS@#Peripheral blood samples of platelet donors from the region were genotyped for HPA-10 alleles by PCR-sequence specific primer (PCR-SSP) and direct sequencing.@*RESULTS@#Among 1401 donors, a rare heterozygote carrier of HPA-10w (a+b+) was identified, which gave an allelic frequency of approximately 0.035%.@*CONCLUSION@#The detection of rare HPA-10bw antigen allele among ethnic Han Chinese from Shandong is useful for the diagnosis and prevention of neonatal alloimmune thrombocytopenia and post-transfusion purpura in the region.


Subject(s)
Alleles , Antigens, Human Platelet/genetics , Asians/genetics , Gene Frequency , Genotype , Humans , Infant, Newborn , Polymorphism, Genetic
7.
Article in Chinese | WPRIM | ID: wpr-928388

ABSTRACT

OBJECTIVE@#To analyze the clinical phenotype and genetic variant in a Chinese pedigree affected with benign familial neonatal convulsion (BFNC).@*METHODS@#Clinical data and peripheral blood samples of the pedigree were obtained with informed consent. Whole exome sequencing (WES) was carried out for the proband. Candidate variants were verified by Sanger sequencing.@*RESULTS@#The pedigree comprised 9 individuals, among whom 4 were affected, including 3 males and 1 female. All patients had developed seizures during the neonatal period, which had ceased in 4 to 6 months. One patient had recurrence in between 1 and 2 years old. Genetic testing has identified a novel nonsense c.810G>A (p.W270X) variant in exon 5 of the KCNQ2 gene, which has co-separated with the BFNC phenotype in the pedigree.@*CONCLUSION@#The patients from this pedigree have conformed to the diagnosis of BFNC with good prognosis, which was in keeping with previously reported cases. The heterozygous c.810G>A (p.W270X) nonsense variant of the KCNQ2 gene probably underlay the pathogenesis of BFNC in this pedigree, which has expanded the mutational spectrum of the disease.


Subject(s)
Asians/genetics , Child, Preschool , China , Epilepsy, Benign Neonatal/genetics , Female , Genetic Testing , Humans , Infant , Male , Mutation , Pedigree
8.
Article in Chinese | WPRIM | ID: wpr-928362

ABSTRACT

OBJECTIVE@#To analyze the clinical features and variants of ABCD1 gene in a Chinese pedigree affected with X-linked adrenoleukodystrophy.@*METHODS@#Clinical data of the proband were collected and analyzed. Potential variant of the ABCD1 gene were analyzed by PCR and Sanger sequencing of the proband, his parents and 100 unrelated healthy individuals.@*RESULTS@#The prominent features of the proband included cerebellar and brainstem lesions, along with increased serum level of very-long chain fatty acids. He was found to harbor a hemizygous c.1509delG (p.L504Sfs*54) variant of the ABCD1 gene, for which his mother was heterozygous. The same variant was not detected in his father and 100 healthy controls.@*CONCLUSION@#X-linked adrenoleukodystrophy has a variety of clinical manifestations. Discovery of the c.1509delG (p.L504Sfs*54), as a novel pathogenic variant of the ABCD1 gene, has enabled diagnosis and genetic counseling for this pedigree.


Subject(s)
Adrenoleukodystrophy/genetics , Asians/genetics , China , Female , Genetic Testing , Humans , Male , Mutation , Pedigree
9.
Article in Chinese | WPRIM | ID: wpr-928360

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a Chinese patient with retinitis pigmentosa (RP).@*METHODS@#Whole exome sequencing (WES) was carried out to screen potential variant in the proband. Candidate variants were determined by taking consideration of clinical phenotype. Sanger sequencing was used to verify the variant in the proband and his parents.@*RESULTS@#The proband was found to harbor compound heterozygous variants of c.8G>A (p.Cys3Tyr) and c.958_959insA (p.Arg320Glnfs*29) in the C2ORF71 gene, which has derived from his father and mother, respectively. Both variants were unreported previously. Based on the ACMG guidelines, they were predicted to be likely pathogenic and pathogenic, respectively.@*CONCLUSION@#The novel compound heterozygous variants of the C2ORF71 gene probably underlay the pathogenesis of RP in the proband. Above finding has enriched the spectrum of C2ORF71 gene mutations and facilitated genetic counseling for the family.


Subject(s)
Asians/genetics , China , Humans , Mutation , Pedigree , Retinitis Pigmentosa/genetics , Whole Exome Sequencing
10.
Article in Chinese | WPRIM | ID: wpr-928358

ABSTRACT

OBJECTIVE@#To explore the clinical features and genetic basis for a Chinese pedigree diagnosed with congenital glycosylation disease (CGD).@*METHODS@#Clinical manifestations of two brothers were analyzed. Whole exome sequencing was carried out for the sib pair. Suspected variants were verified by Sanger sequencing.@*RESULTS@#Both the proband and her younger brother were found to carry compound heterozygous variants of the PMM2 gene, which included a known pathogenic mutation of c.395T>C (p.I132T) and a previously unreported c.448-1(delAG) in the 5' end of exon 6 of the gene.@*CONCLUSION@#The compound heterozygous variants of the PMM2 gene probably underlay the CGD in the sib pair.


Subject(s)
Asians/genetics , China , Female , Glycosylation , Humans , Male , Mutation , Pedigree , Whole Exome Sequencing
11.
Article in English | WPRIM | ID: wpr-927641

ABSTRACT

OBJECTIVE@#To explore the association of single nucleotide polymorphisms (SNPs) of the vitamin D receptor gene ( VDR) with circulating lipids considering gender differences.@*METHODS@#Of the Han Chinese adults recruited from a health examination center for inclusion in the study, the circulating lipids, 25-hydroxyvitamin D (25OHD), and other parameters were measured. The VDR SNPs of Cdx2 (rs11568820), Fok1 (rs2228570), Apa1 (rs7975232), and Taq1 (rs731236) were genotyped with a qPCR test using blood DNA samples, and their associations with lipids were analyzed using logistic regression.@*RESULTS@#In the female participants ( n = 236 with dyslipidemia and 888 without dyslipidemia), multiple genotype models of Fok1 indicated a positive correlation of B (not A) alleles with LDLC level ( P < 0.05). In the male participants ( n = 299 with dyslipidemia and 564 without dyslipidemia), the recessive model of Cdx2 and the additive and recessive models of Fok1 differed ( P < 0.05) between the HDLC-classified subgroups, respectively, and Fok1 BB and Cdx2 TT presented interactions with 25OHD in the negative associations with HDLC ( P < 0.05).@*CONCLUSION@#In the Chinese Han adults included in the study, the Fok1 B-allele of VDR was associated with higher LDLC in females, and the Fok1 B-allele and the Cdx2 T-allele of VDR were associated with lower HDLC in males. The interaction of VD and Fok1 BB or Cdx2 TT in males synergistically decreased HDLC levels.


Subject(s)
Adult , Alleles , Asians/genetics , China/ethnology , Dyslipidemias/genetics , Female , Genetic Predisposition to Disease/genetics , Genotype , Humans , Lipids/blood , Male , Middle Aged , Polymorphism, Single Nucleotide , Receptors, Calcitriol/genetics , Sex Factors , Vitamin D/blood
12.
Article in English | WPRIM | ID: wpr-880666

ABSTRACT

OBJECTIVES@#Due to the genetic feature of high diversity than other DNA markers, short tandem repeat (STR) plays key roles in forensic, anthropology, and population genetics. Newly introduced multiple STR kit is more valuable because of the greatly improved discriminatory power with the increase in the number of STR loci. The genetic polymorphic data are essential for the application and research in specific population. This study aims to investigate the genetic polymorphism of Han population residing in Yuncheng district, Shanxi Province, to evaluate the application of 23 STR loci in forensic personal identification and paternity test, and to explore the genetic relationship of Han population between Yuncheng and other populations.@*METHODS@#A total of 23 STR loci were amplified from 525 healthy unrelated individuals from the Han nationality in Yuncheng, Shanxi Province using the AGCU EX25 amplification kit. The products were detected and separated by ABI 3500 Genetic Analyzer. Alleles were genotyped by GeneMapper ID (Version 3.2) software, and corresponding frequencies and forensic parameters were calculated. We calculated the genetic distance and plotted the neighboring-joining tree with other 13 population.@*RESULTS@#The allele frequency of the 23 STRs ranged from 0.0010 to 0.5090. No deviation from Hardy-Weinberg equilibrium (@*CONCLUSIONS@#These 23 STRs are highly genetic polymorphic and informative in the Han population of Yuncheng, Shanxi Province, which can provide basic data for forensic personal identification, paternity testing, and population genetic research.


Subject(s)
Asians/genetics , China , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , Humans , Microsatellite Repeats/genetics , Polymorphism, Genetic
13.
Article in Chinese | WPRIM | ID: wpr-879614

ABSTRACT

OBJECTIVE@#To investigate the genetic polymorphisms of 21 non-combined DNA index system short tandem repeat (STR) loci in Hainan Li population.@*METHODS@#DNA samples from 339 unrelated healthy individuals of Li population from Hainan Province were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were electrophoresed on an ABI3130 Genetic Analyzer following the manufacturer's instructions. Allele designation was performed with a GeneMapper ID-X by comparison with the allele ladder provided by the corresponding kit.@*RESULTS@#A total of 173 alleles and 489 genotypes were observed for the 21 STR loci, respectively. The frequencies of alleles and genotypes were 0.0010-0.5434 and 0.0020-0.3274, respectively. The heterozygosity varied from 0.639 to 0.833. Discrimination power (DP) was 0.803-0.948, power of exclusion for trio-paternity was 0.416-0.584, power of exclusion for duo-paternity was 0.140-0.238, the polymorphism information content(PIC) was 0.57-0.81, respectively. The total discrimination power (TDP), cumulative probability of exclusion for trio-paternity testing(CPE-trio) and cumulative probability of exclusion for duo-paternity testing (CPE-duo) were 0.999 999 999 999 99, 0.999 999 883 211 752, and 0.987 266, respectively.@*CONCLUSION@#The 21 STR loci are highly polymorphic and informative in the studied population and can be employed as supplementary loci in duo-paternity testing or cases with variant circumstances.


Subject(s)
Asians/genetics , China , DNA , Gene Frequency , Genetics, Population , Humans , Microsatellite Repeats/genetics , Polymorphism, Genetic
14.
Article in Chinese | WPRIM | ID: wpr-879560

ABSTRACT

OBJECTIVE@#To explore the clinical characteristics and genetic basis for a pair of twins affected with hyaline fibromatosis syndrome (HFS).@*METHODS@#Clinical data of the twins were retrospectively analyzed. High-throughput sequencing was carried out to detect potential pathogenic variants. CLUSTALX was employed to analyze cross-species conservation of the mutant amino acids. Impact of the mutations was predicted by using software including PolyPhen-2 and Mutation taster.@*RESULTS@#The pair of twins have featured growth and intelligence retardation, and were found to carry compound heterozygous variants of the ANTXR2 gene including c.1214G>A and c.1074delT, among which c.1214G>A was unreported previously. Both variants were predicted to be pathogenic. In addition to growth and mental delay, the pair of twins also featured hyperplasia of the gum and soft tissue-like masses of the auricle. The younger brother had rupture of the auricle mass during follow-up.@*CONCLUSION@#The patients' condition can probably be attributed to the compound heterozygous variants of the ANTXR2 gene. Above finding has facilitated molecular diagnosis of the patients.


Subject(s)
Asians/genetics , China , Humans , Hyalinosis, Systemic/genetics , Male , Mutation , Pedigree , Receptors, Peptide/genetics , Retrospective Studies
15.
Chinese Medical Journal ; (24): 1138-1145, 2021.
Article in English | WPRIM | ID: wpr-878167

ABSTRACT

BACKGROUND@#Single-nucleotide polymorphisms (SNPs)-associated genes and long non-coding RNAs (lncRNAs) can contribute to human disease. To comprehensively investigate the contribution of lncRNAs to breast cancer, we performed the first genome-wide lncRNA association study on Han Chinese women.@*METHODS@#We designed an lncRNA array containing >800,000 SNPs, which was incorporated into a 96-array plate by Affymetrix (CapitalBio Technology, China). Subsequently, we performed a two-stage genome-wide lncRNA association study on Han Chinese women covering 11,942 individuals (5634 breast cancer patients and 6308 healthy controls). Additionally, in vitro gain or loss of function strategies were performed to clarify the function of a novel SNP-associated gene.@*RESULTS@#We identified a novel breast cancer-associated susceptibility SNP, rs11066150 (Pmeta = 2.34 × 10-8), and a previously reported SNP, rs9397435 (Pmeta = 4.32 × 10-38), in Han Chinese women. rs11066150 is located in NONHSAT164009.1 (lncHSAT164), which is highly expressed in breast cancer tissues and cell lines. lncHSAT164 overexpression promoted colony formation, whereas lncHSAT164 knockdown promoted cell apoptosis and reduced colony formation by regulating the cell cycle.@*CONCLUSIONS@#Based on our lncRNA array, we identified a novel breast cancer-associated lncRNA and found that lncHSAT164 may contribute to breast cancer by regulating the cell cycle. These findings suggest a potential therapeutic target in breast cancer.


Subject(s)
Asians/genetics , Breast Neoplasms/genetics , Case-Control Studies , China , Female , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study , Humans , Polymorphism, Single Nucleotide/genetics , RNA, Long Noncoding/genetics
16.
Article in Chinese | WPRIM | ID: wpr-879475

ABSTRACT

OBJECTIVE@#To analyze the molecular etiology of a Chinese child affected with dihydropyrimidinase deficiency.@*METHODS@#Genomic DNA was extracted from peripheral blood samples of the family members. Pathogenic variant was determined by whole exome sequencing and verified by Sanger sequencing.@*RESULTS@#The child was found to harbor homozygous c.905G>A (p.Arg302Gln) variants in exon 5 of the DPYS gene, for which her parents were both heterozygous carriers.@*CONCLUSION@#The homozygous c.905G>A (p.Arg302Gln) variants of the DPYS gene probably underlies the dihydropyrimidinase deficiency in the child. Above result has enabled genetic counseling and prenatal diagnosis for this family.


Subject(s)
Amidohydrolases/genetics , Asians/genetics , Child , Exons , Female , Humans , Metabolism, Inborn Errors/genetics , Mutation , Pedigree
17.
Braz. j. infect. dis ; 23(6): 388-394, Nov.-Dec. 2019. tab, graf
Article in English | LILACS | ID: biblio-1089306

ABSTRACT

ABSTRACT Host immunogenetic setting is involved in the regulation of human papillomavirus (HPV) infection and development of condyloma acuminatum (CA). We investigated the correlation of two common single nucleotide polymorphisms (SNPs) (−607C/A and −137G/C) of IL-18 with the susceptibility of CA in a large Chinese cohort. Out of 408 CA patients analyzed, 300 had HPV infection transmitted through sexual contact (SC) and 108 through non-sexual contact (NSC). In addition, 360 healthy volunteers were enrolled as controls. SNPs at positions −607C/A and −137G/C in IL-18 promoter were analyzed. Comparing CA patients to healthy controls, no dominant relevance was found between the IL-18 promoter −607 C/A or −137G/C polymorphisms and the CA disease either identified genotypically (p > 0.05) or by allelically (p > 0.05). However, the IL-18 promoter −137G/C polymorphism genotype and allele frequencies in the NSC CA group, but not between in the SC group, were significantly higher than in the controls. There was no dominant relevance between IL-18-607C/A polymorphism genotype and allele frequencies among SC, NSC CA patients, and controls. Our study demonstrates that polymorphism −137G/C in IL-18 promoter is significantly correlated with risk of CA in NSC patients.


Subject(s)
Humans , Male , Female , Condylomata Acuminata/genetics , Interleukin-18/genetics , Polymorphism, Single Nucleotide/genetics , Papillomavirus Infections/complications , Polymorphism, Genetic , Condylomata Acuminata/virology , China , Cohort Studies , Promoter Regions, Genetic , Genetic Predisposition to Disease , Papillomavirus Infections/transmission , Asians/genetics , Alleles , Genotype
18.
An. bras. dermatol ; 94(6): 658-663, Nov.-Dec. 2019. tab, graf
Article in English | LILACS | ID: biblio-1054887

ABSTRACT

Abstract Background: Palmoplantar pustulosis is considered to be a localized pustular psoriasis confined to the palms and soles. Mutation of the IL36RN gene, encoding interleukin-36 receptor antagonist (IL-36Ra), is associated with generalized pustular psoriasis, but IL36RN mutations in Chinese palmoplantar pustulosis patients have not previously been investigated. Objective: The aim of this study was to evaluate the mutation of IL36RN in Chinese patients with palmoplantar pustulosis. Methods: Fifty-one Han Chinese patients with palmoplantar pustulosis were recruited. All exons and exon-intron boundary sequences of IL36RN were amplified in polymerase chain reactions, and Sanger sequencing of the amplicons was performed. Results: Among the 51 palmoplantar pustulosis patients, four different single-base substitutions were identified in nine patients. The mutations were c.140A>G/p.Asn47Ser in five patients, c.258G>A/p.Met86IIe in two patients, and c.115+6T>C and c.169G>A/p.Val57IIe in one patient each. All mutations were heterozygous. Comparison with the human genome database and reported literature suggested that these variants may not be pathogenic mutations causing palmoplantar pustulosis. Furthermore, there was no difference in disease severity, onset age, or disease duration between patients with these heterozygous IL36RN variants and those without (p > 0.1). Study limitation: Lack of the further evaluation of IL36Ra protein in palmoplantar pustulosis lesions. Conclusions: The four variants of IL36RN identified did not appear to be associated with the specific phenotypes of palmoplantar pustulosis.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Psoriasis/genetics , Interleukins/genetics , Mutation , Phenotype , Psoriasis/pathology , China , Sequence Analysis, DNA , Statistics, Nonparametric , Asians/genetics , Amplified Fragment Length Polymorphism Analysis , Genetic Association Studies , Foot Dermatoses/genetics , Foot Dermatoses/pathology , Hand Dermatoses/genetics , Hand Dermatoses/pathology , Heterozygote
19.
Biomédica (Bogotá) ; 39(3): 595-600, jul.-set. 2019. tab, graf
Article in Spanish | LILACS | ID: biblio-1038818

ABSTRACT

Resumen Introducción. Los proyectos del mapa de haplotipos (HapMap) y de los 1.000 genomas han sido fundamentales para la compresión del componente genético de las enfermedades comunes y los fenotipos normales. Sin embargo, la variabilidad genética colombiana incluida en estos proyectos no es representativa del país. Objetivo. Contribuir al conocimiento de la variabilidad genética de la población colombiana a partir del estudio genómico de una muestra de individuos de Bogotá. Materiales y métodos. Se genotipificaron 2'372.784 marcadores genéticos de 32 individuos nacidos en Bogotá y de padres originarios de la misma ciudad utilizando la plataforma Illumina™. Los niveles de variabilidad genética se determinaron y se compararon con los datos disponibles de otras poblaciones del proyecto de los 1.000 genomas. Resultados. Los individuos analizados presentaron una variabilidad genética semejante a la de poblaciones con las que comparten ancestros. No obstante, a pesar de la poca diferenciación genética detectada en la población de Bogotá y en la de Medellín, el análisis de los componentes principales sugiere una composición genética diferente en las dos poblaciones. Conclusiones. El análisis genómico de la muestra de Bogotá permitió detectar similitudes y diferencias con otras poblaciones americanas. El aumento de tamaño de la muestra bogotana y la inclusión de muestras de otras regiones del país permitirán una mejor compresión de la variabilidad genética en Colombia, lo cual es fundamental para los estudios de salud humana, y la prevención y el tratamiento de enfermedades comunes en el país.


Abstract Introduction: The HapMap and the 1000 Genomes projects have been important for understanding the genetic component of common diseases and normal phenotypes. However, the Colombian genetic variability included in these projects is not fully representative of our country. Objective: To contribute to the knowledge of the Colombian genetic variability through the genomic study of a sample of individuals from Bogotá. Materials and methods: A total of 2,372,784 genetic markers were genotyped in 32 individuals born in Bogotá whose parents are from the same region, using the Illumina™ platform. The genetic variability levels were determined and compared with the data available from other populations of the 1000 Genomes Project. Results: The genetic variability detected in the individuals from Bogotá was similar to those with shared ancestry. However, despite the low levels of genetic differentiation between Bogotá and Medellín, populations the principal component analysis suggested a different genetic composition in them. Conclusions: Our genomic analysis of a Bogotá sample allowed us to detect similarities and differences with other American populations. The increase of the Bogotá sample and the inclusion of samples from other regions of the country will improve our understanding of the genetic variability in Colombia, essential for studies of human health and the prevention and treatment of common diseases in our country.


Subject(s)
Female , Humans , Male , Genetic Variation , Haplotypes , Genetic Markers , Human Genome Project , Cities/ethnology , Colombia/ethnology , Polymorphism, Single Nucleotide , Blacks/genetics , American Native Continental Ancestry Group/genetics , Asians/genetics , Whites/genetics
20.
Biomédica (Bogotá) ; 39(3): 601-610, jul.-set. 2019. tab
Article in Spanish | LILACS | ID: biblio-1038819

ABSTRACT

Resumen Introducción. El citocromo CYP2C9 metaboliza, aproximadamente, el 15 % de los fármacos prescritos. Su gen presenta alelos cuyas frecuencias difieren entre grupos étnicos y poblaciones. Los alelos CYP2C9*2 y CYP2C9*3 dan cuenta de una enzima con actividad disminuida cuya frecuencia no ha sido determinada en la población mestiza peruana. Objetivo. Caracterizar la frecuencia de las variantes *2 (rs1799853) y *3 (rs1057910) del gen CYP2C9 en muestras de población mestiza peruana provenientes de Lima, Tacna y Junín. Materiales y métodos. Se hizo un estudio descriptivo, observacional y prospectivo, con muestreo no probabilístico, por conveniencia e incidental. Se incluyeron 218 sujetos según los criterios de inclusión y exclusión; todos los participantes otorgaron su consentimiento informado. El ADN genómico se obtuvo mediante hisopado de mucosa oral, y la detección de los genotipos para los alelos CYP2C9*2 y CYP2C9*3 se hizo mediante reacción en cadena de la polimerasa (PCR) en tiempo real, utilizando sondas TaqMan™. Resultados. Las variantes de CYP2C9*2 y CYP2C9*3 están presentes en la población mestiza peruana con frecuencias de 0,046 y 0,062, respectivamente. El análisis de las frecuencias genotípicas observadas permitió predecir que la frecuencia de fenotipos metabolismo intermedio sería del 15,13 % (CYP2C9*1/*2: 5,96 %; CYP2C9*1/*3: 9,17 %), y la de fenotipos de metabolismo lento, del 3,22 % (CYP2C9*2/*2: 1,38 %; CYP2C9*3/*3: 1,38 %; CYP2C9*2/*3: 0,46 %). Conclusiones. Se lograron determinar las frecuencias genotípicas y alélicas para las variantes *2 y *3 del gen CYP2C9 en una muestra no probabilística de población mestiza peruana. Las frecuencias obtenidas (0,046 y 0,062, respectivamente) están entre las esperadas para una población mestiza sudamericana con ascendencia amerindia, europea, africana y asiática.


Abstract Introduction: CYP2C9 metabolizes approximately 15% of the prescribed drugs. Its gene has alleles whose frequencies differ between ethnic groups and populations. The alleles CYP2C9*2 and CYP2C9*3 account for an enzyme with decreased activity and their frequencies have not been determined in the Peruvian mestizo population. Objective: To characterize the frequencies of the allelic variants *2 (rs1799853) and *3 (rs1057910) of CYP2C9 gen in the Peruvian mestizo population from Lima, Tacna y Junín. Materials and methods: We conducted an observational, prospective cross-sectional study with non-probabilistic, by convenience, and incidental sampling. We included 218 subjects according to the inclusion and exclusion criteria, all of whom had signed the informed consent. We obtained the genomic DNA from oral mucosa swab. For the detection of the CYP2C9*2 and CYP2C9*3 genotypes, we used real-time-polymerase chain reaction with TaqMan® probes. Results: The genotyping revealed that CYP2C9*2 and CYP2C9*3 variants have low frequencies (0.046 and 0.062, respectively). The frequency of intermediate metabolizers was 15.13% (CYP2C9*1/*2: 5.96%; CYP2C9*1/*3: 9.17%) and that of slow metabolizers was 3.22% (CYP2C9*2/*2: 1.38%; CYP2C9*3/*3: 1.38%; CYP2C9*2/*3: 0.46%). Conclusions: It was possible to determine the genotypic and allelic frequencies for the variants *2 and *3 of the CYP2C9 gene in a non-probabilistic sample of the Peruvian mestizo population. The frequencies obtained (0.046 and 0.062, respectively) corresponded to those expected for a South American mestizo population with Amerindian, European, African and Asian ancestry.


Subject(s)
Adult , Female , Humans , Male , Alleles , Cytochrome P-450 CYP2C9/genetics , Gene Frequency , Peru/ethnology , Pharmaceutical Preparations/metabolism , Cross-Sectional Studies , Prospective Studies , Cities/ethnology , Blacks/genetics , American Native Continental Ancestry Group/genetics , Asians/genetics , Whites/genetics , Genotype
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