[Association study of telomere length with idiopathic male infertility].

Telomeres are evolutionary conserved, multifunctional DNA-protein complexes located at the ends of eukaryotic chromosomes. Telomeres maintain chromosome stability and genome integrity and also play an important role in meiosis which aid in synapsis, homologous recombination, and segregation. Sperm telomere has been reported to play an important role in fertilization and embryo development. Nowadays, the association between telomere and reproduction is one of the major areas of interest, however whether sperm telomere associated with male infertility is not clear. In this study, in order to find out the association between Chinese idiopathic infertility and sperm telomere length, we analyzed the difference of sperm telomere length between idiopathic infertile men and normal fertile men, as well as the correlations between sperm telomere length and human semen characteristics. We analyzed 126 Chinese idiopathic infertile men and 138 normal fertile men for sperm telomere length by using quantitative PCR. We found that the relative sperm mean telomere length of infertile men was significantly shorter than that of fertile men (2.894 ± 0.115 vs. 4.016 ± 0.603, P=5.097 x 10⁻5). Both sperm count and semen progressive motility are related with telomere length. Our results suggest that sperm telomere length is associated with idiopathic male infertility of China and we proposed the possibility that shorter telomeres in sperm chromosome will reduce spermatogenesis and sperm functions, which finally affected the fertility of male.

Determination of the 3'UTR region of HLA-B*53:01:03 sequence by next generation sequencing.

The 3'UTR of the HLA-B*53:01:03 allele has been determined by next generation sequencing.

[Association of polymorphisms of PTPN22 and PADI4 genes with rheumatoid arthritis in Yunnan].

OBJECTIVE: To assess the association between genetic polymorphisms of 7 SNPs in PTPN22 and PADI4 genes and susceptibility to rheumatoid arthritis in Yunnan. METHODS: A case-control study was carried out on 192 patients of rheumatoid arthritis and 288 healthy controls. Genotypes of rs33996649 and 1858 loci within PTPN22 gene, and rs11203366 and rs874881 loci within PADI4 gene were determined with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Genotypes of rs1635579, rs2428736 and rs2240340 in PADI4 gene were determined with pyrosequencing. RESULTS: The frequencies of alleles and genotypes of rs2240340 locus in PADI4 gene showed a significant difference between rheumatoid arthritis and controls in Yunnan population (P U+003C 0.05). CONCLUSION: Our results suggested that rs2240340 in PADI4 gene is associated with susceptibility to rheumatoid arthritis in Yunnan.

[Distribution of HLA-G 14 bp insertion/deletion polymorphism and their associations with HLA-A alleles in four Chinese ethnic groups].

Recently, a 14 bp insertion/deletion polymorphism (+14 bp/-14 bp) in exon 8 of the human leucocyte antigen-G (HLA-G) gene has been widely recognized to associate with recurrent miscarriage, autoimmune diseases, hepatocellular carcinoma and other diseases. Our previous studies have shown the distribution characteristics of linguistic family for HLA-G 14 bp insertion/deletion in different ethnic groups. In the present study, we investigated the distribution of HLA-G 14 bp insertion/deletion polymorphism and their subsequent associations with HLA-A alleles in Tu, Yugu, Lisu and Nu ethnic populations based upon the HLA-A genotyping data. Our results showed that the frequencies of the 14 bp insertion/deletion polymorphism were diverse in these four populations while that in the same linguistic subfamily was similar. The significant difference in different linguistic subfamily except for Han and Mongolian language subfamily was identified. In addition, the 14 bp insertion was found to associate with HLA-A alleles in different ethnic populations.

[Association between six single nucleotide polymorphisms of EGLN1 gene and adaptation to high-altitude hypoxia].

To investigate the association between SNPs located in 5'UTR and intron of prolyl hydroxylase 2 (EGLN1 or PHD2) and adaptation to high-altitude hypoxia, the SNPs (rs2066140, rs2808584, rs2491405, rs2486741, rs2486734 and rs21533646) of EGLN1 gene were genotyped using Sequenom MassArray genotyping system in 152 unrelated healthy Tibetan individuals (3 650 m altitude) and 192 Han (5 00 m altitude), and the haplotypes of these SNPs were constructed and analyzed. Our results showed all the homozygous genotypes of six SNPs loci were significantly different between the two groups (P<0.05). The frequencies of haplotypes G-G (rs2066140 and rs2808584) and G-C (rs2486741 and rs2486734) of high-altitude group were significantly different from low-altitude group (P<0.05). In addition, the frequencies of haplotypes C-A (rs2066140 and rs2808584) and C-T (rs2486741 and rs2486734) of high-altitude group were significantly lower than those in low-altitude group (P<0.05). Our results indicate that the polymorphism of homozygous genotype in six SNPs and their haplotypes were associated with adaptation to high-altitude hypoxia.

[Association between gene polymorphisms and myocardial infarction in Han Chinese of Yunnan province].

OBJECTIVE: To determine frequencies of genetic polymorphisms of coagulation factor VII (FVII), coagulation factor FXII (FXII), fibrinogen (FBG) and 9p21 in ethnic Han Chinese from Yunnan province, and to assess the association between such polymorphisms and onset of myocardial infarction (MI). METHODS: One hundred and forty-two patients with MI and 192 healthy controls were analyzed. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and pyrosequencing were used to determine the genotypes of FVII, FXII, FBG and 9p21. RESULTS: No significant difference was found in the frequencies of R353Q, 5'F7, C46T, -148C/T, rs1333049 and rs4977574 loci between the two groups (P> 0.05). However, the frequencies of AA of -455G/A, T and TT of rs1333040, T and TT of rs10116277 and G and GG of rs2383207 were significantly higher in MI group compared with the controls (P< 0.05), whilst the frequencies of CT of rs1333040 and GT of rs10116277 were significantly lower in MI group compared with the controls (P<0.05). CONCLUSION: Polymorphisms of FVII, FXII, -148C/T of FBG and rs1333049 of 9p21 were not associated with myocardial infarction. Polymorphisms of -455G/A of FBG and rs1333040, rs10116277 and rs2383207 of 9p21 may be associated with MI in ethnic Han Chinese from Yunnan province.

[Detection and preliminary study of a family carrying a CCR5Δ32 deletional mutation].

OBJECTIVE: To investigate the frequencies of chemokine (C-C motif) receptor 5 gene (CCR5)Δ32 deletional mutation of in Han and Dai populations from Yunnan province. Immortalized cell lines were derived from a family carrying the CCR5Δ32 mutation. METHODS: Blood samples of 346 Han and 355 Dai individuals were collected for genotyping. The coding regions of CCR5 gene were amplified with PCR followed by agarose gel electrophoresis. Suspected mutations were verified with DNA sequencing. Immortalized cell lines were constructed by using Epstain Barr virus and cyclosporine A. The difference between the cell lines and original blood samples was verified with PCR. RESULTS: One ethnic Han individual was confirmed to be heterozygous for a deletional mutation by sequencing, which has led to discovery of a family with CCR5Δ32. Nine immortalized cell lines were established from this family, and no difference between the cell lines and original blood samples was detected by PCR. CONCLUSION: Together with previous reports, this study has indicated a significant difference in CCR5Δ32 among different ethnic groups in China. Established immortalized cell lines can also provide material for future research.

[Association between Alu insertion polymorphisms and HLA class I alleles in Chinese Lisu and Nu ethnic populations].

OBJECTIVE: To investigate the frequencies of HLA-Alu repeat polymorphisms (AluMICB, AluTF, AluHJ, AluHG and AluHF) in Chinese Lisu and Nu ethnic populations. METHODS: The frequencies of HLA-Alu repeat polymorphisms in above populations were determined with polymerase chain reaction (PCR). The associations between HLA-Alu repeat polymorphisms and HLA-A, HLA-B and HLA-C alleles were also analyzed. Phylogenetic trees were constructed with genetic distance calculated from the frequencies of HLA-Alu repeat polymorphisms. RESULTS: Frequencies of AluTF*2 and AluHF*2 were different between the two populations (P< 0.05), while those of other three insertions were similar. The strength of association between HLA-Alus and HLA alleles were different (P< 0.05) in the two populations. Although AluMICB*2 were associated with HLA-B*56:01 in both populations, the association was stronger in Lisu population (74.0%) but moderate in Nu population (30.7%). HLA-Alus were associated with particular HLA subtypes, e.g., AluHG*2 with certain HLA-A*02 subtypes. By phylogenetic analysis, Lisu and Nu were clustered together with southern Chinese and Thai populations. CONCLUSION: The distribution of HLA-Alus and the strength of associations between HLA-Alus and HLA class I alleles have varied between the two populations. Study of this association may facilitate identification of origins, evolution, progenitor haplotypes and recombination within the HLA class I region.

[Distribution of HLA-C genes and HLA C-B, A-C-B haplotypes in Jinuo, Maonan and Wa ethnic populations in southwest China].

OBJECTIVE: To investigate the distribution of human leukocyte antigen(HLA) class I genes and haplotypes in Jinuo, Maonan and Wa ethnic populations in southwest China. METHODS: Polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing by Luminex was performed to genotype the HLA-C alleles in unrelated healthy individuals in the three populations. HLA C-B, A-C-B haplotypes were computed by combining the previous HLA-A and -B genotyping data using Pypop7.0 software. RESULTS: Eighteen HLA-C genes were identified in the three populations, with 17, 13 and 15 HLA-C genes in Jinuo, Maonan and Wa populations respectively. The alleles with frequency of more than 10% from high to low were C*08:01, C*01:02, C*03:04 and C*07:02 in the Jinuo, C*03:04, C*01:02, C*07:02 and C*08:01 in the Maonan, and C*12:03, C*08:01, C*07:02 and C*04:01 in the Wa. The predominant HLA A-C-B haplotypes were A*02:07-C*01:02-B*46:01, A*11:01-C*08:01-B*15:02 and A*11:01-C*03:04-B*13:01 in the Jinuo, A*11:01-C*03:04-B*13:01, A*02:07-C*01:02-B*46:01, A*11:01-C*08:01-B*15:02 and A*02:03-C*07:02-B*38:02 in the Maonan, and A*11:01-C*08:01-B*15:02, A*11:01-C*12:03-B*15:32 and A*11:01-C*04:01-B*35:01 in the Wa, respectively. CONCLUSION: There were different characteristics in the distributions of HLA-C genes and HLA C-B, A-C-B haplotypes in the Jinuo, Maonan and Wa populations. However, haplotypes C*08:01-B*15:02 and A*11:01-C*08:01-B*15:02 with high frequencies were common in the three populations, which might be the common ancient haplotypes of southern Chinese population. The study of HLA genes and haplotypes in these populations may be of significance in the study of population genetics, transplantation and disease association.

[Establishment of B lymphoblastoid cell lines of Miao pedigree with Bardet-Biedl syndrome].

OBJECTIVE: To establish immortalized lymphoblastoid cell lines of a Miao core pedigree with Bardet-Biedl syndrome (BBS), in order to provide a long-term source of material for research. METHODS: With Epstein-Barr virus transformation of B cells and addition of cyclosporine A to inhibit the activity of T cells, fresh anticoagulated blood samples with heparin were collected from 12 members of the core pedigree, and were used to establish the immortalized lymphoblastoid cell lines of B lymphocytes. RESULTS: Twelve immortalized lymphoblastoid cell lines of the core BBS pedigree were obtained successfully. CONCLUSION: The immortalized B lymphoblastoid cell lines of the Miao pedigree with BBS can preserve the whole genome information and provide long-term research materials for BBS study.

[Association between diversity of hypoxia at different altitude and the polymorphism of EPAS1 gene].

OBJECTIVE: To study the selection effect of endothelial PAS domain protein 1 (EPAS1) gene induced by high altitude hypoxia environment. METHODS: Fourteen single nucleotide polymorphism sites (SNPs) of the EPAS1 gene were genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) in three Tibetan groups (58 samples from Tibetan living in an altitude of about 3700 meters above sea level, 47 from Qinghai province, about 3100 meters above sea level, 43 from Yunnan province, about 2500 meters above sea level), and Han of Shandong (47 samples, about 50 meters above sea level). RESULTS: There were significant differences of most SNP allelic, genotypic and haplotypic frequencies when comparing Han of Shandong, Tibetan of Yunnan with Tibetan of Tibetan and Qinghai. But no difference between Han of Shandong and Tibetan of Yunnan was found. CONCLUSION: The EPAS1 gene might be under hypoxic selection induced by high altitude.

[Polymorphic Alu insertions and their associations with HLA I alleles in Yugu and Zhuang ethnic populations].

Many studies have show that the structurally polymorphic Alu insertion within HLA class I region are useful tools for investigating the origin, evolution and recombination of HLA class I progenitor haplotypes and gene diversity in different ethnic populations. In the present study, we determined the frequencies of HLA-Alus (i.e., AluMICB, AluTF, AluHJ, AluHG, and AluHF) in Zhuang and Yugu ethnic populations at first. Then, combined with HLA genotyping data, we studied associations between HLA-Alus and HLA-A alleles in Zhuang, Yugu, Bulang, Dai, and Hani ethnic populations. Our results showed that (1) the frequencies of five HLA-Alus were 1.5%~35.8% and 9.2%~34.8% in Zhuang and Yugu, respectively; and (2) the results of association between HLA-A alleles and HLA-Alu showed strong association between AluHG insertion and HLA-A 02 subtypes in all populations, association between AluHJ insertion and HLA-A 2402 in all populations, and association between AluHJ insertion and HLA-A 1101, -A 2407 in Bulang. The present study suggested that the distribution of HLA-Alus as well as the associations between HLA-Alus and HLA class I alleles are variable in different ethnic populations. HLA Alus alone or together with the HLA class I alleles are informative genetic markers for the identification of HLA class I allele and variation of haplotype lineages in different populations.

[Variation of CAG repeats in coding region of ATXN2 gene in different ethnic groups].

Toinvestigate CAG repeats variation of ATXN2 gene coding region in six ethnic groups that live in comparatively different environments, to evaluate whether these variations are under positive selection, and to find factors driving selection effects, 291 unrelated healthy individuals were collected from six ethnic groups and their STR geneotyping was performed. The frequencies of alleles and genotypes were counted and thereby Slatkin's linearized Fst values were calculated. The UPGMA tree against this gene was constructed. The MDS analysis among these groups was carried out as well. The results from the linearized Fst values indicated that there were significant evolutionary differences of the STR in ATXN2 gene between Hui and Yi groups, but not among the other 4 groups. Further analysis was performed by combining our data with published data obtained from other groups. These results indicated that there were significant differences between Japanese and other groups including Hui, Hani, Yunnan Mongolian, and Inner Mongolian. Both Hui and Mongolian from Inner Mongolia were significantly different from Han. In conclusion, the six ethnic groups had their own distribution characterizations of allelic frequencies of ATXN2 STR, and the potential cause of frequency changes in rare alleles could be the consequence of positive selection.

[Study of nine single nucleotide polymorphism loci of human HIF1A gene in three Tibetan groups].

OBJECTIVE: To investigate the effect of hypoxia environment induced by altitude on hypoxia inducible factor 1α (HIF1A) gene. METHODS: Nine single nucleotide polymorphism (SNP) loci of the HIF1A gene from three Tibetan groups (Tibet, Qinghai Province and Yunnan Province) were genotyped using PCR-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS: For non-synonymous mutation SNP site, there was no significant difference among the three Tibetan groups, except for SNP rs11549465 between Tibet Tibetan and Yunnan Tibetan, as well as between Qinghai Tibetan and Yunnan Tibetan. Frequencies of genotypes and alleles in rs4899056, rs1957757, rs10873142 and rs3783752 had significant differences between Tibet Tibetan and Yunnan Tibetan, and between Qinghai Tibetan and Yunnan Tibetan (all P<0.05). We also observed that the difference was negatively correlated with the altitude. CONCLUSION: The results suggested that the HIF1A gene might be under hypoxic selection induced by high altitude in the three groups.

[Analysis of the 14 bp insertion/deletion polymorphism in human leukocyte antigen-G gene in Chinese Dai and Han ethnic groups in Yunnan Province].

A 14 bp insertion/deletion polymorphism (+14 bp/-14 bp) in exon 8 of HLA-G gene has been investigated extensively because this polymorphism was associated with HLA-G mRNA stability and could influence HLA-G mRNA expression. In the present study, we genotyped 14 bp insertion/deletion polymorphisms in the HLA-G gene in Dai and Han populations in Yunnan Province. The frequencies of +14 bp in Dai and Han were 31.97% and 40.87%, respectively. The frequency of +14 bp/+14 bp in Dai was lower (8.20%) than that of Han (17.31%). Nevertheless, the frequency of +14 bp/-14 bp was similar in both populations (47.54% in Dai and 47.11% in Han). When compared with other populations, the frequency of 14 bp insertion/deletion of Han was similar to others, whereas the Dai showed significant difference from others and presented it's specific characteristic. We assumed that the distribution characteristic of 14 bp insertion/deletion in Dai might be the results of random genetic drift, but the role of natural selection cannot be excluded.

[Establishment of immortalized cell lines and genetic stability evaluation for a family with spinocerebellar ataxia type 2].

OBJECTIVE: Immortalized cell lines of spinocerebellar ataxia type 2 (SCA2) with Parkinson disease symptoms were established in order to provide experimental material for future study. METHODS: The immortalized cell lines were constructed by using Epstein Barr virus and cyclosporine A. Microsatellite markers were detected to see whether there is any change between the cell lines and the original blood samples, and the genetic stability of the cell lines were evaluated. RESULTS: Twenty-five immortalized cell lines were established successfully from the family and the microsatellite markers were unchanged. CONCLUSION: The karyotypes of the immortal cell lines were normal and the cell lines were genetically stable.

Characterization of the novel KIR3DL1*0150213 and KIR3DL1*112 alleles using sequence-based typing.

KIR3DL1*0150213 differs from KIR3DL1*0150211 at 15 nucleotide positions. KIR3DL1*112 differs from KIR3DL1*03101 at 19 nucleotide substitutions.

[Study on the genetic stability of immortalized cell line of lymphocyte cell transformed by EB virus after long subculture process].

OBJECTIVE: To study the genetic stability of an immortalized cell line transformed by Epstein-Barr virus (EBV) after long subculture process. METHODS: In the present study, the genetic stability including chromosome diploidy, karyotypes and microsatellite DNA were evaluated with chromosome banding techniques and microsatellite DNA detection. The telomerase activity of the immortalized cell line was detected by using the telomerase assay kit. RESULTS: From passage 1 to 30, there were no change of the diploidy, karyotypes of chromosome and microsatellite DNA, and the telomerase activity is negative. CONCLUSION: This study indicates that the immortalized cell line remains stable genetically within limited passages.

[Comparative analysis of the complete mitochondrial genome between Tibetan and Han population].

OBJECTIVE: To construct the haplogroup and perform an analysis of mitochondrial whole-genome sequence in Tibetan and Han Chinese. Variations of nucleotide of mitochondrial DNA (mtDNA) were identified and compared between the Tibetan and Han population. METHODS: The mtDNA whole sequences of 40 Tibetan and 50 Han individuals were sequenced by an Applied Biosystems 3730 DNA automatic sequencer. The sequences were assembled using software phredPhrap16.0, and all assembled sequences were manually verified according to the criterion of rCRS (revised Cambridge Reference Sequence). The haplogroups of mtDNA were constructed using phylogenetic analysis according to the criteria of MITOMAP by Network method. The data were elucidated by integrated methods. RESULTS: Authors' results showed that all the pooled 90 subjects belonged to the Macrohaplogroup M and N, and were classified into 13 haplogroups. No differences were observed among the haplogroups of the two populations except for M9 haplogroup. A total of 21 variants were detected by comparing the mtDNA whole sequences between Tibetan and Han population; of those, 5 variants have not been reported before. In addition, we constructed the haplotypes of 5 variants harboring the D-loop region, and founded prominent difference in both supertype 1 and supertype 2 between Tibetan and Han population. CONCLUSION: The phylogenetic analysis indicates that the Tibetan and Han ethnic groups shared close maternal relationship in origin. The biological implication of the significant variants is worth elucidating; whether they are the results of adaptive selection or neutral selection or pathological variations need to be further studied.

[Distribution of HIV/AIDS associated CCR2-64 I allele of 14 Chinese ethnic populations in South China].

The purpose of the work is to investigate the frequencies and polymorphisms of HIV-1 resistant CCR2-64 I alleles in 14 Chinese populations in South China. The blood samples include 791 unrelated healthy individuals. Whole blood samples were collected randomly and their genomic DNA were extracted with OMEGA Blood Kits. Allelic frequencies were identified by PCR-RFLP analysis. 636 individuals were wild-type homozygous, 104 individuals were CCR2-64 heterozygote and 51 individuals were CCR2-64 homozygous. Distributions of the CCR2-64 I alleles among the populations were in accordance with Hardy-Weinberg equilibrium. The average allele frequencies was 13.6%, and the frequency span of the alleles was 1.6%-30.3%. By statistical analysis, the frequency varied significantly in 14 populations (Plt;0.05). Among them, Zhuang ethnic population had the lowest CCR2-64 I allele, whereas the Lisu ethnic population in Yunnan province had the highest CCR2-64 I allele Conclusion: The frequency of CCR2-64 I allele of 12 ethnic populations were lower than that of Han. The frequency of CCR2-64 I allele between Southern and South-east group showed significant variations. The mutant alleles conferring genetic resistance to HIV-1 and AIDS progression needs to be further studied.