Nucleotide polymorphism of the TNF gene cluster in six Chinese populations

Zhang, Yong-Biao; Zhang, Feng; Lin, Haoran; Shi, Lei; Wang, Panpan; Shi, Li; Gong, Qiang; Li, Xin; Wang, Mei; Hu, Songnian; Chu, Jiayou; Wang, Duen-Mei

doi:10.1038/jhg.2010.33

Cited by 5 publications

(4 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Modern Tibetans have adapted to live in these rigorous conditions, as evidenced by their efficient oxygen utilization, absence of chronic mountain sickness, and high infant survival rate [1] . Although it is known that Tibetans are a branch of East-Asian (EA) populations [2] , [3] , [4] , long-term endurance in the harsh environment has facilitated the divergence of Tibetans from other East-Asian populations with a distinct set of genetic characteristics [5] .…”

Section: Introductionmentioning

confidence: 99%

A Preliminary Study of Copy Number Variation in Tibetans

Zhang

et al. 2012

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Genetic features of Tibetans have been broadly investigated, but the properties of copy number variation (CNV) have not been well examined. To get a preliminary view of CNV in Tibetans, we scanned 29 Tibetan genomes with the Illumina Human-1 M high-resolution genotyping microarray and identified 139 putative copy number variable regions (CNVRs), consisting of 70 deletions, 61 duplications, and 8 multi-allelic loci. Thirty-four of the 139 CNVRs showed differential allele frequencies versus other East-Asian populations, with P values <0.0001. These results indicated a distinct pattern of CNVR allele frequency distribution in Tibetans. The Tibetan CNVRs are enriched for genes in the disease class of human reproduction (such as genes from the DAZ, BPY2, CDY, and HLA-DQ and -DR gene clusters) and biological process categories of “response to DNA damage stimulus” and “DNA repair” (such as RAD51, RAD52, and MRE11A). These genes are related to the adaptive traits of high infant birth weight and darker skin tone of Tibetans, and may be attributed to recent local adaptation. Our results provide a different view of genetic diversity in Tibetans and new insights into their high-altitude adaptation.

show abstract

Section: Introductionmentioning

confidence: 99%

A Preliminary Study of Copy Number Variation in Tibetans

Zhang

et al. 2012

PLoS ONE

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although a more comprehensive review of reference genes is in order, the results shown in Figure give a clear estimation of where IZUMO1 and JUNO lie with respect to genes previously suggested to be under selection in the literature: IZUMO1 Tajima's D indicates balancing selection, whereas JUNO's Tajima's D is consistent with positive selection. The Tajima's D values for the reference genes are reported in Supplementary Table S4, along with some literature values [30][31][32][33][34][35][36][37]. Nucleotide diversity.…”

Section: Resultsmentioning

confidence: 99%

“…Table S4: Tajima's D value analysis of various genes under different types of selection [30][31][32]34]. African versus Non-African populations.…”

Section: Population Groupsmentioning

confidence: 99%

Genetic Diversity in the IZUMO1-JUNO Protein-Receptor Pair Involved in Human Reproduction

Floriano

Allingham

2021

Preprint

View full text Add to dashboard Cite

Fertilization in mammals begins with the union of egg and sperm, an event that starts a cascade of cellular processes. The molecular-level understanding of these processes can guide the development of new strategies for controlling and/or promoting fertilization, and inform researchers and medical professional on the best choice of interventions. The proteins encoded by the IZUMO1 and JUNO genes form a ligand-receptor protein pair involved in the recognition of sperm and egg. Due to their role in the fertilization process, these proteins are potential targets for the development of novel anti-contraceptive, as well as infertility treatments. Here we present a comprehensive analysis of these gene sequences, with the objective of identifying evolutionary patterns that may support their relevance as targets for preventing or improving fertility among humans. JUNO and IZUMO1 gene sequences were identified within the genomes of over 2000 humans sequenced in the 1000 Genomes Project. The human sequences were subjected to analyses of nucleotide diversity, selection neutrality, population-based differentiation (FST), haplotype inference, and whole chromosome scanning for signals of positive or of balancing selection. Derived alleles were determined by comparison to archaic hominin and other primate genomes. The potential effect of common non-synonymous variants on protein-protein interaction was also assessed. IZUMO1 displays higher variability among human individuals than JUNO. Genetic differentiation between continental population pairs was within whole-genome estimates for all but the JUNO gene in the African population group with respect to the other 4 population groups (American, East Asian, South Asian, and European). Tajima's D values demonstrated deviation from neutrality for both genes in comparison to a group of genes identified in the literature as under balancing or positive selection. Tajima's D for IZUMO1 aligns with values calculated for genes presumed to be under balancing selection, whereas JUNO's value aligned with genes presumed to be under positive selection. These inferences on selection are both supported by SNP density, nucleotide diversity and haplotype analysis. A JUNO haplotype carrying 3 derived alleles out of 5, one of which is a missense mutation implicated in polyspermy, was found to be significant in a population of African ancestry. Polyspermy has a disadvantageous impact on fertility and its presence in approximately 30% of the population of African ancestry may be associated to a potentially beneficial role of this haplotype. This role has not been established and may be related to a non-reproductive role of JUNO. The high degree of conservation of the JUNO sequence combined with a dominant haplotype across multiple population groups supports JUNO as a potential target for the development of contraceptive treatments. In addition to providing a detailed account of human genetic diversity across these 2 important and related genes, this study also provides a framework for large population-based studies investigating protein-protein interactions at the genome level.

show abstract

“… 26 Due to the important biological role of TNF and the special position of the gene, the relationship between TNF gene polymorphism and disease has been widely paid attention. 27 TNF has been found to be involved in immune regulation and inflammation.…”

Section: Discussionmentioning

confidence: 99%

The Assessment of TNF-α Gene Polymorphism Association with the Risk of Allergic Rhinitis in the Chinese Han Population

Cui¹,

Li²,

Wang³

2021

IJGM

View full text Add to dashboard Cite

Background Allergic rhinitis (AR) is a non-infectious chronic inflammatory disease of the nasal mucosa that is mainly mediated by IgE after exposure to allergens. Tumor necrosis factor-α has been found to be involved in inflammation response. In the present study, we screened several SNPs of TNF-α gene and analyzed the associations between target SNPs polymorphism and AR. Methods Using an unmatched case–control design, 600 AR patients and 600 healthy controls were enrolled. General characteristics were collected including IgE expression. Univariate and multivariate logistic regression were used to estimate the odds ratio (OR) and 95% confidence interval (CI) of TNF–α gene for AR in dominant model, additive model, recessive model and allele model. The haplotype analyses were performed using rs1799964, rs1800630 and rs769178. Stratified analyses were also performed in gender, age, overweight, smoking, drinking, family history, and asthma history. Results Our multivariate logistic regression indicated that rs1799964, rs1800630 and rs769178 locus polymorphisms are not associated with AR. For rs769178, the GT (OR=2.35, 95% CI:1.82–3.03, P<0.001) and GT+TT (OR=1.89, 95% CI: 1.50–2.38, P<0.001) genotypes present an increased risk for AR compared to GG. The C-G-A-T (OR=2.04, 95% CI: 1.21–3.44, P=0.007) and C-G-C-T (OR=1.29, 95% CI: 1.04–1.62, P=0.024) haplotypes are associated with the increased risk of AR, and the C-G-C-G haplotypes decreased risk of AR (OR=0.75, 95% CI: 0.63–0.88, P=0.001). Stratified analyses shown a significant association between recessive model of rs769178 locus and AR risk in the subgroup of age≤60, overweight and smoking. Cross-over analysis indicated that the effects of TT+GT of genotype combined with smoking or drinking related with AR were associated with AR risk. Conclusion The rs769178 locus polymorph of TNF-α was associated with an increased risk of AR. The haplotypes (C-G-A-T and C-G-C-T) of TNF-α can significantly increase the risk of AR, and C-G-C-G haplotype decreased the risk of AR. There are interactions between rs769178 polymorphism and smoking/drinking for AR risk.

show abstract

Nucleotide polymorphism of the TNF gene cluster in six Chinese populations

Cited by 5 publications

References 52 publications

A Preliminary Study of Copy Number Variation in Tibetans

A Preliminary Study of Copy Number Variation in Tibetans

Genetic Diversity in the IZUMO1-JUNO Protein-Receptor Pair Involved in Human Reproduction

The Assessment of TNF-α Gene Polymorphism Association with the Risk of Allergic Rhinitis in the Chinese Han Population

Contact Info

Product

Resources

About