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Identification of a novel allele HLA-DRB1*1219.

Xiang-min NIE ; Yi ZHANG ; Yun-hai FANG ; Yong-hong SONG ; Yun-long ZHUANG ; Yan LIU ; Chuan-fu ZHU

Chinese Journal of Medical Genetics.2011;28(1):99-102. doi:10.3760/cma.j.issn.1003-9406.2011.01.022

OBJECTIVETo identify a novel HLA DRB1 allele in a Chinese leukemia family.

METHODSA new HLA-DRB1 allele was initially detected by polymerase chain reaction-sequence specific primer and unusual reaction pattern by Luminex RSSO, then DNA sequencing was performed to identify the sequence of the novel allele.

RESULTSThe DNA sequencing revealed the presence of the new allele which differs from the closest matching HLA-DRB1*120201 by a single nucleotide substitution at position (341 C > T in exon 2), resulting in an amino acid change from Ala to Val at coden 85.

CONCLUSIONA novel allele was confirmed by DNA sequencing and has been designated HLA-DRB1*1219 by the WHO Nomenclature Committee.

Alleles ; Amino Acid Sequence ; Base Sequence ; HLA-DR Antigens ; genetics ; HLA-DRB1 Chains ; Humans ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA

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A study on allele frequencies and mismatching proportion of HLA-A, B, Cw, DRB1 and DQB1 on high-resolution donor-recipient typing in Chinese Han population.

Yang LI ; Jun HE ; Xiao-jing BAO ; Qiao-cheng QIU ; Xiao-ni YUAN ; Chao XU ; Wen-ying DI ; Jian ZHANG ; Xue-ming XU ; Zi-xing CHEN

Chinese Journal of Medical Genetics.2011;28(1):92-98. doi:10.3760/cma.j.issn.1003-9406.2011.01.021

OBJECTIVETo analyze the allele frequencies and polymorphism of human leukocyte antigens (HLA) -A, B, Cw, DRB1 and DQB1 between donors-recipients on high-resolution typing; and to analyze the matching and mismatching proportion between donors and recipients.

METHODSHLA high-resolution types were determined by sequence based typing (SBT), sequence specific oligonucleotide probe (SSOP) and sequence specific primer (SSP) on 2540 unrelated Chinese Han individuals including 1168 recipients and 1372 donors, then statistical analyses were carried out.

RESULTSForty-four HLA-A alleles were detected, and among them the frequencies of A*1101, A*2402, A*0201, A*0207, A*3303, A*0206 and A*3001 exceeded 0.05, and accounted for 80.4%. Eighty-one HLA-B alleles were detected, and the frequencies of B*4001, B*4601, B*5801, B*1302 and B*5101 exceeded 0.05, and accounted for 43.0% of total. There were 44 HLA-Cw alleles, among them the frequencies of Cw*0702, Cw*0102, Cw*0304, Cw*0801, Cw*0602, Cw*0303, Cw*0302 and Cw*0401 exceeded 0.05, and were 80.3% of total. There were 61 HLA-DRB1 alleles, the frequencies of DRB1*0901, DRB1*1501, DRB1*1202, DRB1*0803, DRB1*0701, DRB1*0405, DRB1*0301 and DRB1*1101 exceeded 0.05, and were 70.1% of total. Finally, 22 HLA-DQB1 alleles were detected, the frequencies of DQB1*0301, DQB1*0303, DQB1*0601, DQB1*0602, DQB1*0202, DQB1*0302, DQB1*0401, DQB1*0502 and DQB1*0201 exceeded 0.05, and they were 87.4% of total. All the five loci were of heterozygote deficiency. The HLA-A, B and DRB1 loci conformed to Hardy-Weinberg equilibrium (HWE) (P > 0.05); but HLA-Cw and HLA-DQB1 loci did not (P < 0.05). Except several particular genotypes, all the five loci conformed to HWE. After comparing data between donors and recipients, only 22.4% of recipients found HLA matched donors (10/10); 24.6% of recipients found single HLA allele mismatched donors (9/10); 26.3% of recipients had two HLA alleles mismatched donors (8/10).

CONCLUSIONThe characteristics of allele frequencies and polymorphism of HLA-A, B, Cw, DRB1 and DQB1 on high-resolution typing in Chinese Han population is valuable for donor searching in unrelated hematopoietic stem cell transplantation, and it provides genetic basis for donor registry and usage of donor resource for Chinese Marrow Donor Program.

China ; ethnology ; Gene Frequency ; Genetics, Population ; HLA-A Antigens ; genetics ; HLA-B Antigens ; genetics ; HLA-C Antigens ; genetics ; HLA-D Antigens ; genetics ; HLA-DQ Antigens ; genetics ; HLA-DQ beta-Chains ; HLA-DR Antigens ; genetics ; HLA-DRB1 Chains ; Hematopoietic Stem Cell Transplantation ; Histocompatibility Antigens Class I ; genetics ; Histocompatibility Testing ; Humans ; Tissue Donors

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Sequence analysis of a novel human leukocyte antigen allele B*5827.

Chao-xia LU ; Na ZHU ; Qian ZHANG ; Hong HUANG ; Bing-shen KE ; Huai-shui HOU ; Bai-jun SHEN

Chinese Journal of Medical Genetics.2011;28(1):88-91. doi:10.3760/cma.j.issn.1003-9406.2011.01.020

OBJECTIVETo investigate the molecular basis for a novel human leukocyte antigen (HLA) allele B*5827.

METHODSDNA from the proband was analyzed by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing. The amplified product was sequenced bidirectionally.

RESULTSAbnormal HLA-B locus was observed and its nucleotide sequence was different from the known HLA-B allele sequences, with highest homology to HLA-B*5820 allele. It differs from HLA-B*5820 by 8 nucleotide substitutions in exon 3, i.e., nt 290 (G > C), nt 346 (T > A), nt 390 (A > C), nt 404 (G > C), nt 413 (C > G), nt 471 (A > G), nt 486 (A > G) and nt 487 (C > A), resulting in an amino acid change from ser > arg at nt 97, phe >tyr at nt 115, ser > arg at nt 130, thr > ala at nt 157 and thr > glu at nt 162. Nucleotide differences of nt 404 (G > C) and nt 413( C > G) did not change amino acid.

CONCLUSIONThe sequences of the novel allele have been submitted to GenBank (access No.GU071234). A novel HLA class I allele B*5827 has been officially assigned by the WHO HLA Nomenclature Committee in Jan. 2010.

Alleles ; Base Sequence ; Cloning, Molecular ; Genotype ; HLA-B Antigens ; chemistry ; genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA

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Cloning and sequence analysis of 5'untranslated region of human ABO gene.

Ying LIU ; Xian-guo XU ; Kai-rong MA ; Xiao-fei LAN ; Xiao-zhen HONG ; Fa-ming ZHU ; Hang-jun LV ; Li-xing YAN

Chinese Journal of Medical Genetics.2011;28(1):83-87. doi:10.3760/cma.j.issn.1003-9406.2011.01.019

OBJECTIVETo clone and investigate the polymorphism of the 5'-untranslated region (5'-UTR) of the human ABO gene, in order to provide the basis for exploring the transcriptional regulation of the human ABO histo-blood group genes.

METHODSABO phenotypes of 30 unrelated healthy blood donors were determined by serological technique, their genotypes were analyzed by sequencing the exons 6 and 7 of the ABO gene. Nearly 5 kb of the 5'-UTR of ABO gene was obtained by PCR amplification and sequencing was performed bidirectionally. Haplotypes of samples with heterozygous sites in the 5'-UTR of ABO gene were separated and analyzed after cloning.

RESULTSTwenty polymorphic sites were identified in these samples where ABO genotypes were consistent with serological phenotypes. It included sixteen nucleotide sequence variations, one 8 bp deletion, one 6 bp deletion/insertion, one 36 bp insertion and one 43 bp repeats. Among them, 11 were novel polymorphic sites. Seven different haplotypes of 5'-UTR of ABO gene were defined to the cis/trans linkage of those mutations.

CONCLUSIONThere were polymorphisms in the 5'-UTR of ABO gene and the nucleotide sequences near the proximal promoter were conservative.

5' Untranslated Regions ; genetics ; ABO Blood-Group System ; genetics ; Cloning, Molecular ; Genotype ; Haplotypes ; Humans ; Polymorphism, Genetic ; Sequence Analysis, DNA

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Genetic variation and association of STEAP4 gene with metabolic syndrome in Chinese Uygur patients.

Yan-ying GUO ; Nan-fang LI ; Chang-min WANG ; Zhi-tao YAN ; Ju-hong ZHANG ; Hong-mei WANG ; Ling ZHOU ; Wen-li LUO

Chinese Journal of Medical Genetics.2011;28(1):78-82. doi:10.3760/cma.j.issn.1003-9406.2011.01.018

OBJECTIVETo investigate the genetic variations of the six transmembrane epithelial antigen of prostate 4 gene (STEAP4) in Chinese Uygur patients with metabolic syndrome (MetS) and to analyze the association of the representative genetic variations of STEAP4 gene with MetS in the population.

METHODSThe sequences of STEAP4 gene functional region (all exons, exon-intron boundaries and the putative promoter region, including the -1 kb 5'and 3'untranslated regions) were amplified and sequenced for patients with MetS. The representative variations were selected based on the function (missense mutation) and linkage disequilibrxium (γ² > 0.8) and genotyped with TaqMan-PCR method in 1910 general populations (682 MetS and 1228 non-MetS controls). The subjects were selected from the cross-sectional study of obesity, hypertension, diabetes, dyslipidemia from January to February 2007 among Uygur people, a relatively isolated population with a relatively homogeneous environment, in Hextian area in Xinjiang Uygur Autonomous Region.

RESULTS(1) Fourteen novel and six known single nucleotide polymorphisms (SNPs) or mutations, including 2 missense mutations, were identified at the functional region of STEAP4 gene in 96 Uygur patients with MetS. The minor allele frequencies of the SNPs of STEAP4 gene in Uygur population were different from that in European and Chinese Han in Beijing area. (2) The SNP 364G/A (rs34741656, Ala122Thr) was significantly associated with MetS [dominant model P = 0.034, OR = 0.757(95%CI: 0.584-0.982) adjusted for age and gender], and was associated with fasting blood glucose (FBG) (P = 0.049) and 2-hour postprandial glucose (2HPG) (P = 0.027) levels in controls. In this SNP, the AA carriers had lower blood glucose levels compared with subjects carrying GG and GT genotypes. (3) The common haplotype H4 (rs8122/rs1981529/ rs34741656, G-A-A), may be associated with MetS (permutation P = 0.089).

CONCLUSIONSTEAP 4 genetic polymorphisms may be associated with MetS risk in Chinese Uygur population.

Adult ; Aged ; Asian Continental Ancestry Group ; genetics ; China ; ethnology ; Ethnic Groups ; genetics ; Female ; Genetic Predisposition to Disease ; Haplotypes ; Humans ; Male ; Membrane Proteins ; genetics ; Metabolic Syndrome ; etiology ; genetics ; Middle Aged ; Oxidoreductases ; genetics ; Polymorphism, Single Nucleotide

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Association of apolipoprotein A5 gene polymorphism with coronary heart disease in Uygur population of Xinjiang.

Shan YUAN ; Yi-tong MA ; Xiang XIE ; Yi-ning YANG ; Zhen-yan FU ; Xiang MA ; Xiao-mei LI ; Yang XIANG ; Fen LIU ; Bang-dang CHEN

Chinese Journal of Medical Genetics.2011;28(1):73-77. doi:10.3760/cma.j.issn.1003-9406.2011.01.017

OBJECTIVETo investigate the association of the -12238T/C polymorphism of apolipoprotein A5 (APOA5) gene with coronary heart disease (CHD) and the influence of serum lipid levels in Chinese Uygur population of Xinjiang.

METHODSThe -12238T/C polymorphism of APOA5 gene in 344 patients with CHD and 408 controls was analyzed by polymerase chain reaction-restriction fragment length polymorphism; the serum lipid levels were detected as well.

RESULTSThe frequencies of CC, TC and TT genotype were 6.69%, 43.31% and 50.00% in the CHD group, while they were 14.95%, 45.10% and 39.95% in the control group. There was significant difference in the distribution of genotypes between the two groups (P < 0.01). Logistic regression analyses adjusted for age, gender, smoking, serum total cholesterol, presence of hypertension and diabetes revealed that individuals carrying CC genotype had an increased risk of CHD compared with TT genotype (OR = 0.328, 95%CI: 0.154-0.700). There was also significant difference in serum triglyceride level in genotypes between these two groups (P < 0.01). Patients in CHD group who carried CC and TC genotypes had lower serum triglyceride level than the TT genotype carriers.

CONCLUSIONThe -12238T/C polymorphism of APOA5 gene has influence on the serum triglyceride level in Uygur population of Xinjianxg. This polymorphism might be associated with development of CHD, and the CC genotype might be a protective factor in the development of CHD.

Adult ; Aged ; Apolipoprotein A-V ; Apolipoproteins A ; genetics ; Asian Continental Ancestry Group ; genetics ; China ; ethnology ; Coronary Disease ; blood ; ethnology ; genetics ; Ethnic Groups ; genetics ; Female ; Genotype ; Humans ; Logistic Models ; Male ; Middle Aged ; Polymorphism, Genetic ; Triglycerides ; blood

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No association of K469E polymorphism of intercellular adhesion molecule-1 with rheumatoid arthritis.

Zhao-lin YUAN ; Xiao-xue ZHANG ; Bo SHEN ; Min ZHU ; Wei XU ; Jun LI ; Jian-xin LV

Chinese Journal of Medical Genetics.2011;28(1):69-72. doi:10.3760/cma.j.issn.1003-9406.2011.01.016

OBJECTIVETo investigate the association of the intercellular adhesion molecule-1 gene (ICAM-1) K469E polymorphism and rheumatoid arthritis (RA).

METHODSTwo hundred and seventy-five patients with RA and 254 healthy individuals were collected and enrolled in the study. The K469E polymorphism of ICAM-1 gene was analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).

RESULTSThe genotype frequencies of KK, KE and EE of K469E polymorphism were 0.535,0.411 and 0.054 respectively in the RA patients, and 0.512,0.437 and 0.051 respectively in the healthy individuals, and there was no significant difference between the two groups (chi² = 0.371, P = 0.831). The frequencies of the K469 allele were 0.74 and 0.73 in the RA patients and the controls respectively (chi² = 0.127, P = 0.721, OR = 1.051, 95%CI:0.800-1.381). No significant difference was observed in KK + KE genotype frequencies between the two groups (P = 0.863), with an odds ratio of 0.935 (95%CI:0.436-2.005).

CONCLUSIONThe K469E polymorphism of the ICAM-1 gene was not associated with the susceptibility of rheumatoid arthritis.

Adult ; Aged ; Aged, 80 and over ; Arthritis, Rheumatoid ; genetics ; Disease Susceptibility ; Female ; Genotype ; Humans ; Intercellular Adhesion Molecule-1 ; genetics ; Male ; Middle Aged ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length

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Negative association of STAMP2 gene polymorphisms with essential hypertension in Xinjiang Uygur population.

Yun-wei BI ; Chang-min WANG ; Zhi-tao YAN ; Nan-fang LI ; Yan-ying GUO ; Hong-mei WANG ; Xiao-guang YAO ; Deng-pan LIANG

Chinese Journal of Medical Genetics.2011;28(1):64-68. doi:10.3760/cma.j.issn.1003-9406.2011.01.015

OBJECTIVETo investigate the relationship between the genetic polymorphisms of the six transmembrane protein of prostate 2 gene (STAMP2) and essential hypertension in Xinjiang Uygur population.

METHODSThe sequences of STAMP2 gene functional region were sequenced in Xinjiang Uygur population with hypertension. The representative variations selected were genotyped by TaqMan-PCR method in 2047 Uygur individuals, including 810 patients with hypertension and 1237 healthy subjects. The association of the genetic variations of the STAMP2 gene with hypertension in Uygur was analyzed.

RESULTSIn the three representative variations (rs8122, rs1981529 and rs34741656) genotyped, there were no significant differences in genotype distribution and allele frequencies between the essential hypertension and control groups (P > 0.05). In ANCOVA analysis, none of the polymorphisms was significantly associated with systolic blood pressure and diastolic blood pressure (P > 0.05). There were no significant differences in haplotype frequencies between the two groups either(P > 0.05).

CONCLUSIONThere was no association of the three polymorphisms (rs8122, rs1981529 and rs34741656) in the STAMP2 gene with essential hypertension in Xinjiang Uygur population.

Adult ; Aged ; Asian Continental Ancestry Group ; genetics ; China ; ethnology ; Ethnic Groups ; genetics ; Female ; Humans ; Hypertension ; genetics ; Logistic Models ; Male ; Membrane Proteins ; genetics ; Middle Aged ; Oxidoreductases ; genetics ; Polymorphism, Genetic

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Association of haptoglobin 1/2 polymorphism with coronary heart disease in Chinese.

Hai-bo LIU ; Yu-ping SHI ; Xiao-fang GUO ; Jiang SHAN ; Geng XU

Chinese Journal of Medical Genetics.2011;28(1):60-63. doi:10.3760/cma.j.issn.1003-9406.2011.01.014

OBJECTIVETo assess the association of haptoglobin (HP)1/2 polymorphism with coronary heart disease (CHD) in Chinese Hans.

METHODSOne hundred and eighty-nine CHD patients and 242 healthy controls confirmed with angiography were recruited. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was utilized to genotype the HP1 and HP2 alleles and genotype frequencies in cases and controls were compared.

RESULTSThe frequency of HP2-2 genotype was significantly higher in CHDs than in controls (0.54 vs.0.35, P = 0.000). The HP2-2 genotype significantly increased the risk for CHD in univariable analysis (OR = 2.166, 95%CI: 1.467-3.196). Multifactor Logistic regression analysis indicated that HP2-2 genotype is an independent risk factor to CHD (P = 0.002; OR = 2.101, 95%CI: 1.311-3.367). Similarly, the HP2 allele frequency in the CHD group was significantly higher than that in the control subjects (0.74 vs.0.61, P = 0.000).

CONCLUSIONThe HP2-2 genotype is associated with CHD in Chinese. HP2-2 genotype may be an independent risk factor to CHD, and HP2 allele may be a genetic susceptibility factor to CHD in Chinese.

Adult ; Aged ; Asian Continental Ancestry Group ; genetics ; Coronary Disease ; genetics ; Female ; Gene Frequency ; Genotype ; Haptoglobins ; genetics ; Humans ; Logistic Models ; Male ; Middle Aged ; Polymorphism, Genetic

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Genetic counseling and clinical outcome of fetus with de novo chromosomal aberrations.

Qi-chang WU ; Hui KONG ; Li SUN ; Wen-bo WANG ; Yun-sheng GE ; Ya-song XU ; Yu-lin ZHOU

Chinese Journal of Medical Genetics.2011;28(1):56-59. doi:10.3760/cma.j.issn.1003-9406.2011.01.013

OBJECTIVETo analyze the chromosome rearrangements and clinical outcome in fetus detected at prenatal diagnosis, and provide information for genetic counseling about de novo chromosomal aberrations.

METHODSFrom January 2006 to December 2009, we found 12 cases of de novo chromosomal aberrations in 2 583 cases of prenatal cytogenetic analyses and reviewed the karyotypes, other experimental analyses data, fetal ultrasound findings and clinical outcomes.

RESULTSOut of the 12 de novo chromosomal aberrations, 10 had unbalanced translocations and 2 had balanced reciprocal translocations. Eight of the 10 unbalanced translocation cases were terminated therapeutically, and 2 were delivered with full term. Neonates were phenotypically normal in the 2 cases with unbalanced translocations, but 1 had language retardation when followed up. The two balanced translocation cases were delivered with full term, and the neonates were phenotypically normal and clinical examinations were normal too.

CONCLUSIONDetailed cytogenetic and molecular study will be adjunctive tools for predicting the phenotype of fetus with de novo chromosomal aberrations. Fetal ultrasound examination will provide convincible demonstration to determine the outcome of pregnancy.

Chromosome Aberrations ; Female ; Genetic Counseling ; Humans ; In Situ Hybridization, Fluorescence ; Pregnancy ; Pregnancy Outcome ; Prenatal Diagnosis

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