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1.
Chinese Journal of Medical Genetics ; (6): 483-489, 2023.
Article in Chinese | WPRIM | ID: wpr-981775

ABSTRACT

OBJECTIVE@#To provide prenatal diagnosis, pedigree analysis and genetic counseling for a pregnant woman who had given birth to a child featuring global developmental delay.@*METHODS@#A pregnant woman who underwent prenatal diagnosis at the Affiliated Hospital of Southwest Medical University in August 2021 was selected as the study subject. Peripheral blood samples were collected from the woman, her husband and child, in addition with amniotic fluid sample during mid-pregnancy. Genetic variants were detected by G-banded karyotyping analysis and copy number variation sequencing (CNV-seq). Pathogenicity of the variant was predicted based on the guidelines from the American College of Medical Genetics and Genomics (ACMG). Candidate variant was traced in the pedigree to assess the recurrence risk.@*RESULTS@#The karyotypes of the pregnant woman, her fetus, and affected child were 46,XX,ins(18)(p11.2q21q22), 46,X?,rec(18)dup(18)(q21q22)ins(18)(p11.2q21q22)mat and 46,XY,rec(18)del(18)(q21q22)ins(18)(p11.2q21q22)mat, respectively. Her husband was found to have a normal karyotype. CNV-seq has revealed a 19.73 Mb duplication at 18q21.2-q22.3 in the fetus and a 19.77 Mb deletion at 18q21.2-q22.3 in her child. The duplication and deletion fragments were identical to the insertional fragment in the pregnant woman. Based on the ACMG guidelines, the duplication and deletion fragments were both predicted to be pathogenic.@*CONCLUSION@#The intrachromosomal insertion of 18q21.2-q22.3 carried by the pregnant woman had probably given rise to the 18q21.2-q22.3 duplication and deletion in the two offspring. Above finding has provided a basis for genetic counseling for this pedigree.


Subject(s)
Child , Female , Humans , Pregnancy , Male , DNA Copy Number Variations , East Asian People , Pedigree , Prenatal Diagnosis/methods , Chromosomes, Human, Pair 18/genetics , Fetus , INDEL Mutation
2.
Journal of Zhejiang University. Science. B ; (12): 241-248, 2022.
Article in English | WPRIM | ID: wpr-929055

ABSTRACT

Due to the virtues of no stutter peaks, low rates of mutation, and short amplicon sizes, insertion/deletion (InDel) polymorphism is an indispensable tool for analyzing degraded DNA samples from crime scenes for human identifications (Wang et al., 2021). Herein, a self-developed panel of 43 InDel loci constructed previously by our group was utilized to evaluate the genetic diversities and explore the genetic background of the Han Chinese from Beijing (HCB) including 301 random healthy individuals. The lengths of amplicons at 43 InDel loci in this panel ranged from 87 to 199 bp, which indicated that the panel could be used as an effective tool to utilize highly degraded DNA samples for human identity testing. The loci in this panel were validated and performed well for forensic degraded DNA samples (Jin et al., 2021). The combined discrimination power (PD) and combined probability of exclusion (PE) values in this panel indicated that the 43 InDel loci could be used as the candidate markers in personal identification and parentage testing of HCB. In addition, population genetic relationships between the HCB and 26 reference populations from five continents based on 19 overlapped InDel loci were displayed by constructing a phylogenetic tree, principal component analysis (PCA), and population genetic structure analysis. The results illustrated that the HCB had closer genetic relationships with the Han populations from Chinese different regions.


Subject(s)
Humans , Beijing , China , Forensic Genetics/methods , Gene Frequency , Genetics, Population , INDEL Mutation , Phylogeny
3.
Journal of Forensic Medicine ; (6): 739-746, 2022.
Article in English | WPRIM | ID: wpr-984166

ABSTRACT

OBJECTIVES@#To investigate the genetic information of 57 autosomal InDel loci (A-InDels) included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine.@*METHODS@#A total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations.@*RESULTS@#After Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10-24, CPEduo was 0.999 062 660, and CPEtrio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations.@*CONCLUSIONS@#The 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.


Subject(s)
Humans , Genetics, Population , Asian People/genetics , Polymorphism, Genetic , Gene Frequency , INDEL Mutation , China , Microsatellite Repeats , Genetic Loci
4.
Journal of Forensic Medicine ; (6): 733-738, 2022.
Article in English | WPRIM | ID: wpr-984165

ABSTRACT

OBJECTIVES@#To investigate the genetic polymorphism of InDel loci in SifalnDel 45plex system in the Han population in Jiangsu Province and the Mongolian population in Inner Mongolia, and to evaluate the effectiveness of the system in forensic medicine.@*METHODS@#SifaInDel 45plex system was used for genotyping in blood samples of 398 unrelated individuals from the above two populations, and allele frequencies and population genetic parameters of the two populations were calculated respectively. Eight intercontinental populations in the gnomAD database were used as reference populations. The genetic distances between the two studied populations and eight reference populations were calculated based on the allele frequencies of 27 autosomal-InDels (A-InDels). The phylogenetic trees and multidimensional scaling (MDS) analysis diagrams were constructed accordingly.@*RESULTS@#Among two studied populations, the 27 A-InDels and 16 X-InDels showed no linkage disequilibrium between each other and the allele frequency distributions were in Hardy-Weinberg equilibrium. The CDP of the 27 A-InDels in two studied populations were all higher than 0.999 999 999 9, and the CPEtrio were all less than 0.999 9. The CDP of the 16 X-InDels in Han in Jiangsu and Mongolian in Inner Mongolia female and male samples were 0.999 997 962, 0.999 998 389, and 0.999 818 940, 0.999 856 063, respectively. The CMECtrio were all less than 0.999 9. The results of population genetics showed that the Jiangsu Han nationality, Inner Mongolia Mongolian nationality and East Asian population clustered into one branch, showing closer genetic relationship. The other 7 intercontinental populations clustered into another group. And the above 3 populations displayed distant genetic relationships with the other 7 intercontinental populations.@*CONCLUSIONS@#The InDels in the SifaInDel 45plex system have good genetic polymorphism in the two studied populations, which can be used for forensic individual identification or as an effective complement for paternity identification, and to distinguish different intercontinental populations.


Subject(s)
Humans , Phylogeny , Gene Frequency , Polymorphism, Genetic , Genetics, Population , Asian People/genetics , China , INDEL Mutation
5.
Journal of Forensic Medicine ; (6): 611-617, 2022.
Article in English | WPRIM | ID: wpr-984155

ABSTRACT

OBJECTIVES@#The previously established 38-plex InDel system was optimized and its performance was validated according to the Scientific Working Group on DNA Analysis Method (SWGDAM) application guidelines. The ancestry inference accuracy of individuals from East Asian, European, African and mixed populations was verified.@*METHODS@#DNA standard sample 9947A was used as the template to establish the optimal amplification conditions by adjusting primer balance, Mg2+ final concentration and optimizing PCR thermal cycle parameters and amplification volume. The allelic dropout, nonspecific amplification and whether the origin of the inferred samples matched the known information were compared to evaluate the performance of this system.@*RESULTS@#The optimal dosage of this system was 0.125-2 ng DNA template. The results of InDel typing were accurate, the amplification equilibrium was good, and the species specificity was good. This system showed certain tolerance to DNA samples including the inhibitor such as hemoglobin (≤80 μmol/L), indigo (≤40 mmol/L), calcium ion (≤1.0 mmol/L), and humic acid (≤90 ng/μL). The system enabled the direct amplification of DNA from saliva and blood on filter paper, and the results of ethnic inference were accurate. The system successfully detected the mixed DNA sample from two individuals. The test results of the system for common biological materials in practical cases were accurate.@*CONCLUSIONS@#The results of the 38-plex InDel system are accurate and reliable, and the performance of the system meets the requirement of the SWGDAM guidelines. This system can accurately differentiate the ancestry origins of individuals from African, European, East Asian, and Eurasian populations and can be implemented in forensic practice.


Subject(s)
Humans , Polymorphism, Single Nucleotide , Genotype , Polymerase Chain Reaction , DNA/genetics , DNA Fingerprinting/methods , INDEL Mutation , Genetics, Population , Gene Frequency
6.
Journal of Forensic Medicine ; (6): 531-537, 2020.
Article in English | WPRIM | ID: wpr-985149

ABSTRACT

Objective To investigate the population genetic data of 47 autosomal insertion/deletion (InDel) polymorphism genetic markers involved in AGCU InDel 50 kit in Guangdong Han, Guangxi Zhuang, Guangxi Yao, Guangxi Jing, and Guangxi Mulam, and to evaluate their application in forensic DNA identification. Methods Multiplex amplification of the 768 unrelated individuals from the 5 ethnic groups mentioned above was performed with the AGCU InDel 50 kit. Genotyping was carried out by 3500xL gene analyzer, population genetic parameters were gathered and polymorphism analysis was performed. Results No linkage disequilibrium was found among 47 autosomal InDel loci in the 5 ethnic groups. The distribution of genotype frequency of 47 autosomal InDel loci confirmed to the Hardy-Weinberg equilibrium in Guangdong Han and Guangxi Zhuang. Except for rs139934789, the other 46 loci confirmed to the Hardy-Weinberg equilibrium in Guangxi Yao, Guangxi Jing, and Guangxi Mulam. The results of genetic variation analysis among the populations showed that 1.12% of genetic variation was caused by ethnic group differences. The cumulative discrimination power of 47 autosomal InDel loci for the 5 ethnic groups were all above 0.999 999 999 999 999. The cumulative probability of exclusion for each ethnic group was less than 0.999 9. The two Y-InDels were identified in all male individuals and were absent in all female individuals. Conclusion Except for rs139934789, the other 46 InDel loci have a relatively good genetic polymorphism in the 5 Chinese ethnic groups, and can be used for forensic individual identification and as effective supplements for paternity testing.


Subject(s)
Female , Humans , Male , Asian People/genetics , China , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , INDEL Mutation , Microsatellite Repeats , Polymorphism, Genetic
7.
China Journal of Chinese Materia Medica ; (24): 1342-1349, 2020.
Article in Chinese | WPRIM | ID: wpr-1008577

ABSTRACT

The molecular markers(cpSSR, cpSNP and cpIndel) were developed based on the whole genome sequence of Panax notoginseng chloroplast genome, which provide a powerful tool for the evaluation and analysis of the future P. notoginseng germplasm resources. The 89 P. notoginseng samples from 9 groups were used for the experiment, and the data for the study were derived from NCBI and the GenBank numbers were: KJ566590, KP036468, KR021381 and KT001509. Through sequence alignment, 30 polymorphic sites(SNP and Indel) were identified, including 16 cpSNP and 14 cpIndel; cpSNP and cpIndel accounted for far more than the gene region in the intergenic region. The developed cpSSR reached 87-89, the repeat unit was mainly composed of trinucleotide, accounting for 70%-71%, and the dinucleotide was the least, accounting for 7%. Eighteen cpDNA molecular markers were developed, including 7 cpSSR primers, 6 cpIndel primers, and 5 cpSNP primers. The MatK gene and ycf1 primers were chosen as control. According to the results of DNA gel electrophoresis, cpSSR-5, pgcpir019 and pncp08 can be used to distinguish different cultivated populations of P. notoginseng. Among them, cpSSR-5 and pgcpir019 can also be used to distinguish the inter-species resources of ginseng by comprehensive sequence length, population π value and average nucleotide difference. However, pncp08 can only be used to distinguish different populations of P. notoginseng. In addition, the effect of distinguishing the groups of P. notoginseng, which the primer pncp-M(based on the MatK gene) is weaker than the cpSSR-5, pgcpir019 and pncp08.


Subject(s)
DNA, Chloroplast/genetics , Genetic Markers , Genetics, Population , INDEL Mutation , Panax notoginseng/genetics , Polymorphism, Single Nucleotide , Sequence Alignment
8.
Journal of Forensic Medicine ; (6): 545-552, 2019.
Article in English | WPRIM | ID: wpr-985044

ABSTRACT

Objective To explore the genetic background and structure of Urumqi Mongolians, the previously developed 39-AIM-InDels panel for ancestry inference was utilized in the present study. Methods The blood samples of 145 unrelated healthy Urumqi Mongolian individuals were collected and genotyped. The compositions of ancestry information of Urumqi Mongolians were studied with 17 different populations from three continents (East Asia, Europe and Africa) as reference populations. Then, multiple population genetics and bioinformatics analysis methods were applied, the Fst and DA values between matched populations were compared and analyzed, PCA analysis was performed and a phylogenetic tree was constructed. The proportions of ancestry information components of Urumqi Mongolians were analyzed with Structure software, etc. Results The ancestry information components of Urumqi Mongolian group in different intercontinental populations accounted for 89%, 7%, and 3% of East Asian, European, and African populations, respectively. Compared with other intercontinental populations, Urumqi Mongolian group and East Asian populations have lower Fst and DA values, and they were in the same cluster in PCA analysis as well. In a phylogenetic tree, the Urumqi Mongolian group was in the same branch as East Asian populations. Conclusion Urumqi Mongolian group had relatively close genetic relationships with East Asian populations, and the proportion of its East Asian ancestry was about 89%.


Subject(s)
Humans , Asian People/genetics , Forensic Genetics , Gene Frequency , Genetics, Population , INDEL Mutation , Phylogeny , Polymorphism, Single Nucleotide
9.
Rev. bras. ginecol. obstet ; 40(10): 631-641, Oct. 2018. tab, graf
Article in English | LILACS | ID: biblio-977788

ABSTRACT

Abstract Objective Previous studies investigating the association between angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism and recurrent pregnancy loss (RPL) risk has provided inconsistent results. The aim of our study was to assess the association between the ACE I/D polymorphism and risk of RPL. Methods All studies published up to January 30, 2018 on the association of ACE I/D polymorphism with RPL were identified by searching the PubMed, Web of Knowledge, and Google scholar databases. Results A total of 26 case-control studies with 3,140 RPL cases and 3,370 controls were included in themeta-analysis. Overall, there was a significant association between ACE I/D polymorphism and RPL risk under the allele model (I versus D: odds ratio [OR] = 0.538, 95% confidence interval [CI] = 0.451-0.643, p 0.001), the homozygote model (II versus DD: OR = 0.766, 95% CI = 0.598-0.981, p = 0.035) and the recessive model (II versus ID + DD: OR = 0.809, 95% CI = 0.658-0.994, p = 0.044). Subgroup analysis by ethnicity showed that there was a significant association between ACE I/D polymorphism and increased risk of RPL in Caucasian and West-Asian populations, but not in East-Asians. When stratified by number of recurrent miscarriages (RMs), a significant association between ACE I/D polymorphism and increased risk of RPL was detected in the group of studies with ≥ 2 RMs, but not in studies with ≥ 3 RMs. Conclusion Themeta-analysis suggests that ACE I/D polymorphism is associated with increased risk of RPL. The ACE I/D polymorphism may be a risk factor for RPL in Caucasian and West-Asian populations, but not in East-Asians.


Subject(s)
Humans , Female , Pregnancy , Abortion, Habitual/genetics , Peptidyl-Dipeptidase A/genetics , Polymorphism, Single Nucleotide , Case-Control Studies , INDEL Mutation
10.
Braz. j. microbiol ; 49(2): 429-442, Apr.-June 2018. tab, graf
Article in English | LILACS | ID: biblio-889226

ABSTRACT

Abstract Bacteria are important sources of cellulases with various industrial and biotechnological applications. In view of this, a non-hemolytic bacterial strain, tolerant to various environmental pollutants (heavy metals and organic solvents), showing high cellulolytic index (7.89) was isolated from cattle shed soil and identified as Bacillus sp. SV1 (99.27% pairwise similarity with Bacillus korlensis). Extracellular cellulases showed the presence of endoglucanase, total cellulase and β-glucosidase activities. Cellulase production was induced in presence of cellulose (3.3 times CMCase, 2.9 times FPase and 2.1 times β-glucosidase), and enhanced (115.1% CMCase) by low-cost corn steep solids. An in silico investigation of endoglucanase (EC 3.2.1.4) protein sequences of three Bacillus spp. as query, revealed their similarities with members of nine bacterial phyla and to Eukaryota (represented by Arthropoda and Nematoda), and also highlighted of a convergent and divergent evolution from other enzymes of different substrate [(1,3)-linked beta-d-glucans, xylan and chitosan] specificities. Characteristic conserved signature indels were observed among members of Actinobacteria (7 aa insert) and Firmicutes (9 aa insert) that served as a potential tool in support of their relatedness in phylogenetic trees.


Subject(s)
Animals , Cattle , Bacillus/enzymology , Cellulase/genetics , Cellulase/metabolism , Evolution, Molecular , Bacillus/growth & development , Bacillus/isolation & purification , Cellulose/metabolism , Computational Biology , Feces/microbiology , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Enzymologic , INDEL Mutation , Sequence Analysis, DNA , Sequence Homology , Substrate Specificity , Zea mays/metabolism
11.
Electron. j. biotechnol ; 31: 44-47, Jan. 2018. tab, graf
Article in English | LILACS | ID: biblio-1022247

ABSTRACT

Background: Strong artificial selection and/or natural bottle necks may limit genetic variation in domesticated species. Lupinus luteus, an orphan temperate crop, has suffered diversity reductions during its bitter/sweet alkaloid domestication history, limiting breeding efforts and making molecular marker development a difficult task. The main goal of this research was to generate new polymorphic insertion­deletion (InDel) markers to aid yellow lupin genetics and breeding. By combining genomic reduction libraries and next generation sequencing, several polymorphic InDel markers were developed for L. luteus L. Results: A total of 118 InDel in silico polymorphic markers were identified. Eighteen InDel primer sets were evaluated in a diverse L. luteus core collection, where amplified between 2­3 alleles per locus. Observed heterozygosity (HO; 0.0648 to 0.5564) and polymorphic information content (PIC; 0.06 to 0.48) estimations revealed a moderate level of genetic variation across L. luteus accessions. In addition, ten and nine InDel loci amplified successfully Lupinus hispanicus Boiss & Reut, and Lupinus mutabilis Sweet, respectively, two L. luteus close relatives. PCA analysis identified two L. luteus clusters, most likely explained by the domestication species history. Conclusion: The development of InDel markers will facilitate the study of genetic diversity across L. luteus populations, as well as among closely related species.


Subject(s)
Genetic Variation , Genetic Markers , Lupinus/genetics , INDEL Mutation , High-Throughput Nucleotide Sequencing
12.
Journal of Forensic Medicine ; (6): 420-427, 2018.
Article in English | WPRIM | ID: wpr-984956

ABSTRACT

Genetic markers in forensic DNA typing experienced the variable number of tandem repeats (VNTR) sequences and the short tandem repeats (STR) sequences. With the emerge of sequencing technology, the third generation of genetic markers were found out, which usually have two alleles including single nucleotide polymorphism (SNP) and insertion/deletion (InDel), also known as biallelic genetic markers. Because of the insertions or deletions of DNA fragments, InDel genetic marker reveals DNA fragment length polymorphism and widely distributes across the whole genome. InDel genetic marker is numerous and has the characteristics of STR and SNP genetic markers, which has been applied in the fields of genetics and anthropology. This review focuses on the research progress of InDel genetic marker in forensic science, aiming to review and summarize the main research findings in recent years and provide clues for future researches.


Subject(s)
Alleles , DNA/genetics , DNA Fingerprinting , Forensic Genetics , Genetic Markers , INDEL Mutation , Microsatellite Repeats , Polymorphism, Single Nucleotide
13.
Journal of Zhejiang University. Science. B ; (12): 620-629, 2018.
Article in English | WPRIM | ID: wpr-1010399

ABSTRACT

Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics strategy for the high-throughput screening of induced mutations. γ radiation, which often induces both insertion/deletion (Indel) and point mutations, has been widely used in mutation induction and crop breeding. The present study aimed to develop a simple, high-throughput TILLING system for screening γ ray-induced mutations using high-resolution melting (HRM) analysis. Pooled rice (Oryza sativa) samples mixed at a 1:7 ratio of Indel mutant to wild-type DNA could be distinguished from the wild-type controls by HRM analysis. Thus, an HRM-TILLING system that analyzes pooled samples of four M2 plants is recommended for screening γ ray-induced mutants in rice. For demonstration, a γ ray-mutagenized M2 rice population (n=4560) was screened for mutations in two genes, OsLCT1 and SPDT, using this HRM-TILLING system. Mutations including one single nucleotide substitution (G→A) and one single nucleotide insertion (A) were identified in OsLCT1, and one trinucleotide (TTC) deletion was identified in SPDT. These mutants can be used in rice breeding and genetic studies, and the findings are of importance for the application of γ ray mutagenesis to the breeding of rice and other seed crops.


Subject(s)
Crops, Agricultural/radiation effects , Gamma Rays , Genetic Techniques , Genome, Plant , Homozygote , INDEL Mutation , Mutagenesis , Oryza/radiation effects , Plant Breeding , Polymerase Chain Reaction , Seeds , Sequence Analysis, DNA , Sequence Deletion
14.
Salud pública Méx ; 59(5): 540-547, Sep.-Oct. 2017. tab
Article in English | LILACS | ID: biblio-903806

ABSTRACT

Abstract: Objective: To evaluate if variants in the genes CYP1A1 (T3801C and A4889G), CYP1B1 (G119T), GSTM1 (indel) and GSTT1 (indel) are associated with breast cancer (BC) among Mexican women. Materials and methods: 952 incident cases with histologically confirmed BC were matched by age (± 5 years) and zone of residence with 998 healthy population controls. Genetic variants in genes CYP1A1, CYP1B1, GSTM1 and GSTT1were genotyped by allelic discrimination and multiplex PCR. In a subsample of women, 105 markers for ancestry were determined. Results: An increased BC risk, independent of other BC risk factors, was observed among carriers of CYP1B1 G119T genotype (T/T vs. G/G: OR=1.9; 95%CI 1.4-2.5). Conclusion: Our results support the existence of genetic susceptibility for BC conferred by CYP1B1 G119T variant among Mexican women.


Resumen: Objetivo: Evaluar si las variantes en los genes CYP1A1 (T3801C y A4889G), CYP1B1 (G119T), GSTM1 (indel) yGSTT1 (indel), se asocian con el cáncer de mama (CM) en mujeres mexicanas. Material y métodos: Se parearon por edad (± 5 años) y zona de residencia 952 casos incidentes de CM histológicamente confirmado con 998 controles sanos poblacionales. Se genotipificaron variantes en los genes CYP1A1, CYP1B1, GSTM1 y GSTT1 por discriminación alélica y PCR multiplex. En una submuestra de mujeres, se determinaron 105 marcadores de ancestría. Resultados: Se observó un aumento del riesgo de CM, independiente de otros factores de riesgo, entre las portadoras del genotipo CYP1B1 G119T (T/T vs. G/G: RM=1.9; 95%CI 1.4-2.5). Conclusiones: Nuestros resultados soportan la existencia de susceptibilidad genética para CM conferida por la variante CYP1B1 G119T en mujeres mexicanas.


Subject(s)
Humans , Female , Adolescent , Adult , Middle Aged , Aged , Young Adult , Breast Neoplasms/genetics , Cytochrome P-450 CYP1A1/genetics , Polymorphism, Single Nucleotide , INDEL Mutation , Cytochrome P-450 CYP1B1/genetics , Glutathione Transferase/genetics , Breast Neoplasms/epidemiology , Case-Control Studies , Risk , Africa/ethnology , Multiplex Polymerase Chain Reaction , Mexico/epidemiology
15.
Journal of Forensic Medicine ; (6): 271-276, 2017.
Article in Chinese | WPRIM | ID: wpr-984891

ABSTRACT

OBJECTIVES@#To study the genetic polymorphisms of 30 insertion/deletion (InDel) loci and evaluate their forensic application in Ewenki ethnic group from Inner Mongolia.@*METHODS@#Peripheral blood samples were collected from 87 unrelated healthy individuals in Ewenki ethnic group. Genomic DNA were extracted, and 30 InDel loci of the samples were multiplex amplified and genotyped. Hardy-Weinberg balance tests were preformed for all loci and genetic parameters were calculated by modified PowerStats v1.2 software. The linkage disequilibrium between loci were tested by SNPAnalyzer v2.0 software. Based on the allele frequencies of 30 InDel loci, the genetic relationships between Ewenki ethnic group and other populations were evaluated by analysis of molecular variance, principal component analysis and phylogenetic reconstruction.@*RESULTS@#After correction, 30 InDel loci conformed to Hardy-Weinberg equilibrium. It was found that the pairwise InDel loci were in linkage equilibrium after Bonferroni correction. The results of population genetics indicated that Ewenki ethnic group had close genetic relationships with Henan Han and Beijing Han populations; whereas it was significantly different from several populations in Europe and Mexico.@*CONCLUSIONS@#There are relatively high genetic polymorphisms on 30 InDel loci of Ewenki ethnic group from Inner Mongolia, which can be used as a helpful supplement application for STR detection system.


Subject(s)
Humans , Asian People/genetics , Beijing , China/epidemiology , DNA , Ethnicity/genetics , Gene Frequency , Genetic Loci , Genetics, Population , Genotype , INDEL Mutation , Linkage Disequilibrium , Microsatellite Repeats , Phylogeny , Polymorphism, Genetic , Social Behavior
16.
Egyptian Journal of Medical Human Genetics [The]. 2017; 18 (2): 187-191
in English | IMEMR | ID: emr-188481

ABSTRACT

Background: Angiotensin I-converting enzyme [ACE] has two homologous catalytic domains, the N- and C-domains. Our previous study suggested that Alu insertion [I allele] in the intron 16 of ACE resulted in premature codon termination. The I allele has only one active site in the N-domain while the Alu deletion [D allele] still has two active sites of ACE. Therefore the effect of I/ D polymorphism of ACE on the enzyme's ability to catalyse bradykinin is still not widely known


Aims: This study aimed to examine the serum bradykinin level in hypertensive patients with I/D polymorphism of ACE, who were treated with ACE inhibitor


Subjects and methods: The serum bradykinin and I/D polymorphism have been detected in 64 hypertensive patients taking ACE inhibitor [lisinopril or captopril] for at least eight weeks with good medication adherence. The binding affinity of ACE with its receptor was calculated by molecular docking


Results: The findings show that genotype II is more frequent in the population the researchers observed [53.12%] compared to ID [23.44%] and DD [23.44%] variances. On the other hand, the bradykinin level is not affected by genotype of the ACE genes on the population. Bradykinin increases in patients with genotype II who are given captopril, but decreases in patients treated with lisinopril. Nevertheless, there is no statistically significant difference


Conclusion: This study suggests that the polymorphism might not significantly affect the serum bra-dykinin level in hypertensive patients taking ACE inhibitors


Subject(s)
Humans , Female , Male , Adult , Middle Aged , Aged , Aged, 80 and over , Peptidyl-Dipeptidase A , Polymorphism, Genetic , Alu Elements , INDEL Mutation , Angiotensin-Converting Enzyme Inhibitors , Bradykinin , Angiotensins
17.
The Korean Journal of Gastroenterology ; : 181-186, 2017.
Article in English | WPRIM | ID: wpr-7492

ABSTRACT

Multiple endocrine neoplasia type 1 (MEN1) syndrome is a relatively rare disease, characterized by the occurrence of multiple endocrine tumors in the parathyroid and pituitary glands as well as the pancreas. Here, we report a case of MEN1 with neuroendocrine tumors (NETs) in the stomach, duodenum, and pancreas. A 53-year-old man visited our hospital to manage gastric NET. Five years prior to his visit, he had undergone surgery for incidental meningioma. His brother had pancreatic nodules and a history of surgery for adrenal adenoma. His brother's daughter also had pancreatic nodules, but had not undergone surgery. The lesion was treated by endoscopic submucosal dissection and diagnosed as a grade 1 NET. Another small NET was detected in the second duodenal portion, resected by endoscopic submucosal dissection, which was also diagnosed as a grade 1 NET. During evaluation, three nodules were detected in the pancreas, and no evidence of pituitary, parathyroid tumors, or metastasis was observed. After surgery, the pancreatic lesions were diagnosed as NETs, with the same immunohistochemical patterns as those of the stomach and duodenum. Genetic testing was performed, and a heterozygous mutation was detected in the MEN1 gene, which is located on 11q13.


Subject(s)
Humans , Middle Aged , Adenoma , Duodenum , Endoscopy , Genetic Testing , Germ-Line Mutation , INDEL Mutation , Meningioma , Multiple Endocrine Neoplasia Type 1 , Neoplasm Metastasis , Neuroendocrine Tumors , Nuclear Family , Pancreas , Pituitary Gland , Rare Diseases , Siblings , Stomach
19.
Saudi Medical Journal. 2015; 36 (2): 176-180
in English | IMEMR | ID: emr-178073

ABSTRACT

To investigate the association between angiotensin-converting enzyme [ACE] insertion/deletion [I/D] polymorphism and rheumatic heart disease [RHD] in Saudi patients. A case-control study was conducted in Saudi RHD patients. Genomic DNA was isolated from 99 RHD patients attending the Pediatric Cardiology Clinic at the Maternity and Children Hospital, Al-Madinah, Saudi Arabia from March 2013 to June 2014, and from 145 age- and gender-matched controls. Patient clinical records were reviewed to report major and minor modified Jones' criteria for diagnosis. The diagnosis was confirmed by echocardiography. The ACE I/D polymorphism was identified by polymerase chain reaction. A significant difference in ACE D allele carriage [DD+ID] distribution between RHD cases and controls was identified [p=0.02, odds ratio = 3.6, 95% confidence interval: 1.2-10.8]. The D allele carriage was significantly associated with development of mitral valve lesions alone [p=0.03]. The ACE I/D polymorphism is associated with an increased risk of RHD in the Saudi population. Further studies are needed to confirm our findings and to understand the molecular mechanisms underlying this association


Subject(s)
Humans , Male , Female , INDEL Mutation , Polymorphism, Genetic , Rheumatic Heart Disease , Case-Control Studies , Polymerase Chain Reaction
20.
Chinese Journal of Medical Genetics ; (6): 410-414, 2015.
Article in Chinese | WPRIM | ID: wpr-239457

ABSTRACT

<p><b>OBJECTIVE</b>To analyze the genetic data of 30 insertion and deletion polymorphisms (InDel) loci included in an InvestigatorR DIPplex diagnostic kit, and to evaluate the forensic application in ethnic Tibetan population from China.</p><p><b>METHODS</b>By detecting 226 unrelated individuals with the Investigator(R) DIPplex kit, allelic frequencies and population genetics parameters of the 30 InDels were statistically analyzed and compared with available data derived from other populations from various regions.</p><p><b>RESULTS</b>After the Bonferroni correction at a 95% significance level (P=0.0017), no significant departures from the Hardy-Weinberg equilibrium were observed except for the HLD114 locus. Linkage disequilibrium test showed no significant allelic association between all 30 loci after the Bonferroni's correction. The average heterozygosity (Ho) of all loci was 0.4125, the mean discrimination power (DP) was 0.5618, the mean polymorphism information content (PIC) was 0.3280, and the combined discrimination power (TDP) was 0.999999999990. The combined power of exclusion of all loci was 0.987 849 91 in trio cases and 0.94977125 in duo cases. Genetic distance between Tibetan and Han from Beijing was minimum (0.0068) in the 5 populations, while genetic distance between Tibetan and Uygur was maximal (0.0215).</p><p><b>CONCLUSION</b>Multiplex detection has revealed that these 30 InDel loci have a moderate distribution of genetic polymorphism among ethnic Tibetan group residing in Tibet, China.</p>


Subject(s)
Adult , Female , Humans , Male , Middle Aged , Young Adult , Asian People , Ethnology , Genetics , Gene Frequency , INDEL Mutation , Linkage Disequilibrium , Polymorphism, Genetic , Tibet , Ethnology
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