Systematic reviews of genetic association studies. Human Genome Epidemiology Network

TNF-α gene promoter polymorphisms contribute to periodontitis susceptibility: evidence from 46 studies

AIM

Tumour necrosis factor-alpha (TNF-α) plays a critical role in the pathogenesis of periodontal disease. TNF-α gene polymorphisms can influence the TNF-α production. Many studies have focused the association between TNF-α gene promoter polymorphisms and periodontitis risk, but these results are still controversial.

MATERIALS AND METHODS

A meta-analysis was performed to assess the effect of TNF-α -308G/A (rs1800629), -238G/A (rs361525) and -863C/A (rs1800630) polymorphisms on either chronic (CP) or aggressive periodontitis (AgP) risk. Odds ratios (ORs) along with their 95% confidence intervals (CIs) were calculated to assess the strength of the association. Forty-six studies involving 5186 cases and 6683 controls were retrieved and analyzed.

RESULTS

The TNF-α -308G/A AA genotype was associated with increased CP risk in Asians, non-smoking Asians and Caucasians, and this polymorphism was significantly associated with elevated risk of AgP in Asians and Caucasians. Asian individuals carrying AA genotype had a significantly increased risk for -863C/A. No significant association was identified between TNF -238G/A polymorphism and CP.

CONCLUSIONS

These findings supported that TNF-α -308G/A and -863C/A polymorphisms may contribute to the susceptibility of periodontitis.

Integrative genomic analysis for the discovery of biomarkers in prostate cancer

Genome-wide association studies (GWAS) have achieved great success in identifying single nucleotide polymorphisms (SNPs, herein called genetic variants) and genes associated with risk of developing prostate cancer. However, GWAS do not typically link the genetic variants to the disease state or inform the broader context in which the genetic variants operate. Here, we present a novel integrative genomics approach that combines GWAS information with gene expression data to infer the causal association between gene expression and the disease and to identify the network states and biological pathways enriched for genetic variants. We identified gene regulatory networks and biological pathways enriched for genetic variants, including the prostate cancer, IGF-1, JAK2, androgen, and prolactin signaling pathways. The integration of GWAS information with gene expression data provides insights about the broader context in which genetic variants associated with an increased risk of developing prostate cancer operate.

Association between apolipoprotein E genotype and cancer susceptibility: a meta-analysis

BACKGROUND

Apolipoprotein E (ApoE), a protein primarily involved in lipoprotein metabolism, occurs in three isoforms (E2, E3 and E4). Studies evaluating the association between APOE genotype and incidence of malignancies have given inconclusive results.

OBJECTIVE

The objective of the present study was to analyze the association between APOE genotype and incidence of cancer by a meta-analysis.

METHODS

We conducted a literature search in the electronic databases for studies with information on APOE genotype in malignancies. Sixteen studies (14 case-control and 2 cohort; 77,970 controls and 12,010 cases) were included for the present meta-analysis. Pooled odds ratios (OR) with 95 % confidence intervals (CI) were calculated assuming a random-effect model for all the genotypes and alleles. Subgroup analyses based on study design, ethnicity of populations, site of cancer and source of controls were performed as a post hoc measure. Appropriate tests to detect heterogeneity, publication bias and sensitivity were done at all stages. The review protocol is registered with the PROSPERO database vide registration number CRD42013006496.

RESULTS

The pooled effect measure for the comparisons did not reveal an association in primary analyses. In the subgroup analyses, we observed a negative association between APOE4+ genotypes and overall risk of cancer in the cohort study subgroup (pooled OR 0.86; 95 % CI 0.82-0.91; p < 0.00001; I (2) = 0 %). Sensitivity analyses did not alter the overall pooled effect measure, and there were no evidences to suggest a publication bias.

CONCLUSION

Overall, the present meta-analysis did not show any association between APOE alleles and genotypes with incidence of cancer in general.

Effect of cytotoxic T-lymphocyte antigen-4, TNF-alpha polymorphisms on osteosarcoma: evidences from a meta-analysis

OBJECTIVE

Previous studies have investigated the role of cytotoxic T-lymphocyte antigen-4 (CTLA-4) and tumor necrosis factor-alpha (TNF-α) in carcinogenesis of osteosarcoma, but their results were inconsistent. We aimed to clarify the associations between CTLA-4, TNF-α polymorphism and osteosarcoma risk by using meta-analysis.

METHODS

We searched relevant studies without language restriction in PubMed, EMbase, Cochrane Library, Google Scholar databases, Chinese National Knowledge Infrastructure (CNKI) and conference literature in humans published prior to March 2013. The strengths of the associations between genetic variants and osteosarcoma risk were estimated by odds ratio (OR) with 95% confidence interval (95% CI).

RESULTS

A total of seven studies with 1,198 osteosarcoma patients and 1,493 controls were selected. Four studies were eligible for CTLA-4 (1,003 osteosarcoma and 1,162 controls), and three studies for TNF-α (195 osteosarcoma and 331 controls). Pooled results showed that rs231775 polymorphism of CTLA-4 was associated with osteosarcoma risk (GG vs. AA: OR=1.63, 95% CI=1.24-2.13; GG + GA vs. AA: OR=1.56, 95% CI=1.21-2.01; AA + GA vs. GG: OR=0.83, 95% CI=0.71-0.97; G vs. A: OR=1.21, 95% CI=1.08-1.36). No significant heterogeneity was observed across the studies. No significant associations were found between rs5742909 polymorphism of CTLA-4 or rs1800629 polymorphism of TNF-α and osteosarcoma risk.

CONCLUSIONS

These results suggest that the rs231775 polymorphism of CTLA-4 may play an important role in carcinogenesis of osteosarcoma.

Association of interleukin-10 polymorphisms with risk of irritable bowel syndrome: A meta-analysis

AIM: To clarify the current understanding of the association between interleukin-10 (IL-10) polymorphisms and the risk of irritable bowel syndrome (IBS).

METHODS: We searched for studies in any language recorded in PubMed, Embase and Cochrane library before August 2013. The associations under allele contrast model, codominant model, dominant model, and recessive model were analyzed. The strengths of the association between IL-10 polymorphisms and IBS risk were estimated using odds ratios (OR) with 95% confidence interval (CI). Fixed effects model was used to pool the result if the test of heterogeneity was not significant, otherwise the random-effect model was selected.

RESULTS: Eight case-control studies analyzing three single-nucleotide polymorphisms rs1800870 (-1082 A/G), rs1800871 (-819C/T), and rs1800872 (-592A/C) of the IL-10 gene, which involved 928 cases and 1363 controls, were eligible for our analysis. The results showed that rs1800870 polymorphisms were associated with a decreased risk of IBS (GG+GA vs AA: OR = 0.80, 95%CI: 0.66-0.96), (AA+GA vs GG: OR = 0.68, 95%CI: 0.52-0.90). Subgroup analysis revealed such association only existed in Caucasian ethnicity (AA+GA vs GG, OR = 0.70, 95%CI: 0.55-0.89). The rs1800872 polymorphisms were associated with an increased risk of IBS in Asian ethnicity (CC vs GG: OR = 1.29, 95%CI: 1.01-1.16). There were no associations between rs1800871 polymorphisms and the IBS risk.

CONCLUSION: The results suggest that IL-10 rs1800870 confers susceptibility to the risk of IBS in Caucasian ethnicity, and the rs1800872 may associate with IBS risk in Asians. However, no significant associations are found between rs1800871 and IBS risk.

Apolipoprotein E genotype, cardiovascular biomarkers and risk of stroke: systematic review and meta-analysis of 14,015 stroke cases and pooled analysis of primary biomarker data from up to 60,883 individuals

BACKGROUND

At the APOE gene, encoding apolipoprotein E, genotypes of the ε2/ε3/ε4 alleles associated with higher LDL-cholesterol (LDL-C) levels are also associated with higher coronary risk. However, the association of APOE genotype with other cardiovascular biomarkers and risk of ischaemic stroke is less clear. We evaluated the association of APOE genotype with risk of ischaemic stroke and assessed whether the observed effect was consistent with the effects of APOE genotype on LDL-C or other lipids and biomarkers of cardiovascular risk.

METHODS

We conducted a systematic review of published and unpublished studies reporting on APOE genotype and ischaemic stroke. We pooled 41 studies (with a total of 9027 cases and 61,730 controls) using a Bayesian meta-analysis to calculate the odds ratios (ORs) for ischaemic stroke with APOE genotype. To better evaluate potential mechanisms for any observed effect, we also conducted a pooled analysis of primary data using 16 studies (up to 60,883 individuals) of European ancestry. We evaluated the association of APOE genotype with lipids, other circulating biomarkers of cardiovascular risk and carotid intima-media thickness (C-IMT).

RESULTS

The ORs for association of APOE genotypes with ischaemic stroke were: 1.09 (95% credible intervals (CrI): 0.84-1.43) for ε2/ε2; 0.85 (95% CrI: 0.78-0.92) for ε2/ε3; 1.05 (95% CrI: 0.89-1.24) for ε2/ε4; 1.05 (95% CrI: 0.99-1.12) for ε3/ε4; and 1.12 (95% CrI: 0.94-1.33) for ε4/ε4 using the ε3/ε3 genotype as the reference group. A regression analysis that investigated the effect of LDL-C (using APOE as the instrument) on ischaemic stroke showed a positive dose-response association with an OR of 1.33 (95% CrI: 1.17, 1.52) per 1 mmol/l increase in LDL-C. In the separate pooled analysis, APOE genotype was linearly and positively associated with levels of LDL-C (P-trend: 2 × 10(-152)), apolipoprotein B (P-trend: 8.7 × 10(-06)) and C-IMT (P-trend: 0.001), and negatively and linearly associated with apolipoprotein E (P-trend: 6 × 10(-26)) and HDL-C (P-trend: 1.6 × 10(-12)). Associations with lipoprotein(a), C-reactive protein and triglycerides were non-linear.

CONCLUSIONS

In people of European ancestry, APOE genotype showed a positive dose-response association with LDL-C, C-IMT and ischaemic stroke. However, the association of APOE ε2/ε2 genotype with ischaemic stroke requires further investigation. This cross-domain concordance supports a causal role of LDL-C on ischaemic stroke.

The -159C/T polymorphism in the CD14 gene and cancer risk: a meta-analysis

Purpose

The -159C/T polymorphism in the cluster of differentiation (CD)14 gene has been extensively studied for an association with cancer; however, results from replication studies have been inconclusive. The aim of this study was to perform a comprehensive assessment of the possible association between the -159C/T polymorphism in the CD14 gene and cancer risk, by meta-analysis.

Methods

We searched in PubMed, Embase, and other databases, covering all case-control studies on the possible association between CD14 -159C/T gene polymorphism and cancer risk. Data were extracted and statistical analyses were performed using RevMan 5.0 and STATA 12.0 software.

Results

A total of 12 case-control studies met our inclusion criteria, including 2,498 cases and 2,696 controls. The combined analysis indicated that the CD14 -159C/T gene polymorphism didn’t confer risk for cancer – the recessive model (TT versus (vs) CT + CC), showed odds ratio (OR) =1.01, 95% confidence interval (CI) =0.82–1.23 (P=0.94), while the dominant model (TT + TC vs CC) showed OR =0.81, 95% CI =0.66–1.00 (P=0.05). A subgroup analysis by ethnicity showed that the cancer risk associated with CD14 -159C/T gene polymorphism was significantly decreased among Caucasians for the TC + TT vs CC comparison (OR =0.83, 95% CI =0.70–0.98 [P=0.03]). The subgroup analysis by cancer type suggested that the CD14 -159C/T gene polymorphism was not associated with gastric cancer risk.

Conclusion

The evidence from the present meta-analysis did not support the CD14 -159C/T gene polymorphism as a genetic risk factor for cancer. Further studies on different cancer types and ethnicities are needed to validate our findings.

Aggrecan variable number of tandem repeat polymorphism and lumbar disc degeneration: a meta-analysis

STUDY DESIGN

Data on the association between the ACAN (encoded for aggrecan core protein) variable number of tandem repeat (VNTR) polymorphism and lumbar disc degeneration are conflicting, so we performed a meta-analysis.

OBJECTIVE

Aggrecan is involved in the shock absorbing function of the lumbar disc; we performed a meta-analysis to assess the association between ACAN VNTR and lumbar degeneration.

SUMMARY OF BACKGROUND DATA

To perform a meta-analysis, we searched for studies published until September 2012, using electronic databases (PubMed, EMBASE, and China National Knowledge Infrastructure). Eight studies involving 965 cases of lumbar disc degeneration and 982 control subjects were identified.

METHODS

Assessment for eligibility and extraction of data were performed by 2 independent investigators. We extracted allele frequency for each study. We calculated the pooled odds ratios (ORs) and 95% confidence intervals (CI) to assess the strength of the association between the ACAN VNTR polymorphism and lumbar disc degeneration risk.

RESULTS

Results from the allele model suggested an increased risk of lumbar disc degeneration for the shorter alleles carriers compared with the normal alleles and longer alleles (OR = 1.54, 95% CI: 1.04-2.30, P = 0.03). In subgroup analysis by ethnicity, significant increased risks were found among Asians with shorter alleles (OR=1.65, 95% CI: 1.17-2.33, P = 0.004).

CONCLUSION

Our results suggest an increased risk of shorter alleles compared with normal alleles and longer alleles against lumbar disc degeneration among populations especially among Asian descent. Such association may not be statistically significant in European populations.

Comprehensive assessment and network analysis of the emerging genetic susceptibility landscape of prostate cancer

Background

Recent advances in high-throughput genotyping have made possible identification of genetic variants associated with increased risk of developing prostate cancer using genome-wide associations studies (GWAS). However, the broader context in which the identified genetic variants operate is poorly understood. Here we present a comprehensive assessment, network, and pathway analysis of the emerging genetic susceptibility landscape of prostate cancer.

Methods

We created a comprehensive catalog of genetic variants and associated genes by mining published reports and accompanying websites hosting supplementary data on GWAS. We then performed network and pathway analysis using single nucleotide polymorphism (SNP)-containing genes to identify gene regulatory networks and pathways enriched for genetic variants.

Results

We identified multiple gene networks and pathways enriched for genetic variants including IGF-1, androgen biosynthesis and androgen signaling pathways, and the molecular mechanisms of cancer. The results provide putative functional bridges between GWAS findings and gene regulatory networks and biological pathways.

MNS16A tandem repeats minisatellite of human telomerase gene and cancer risk: a meta-analysis

Background

Researchers have provided evidence that telomere dysfunction play an important role in cancer development. MNS16A is a polymorphic tandem repeats minisatellite of human telomerase (hTERT) gene that influences promoter activity of hTERT and thus implicates to relate with risk of several malignancies. However, results on association between MNS16A and cancer risk remain controversial. We therefore conduct a meta-analysis to derive a more precise estimation of association between MNS16A and cancer risk.

Methods

A systematic literature search was conducted by searching PubMed, ISI Web of Knowledge, Human Genome and Epidemiology Network Navigator and Google Scholar digital database for publications on associations between MNS16A and cancer risk. Variants with statistically significant associations by meta-analysis were assessed using Venice criteria.

Results

10 case-control articles enrolling 6101 cases and 10521 controls were brought into our meta-analysis. The relationships were strong epidemiological credibility in cerebral cancer and breast cancer population (P for heterogeneity > 0.1). The cumulative analysis in chronologic order suggested a clear tendency towards a significant association with additional study samples.

Conclusions

The results provided a more accurate depiction of the role of MNS16A in cerebral cancer and breast cancer susceptibility. Additional larger studies were warranted to validate our findings.

Meta-analyses of the 5-HTTLPR polymorphisms and post-traumatic stress disorder

Objective

To conduct a meta-analysis of all published genetic association studies of 5-HTTLPR polymorphisms performed in PTSD cases

Methods Data Sources

Potential studies were identified through PubMed/MEDLINE, EMBASE, Web of Science databases (Web of Knowledge, WoK), PsychINFO, PsychArticles and HuGeNet (Human Genome Epidemiology Network) up until December 2011. Study Selection: Published observational studies reporting genotype or allele frequencies of this genetic factor in PTSD cases and in non-PTSD controls were all considered eligible for inclusion in this systematic review. Data Extraction: Two reviewers selected studies for possible inclusion and extracted data independently following a standardized protocol. Statistical analysis: A biallelic and a triallelic meta-analysis, including the total S and S' frequencies, the dominant (S+/LL and S'+/L'L') and the recessive model (SS/L+ and S'S'/L'+), was performed with a random-effect model to calculate the pooled OR and its corresponding 95% CI. Forest plots and Cochran's Q-Statistic and I² index were calculated to check for heterogeneity. Subgroup analyses and meta-regression were carried out to analyze potential moderators. Publication bias and quality of reporting were also analyzed.

Results

13 studies met our inclusion criteria, providing a total sample of 1874 patients with PTSD and 7785 controls in the biallelic meta-analyses and 627 and 3524, respectively, in the triallelic. None of the meta-analyses showed evidence of an association between 5-HTTLPR and PTSD but several characteristics (exposure to the same principal stressor for PTSD cases and controls, adjustment for potential confounding variables, blind assessment, study design, type of PTSD, ethnic distribution and Total Quality Score) influenced the results in subgroup analyses and meta-regression. There was no evidence of potential publication bias.

Conclusions

Current evidence does not support a direct effect of 5-HTTLPR polymorphisms on PTSD. Further analyses of gene-environment interactions, epigenetic modulation and new studies with large samples and/or meta-analyses are required.

Genetic association studies in female reproduction: from candidate-gene approaches to genome-wide mapping

Many genetic association studies have been performed to investigate disorders of female reproduction, such as polycystic ovary syndrome, premature ovarian failure and endometriosis. These disorders typically manifest heterogeneously, and their pathogeneses are influenced by polygenic and environmental factors. Researchers evaluating these genetic associations have chosen candidate genes related to hormone action, steroid biosynthesis, inflammatory cytokines and autoimmune factors. Several of these genes have yielded statistically significant associations with female reproductive disorders; however, few associations have been robust and reproducible. Whole-genome association studies generate more reliable and unbiased results and represent a breakthrough in genetic studies of female reproduction. Nevertheless, to date only a very small fraction of the overall heritability has been identified and so further studies are needed.

Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer

Genome-wide association studies (GWAS) have achieved great success in identifying common variants associated with increased risk of developing breast cancer. However, GWAS do not typically provide information about the broader context in which genetic variants operate in different subtypes of breast cancer. The objective of this study was to determine whether genes containing single nucleotide polymorphisms (SNPs, herein called genetic variants) are associated with different subtypes of breast cancer. Additionally, we sought to identify gene regulator networks and biological pathways enriched for these genetic variants. Using supervised analysis, we identified 201 genes that were significantly associated with the six intrinsic subtypes of breast cancer. The results demonstrate that integrative genomics analysis is a powerful approach for linking GWAS information to distinct disease states and provide insights about the broader context in which genetic variants operate in different subtypes of breast cancer.

Detection of ancestry informative HLA alleles confirms the admixed origins of Japanese population

The polymorphisms in the human leukocyte antigen (HLA) region are powerful tool for studying human evolutionary processes. We investigated genetic structure of Japanese by using five-locus HLA genotypes (HLA-A, -B, -C, -DRB1, and -DPB1) of 2,005 individuals from 10 regions of Japan. We found a significant level of population substructure in Japanese; particularly the differentiation between Okinawa Island and mainland Japanese. By using a plot of the principal component scores, we identified ancestry informative alleles associated with the underlying population substructure. We examined extent of linkage disequilibrium (LD) between pairs of HLA alleles on the haplotypes that were differentiated among regions. The LDs were strong and weak for pairs of HLA alleles characterized by low and high frequencies in Okinawa Island, respectively. The five-locus haplotypes whose alleles exhibit strong LD were unique to Japanese and South Korean, suggesting that these haplotypes had been recently derived from the Korean Peninsula. The alleles characterized by high frequency in Japanese compared to South Korean formed segmented three-locus haplotype that was commonly found in Aleuts, Eskimos, and North- and Meso-Americans but not observed in Korean and Chinese. The serologically equivalent haplotype was found in Orchid Island in Taiwan, Mongol, Siberia, and Arctic regions. It suggests that early Japanese who existed prior to the migration wave from the Korean Peninsula shared ancestry with northern Asian who moved to the New World via the Bering Strait land bridge. These results may support the admixture model for peopling of Japanese Archipelago.

Association of plasminogen activator inhibitor-type 1 (-675 4G/5G) polymorphism with pre-eclampsia: systematic review

BACKGROUND AND AIMS

Excessive generation of plasminogen activator inhibitor-type 1 (PAI-1) is implicated in the pathogenesis of pre-eclampsia and related conditions. The PAI-1 (-675 4G/5G) promoter polymorphism (rs1799889) affects transcriptional activity and is a putative genetic risk factor for pre-eclampsia. The aim of this study was identify, appraise and synthesise the available evidence for the association of the PAI-1 (-675 4G/5G) polymorphism with pre-eclampsia.

METHODS

Systematic review and random effects meta-analysis of genetic association studies.

RESULTS

We found 12 eligible genetic association studies in which a total of 1511 women with pre-eclampsia, eclampsia or HELLP syndrome and 3492 controls participated. The studies were generally small (median number of cases 102, range 24 to 403) and underpowered to detect plausible association sizes. Meta-analysis of all of the studies detected statistically significant gene-disease associations in the recessive [pooled odds ratio 1.28 (95% confidence interval 1.09, 1.50); population attributable risk 7.7%] and dominant [pooled odds ratio 1.21 (95% confidence interval 1.01, 1.44); population attributable risk 13.7%] models. We did not find evidence of statistical heterogeneity, funnel plot asymmetry or small study bias.

CONCLUSIONS

These data suggest that the fibrinolytic pathway regulated by the PAI-1 gene may contribute to the pathogenesis of pre-eclampsia and related conditions. This association, if confirmed in larger genetic association studies, may inform research efforts to develop novel interventions or help to prioritise therapeutic targets that merit evaluation in randomised clinical trials.

An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer

Genome-wide association studies (GWAS) have identified genetic variants associated with an increased risk of developing breast cancer. However, the association of genetic variants and their associated genes with the most aggressive subset of breast cancer, the triple-negative breast cancer (TNBC), remains a central puzzle in molecular epidemiology. The objective of this study was to determine whether genes containing single nucleotide polymorphisms (SNPs) associated with an increased risk of developing breast cancer are connected to and could stratify different subtypes of TNBC. Additionally, we sought to identify molecular pathways and networks involved in TNBC. We performed integrative genomics analysis, combining information from GWAS studies involving over 400,000 cases and over 400,000 controls, with gene expression data derived from 124 breast cancer patients classified as TNBC (at the time of diagnosis) and 142 cancer-free controls. Analysis of GWAS reports produced 500 SNPs mapped to 188 genes. We identified a signature of 159 functionally related SNP-containing genes which were significantly (P <10⁻⁵) associated with and stratified TNBC. Additionally, we identified 97 genes which were functionally related to, and had similar patterns of expression profiles, SNP-containing genes. Network modeling and pathway prediction revealed multi-gene pathways including p53, NFkB, BRCA, apoptosis, DNA repair, DNA mismatch, and excision repair pathways enriched for SNPs mapped to genes significantly associated with TNBC. The results provide convincing evidence that integrating GWAS information with gene expression data provides a unified and powerful approach for biomarker discovery in TNBC.

The -159C/T polymorphism in the CD14 gene and tuberculosis risk: a meta-analysis

BACKGROUND

The -159C/T polymorphism in the CD14 gene has been implicated in susceptibility to tuberculosis, but the results were inconclusive. The present meta-analysis aimed to perform a comprehensive assessment of the literature on the possible association between the -159C/T polymorphism and tuberculosis risk.

METHODS

We searched in Pubmed and Embase for studies evaluating the association between the -159C/T gene polymorphism and tuberculosis risk. Data were extracted and statistical analysis was performed using Revman 5.1 and STATA 12.0 software.

RESULTS

A total of seven case-control studies involving 3253 subjects (1,574 tuberculosis cases and 1,679 controls) were included. Combined analysis revealed an obvious association between this polymorphism and tuberculosis risk (odds ratio=1.66 and 95% confidence interval: 1.23-2.25, P<0.05 for TT vs. TC+ CC). Sub-group analysis by ethnicity suggested that the risk of tuberculosis associated with the -159C/T polymorphism was significantly elevated among Asians (odds ratio=1.87 and 95% confidence interval: 1.58-2.21, P<0.05 for TT vs. TC+ CC).

CONCLUSION

This meta-analysis suggests that the -159C/T polymorphism in the CD14 gene contributes to tuberculosis susceptibility. To further investigate gene-gene and gene-environment interactions between this polymorphism and tuberculosis risk, more studies are needed.

Genetic characteristics of Sasang typology: a systematic review

A systematic review on studies related to the genetic characteristics of Sasang types was conducted with the goal of delineating genetic characteristics of Sasang typology. Six electronic databases of up to the March 2011 were examined with the key words of Sasang typology, constitution, and genetics in both Korean and English. Predefined review criteria were used, including demographic characteristics, type classification methods, genotyping methods, and genotypes. Fifty-nine potentially relevant studies were identified and 40 peer reviewed research articles that contained genetic data were included. Fourteen articles reported statistically significant differences among Sasang types, which are heritability, structural variation, genome-wide screening, and pathophysiological function. Although significant genotypes were reported with vWA, CSF1PO, Penta D, HLA-Cw*04, HLA-Cw*07, PPAR-γ, MDR1, IL-α, IL-β, and IL-6 receptor, results of the review indicate that there was no conclusive genotype related to the Sasang typology. Considering the features of Sasang typology, it is recommended that the macroscopic systems medical approach on genetics be employed, rather than the single genes association approach.

Telomerase reverse transcriptase locus polymorphisms and cancer risk: a field synopsis and meta-analysis

BACKGROUND

Several recent studies have provided evidence that polymorphisms in the telomerase reverse transcriptase (TERT) gene sequence are associated with cancer development, but a comprehensive synopsis is not available. We conducted a systematic review and meta-analysis of the available molecular epidemiology data regarding the association between TERT locus polymorphisms and predisposition to cancer.

METHODS

A systematic review of the English literature was conducted by searching PubMed, Embase, Cancerlit, Google Scholar, and ISI Web of Knowledge databases for studies on associations between TERT locus polymorphisms and cancer risk. Random-effects meta-analysis was performed to pool per-allele odds ratios for TERT locus polymorphisms and risk of cancer, and between-study heterogeneity and potential bias sources (eg, publication and chasing bias) were assessed. Because the TERT locus includes the cleft lip and palate transmembrane 1-like (CLPTM1L) gene, which is in linkage disequilibrium with TERT, CLPTM1L polymorphisms were also analyzed. Cumulative evidence for polymorphisms with statistically significant associations was graded as "strong," "moderate," and "weak" according to the Venice criteria. The joint population attributable risk was calculated for polymorphisms with strong evidence of association.

RESULTS

Eighty-five studies enrolling 490 901 subjects and reporting on 494 allelic contrasts were retrieved. Data were available on 67 TERT locus polymorphisms and 24 tumor types, for a total of 221 unique combinations of polymorphisms and cancer types. Upon meta-analysis, a statistically significant association with the risk of any cancer type was found for 22 polymorphisms. Strong, moderate, and weak cumulative evidence for association with at least one tumor type was demonstrated for 11, 9, and 14 polymorphisms, respectively. For lung cancer, which was the most studied tumor type, the estimated joint population attributable risk for three polymorphisms (TERT rs2736100, intergenic rs4635969, and CLPTM1L rs402710) was 41%. Strong evidence for lack of association was identified for five polymorphisms in three tumor types.

CONCLUSIONS

To our knowledge, this is the largest collection of data for associations between TERT locus polymorphisms and cancer risk. Our findings support the hypothesis that genetic variability in this genomic region can modulate cancer susceptibility in humans.

Tumour necrosis factor gene polymorphisms and migraine: a systematic review and meta-analysis

BACKGROUND

Data on the association between TNFα and TNFβ gene polymorphisms and migraine are conflicting.

METHODS

We performed a systematic review and meta-analysis of studies published until January 2011. We used data from published papers and as provided after contact with the authors. We calculated study specific odds ratios (OR) and 95% confidence intervals (CI) assuming additive, dominant, and recessive genetic models as well as pooled effect estimates.

RESULTS

Among the ten studies identified, the best evidence is available for the TNFα -308G>A and TNFβ 252A > G polymorphisms indicating no overall association with migraine. Subgroup analyses suggested that the A allele of the TNFα -308G > A variant more than doubles the risk for migraine among populations with a heterogeneous ethnic background, which was driven by associations for migraine without aura (additive model: pooled OR = 2.87, 95% CI 1.86-4.43). Further, the risk for migraine with aura was increased among Asian populations (additive model: pooled OR = 1.71, 95% CI 1.07-2.71). Both observed effects were stronger among females than males.

CONCLUSIONS

Our results indicate no overall association between TNFα and TNFβ gene variants and migraine. However, associations differed among specific populations. Our findings need to be treated with caution and further targeted research is warranted to evaluate population-specific effects including population stratification.

Research methods for meta-analyses

Meta-analysis uses numerical tools to pool data and to estimate a summary effect size for the comparison of two interventions from a set of randomised controlled trials identified in a systematic review. An effect size is a single number that expresses the difference in outcome from the interventions. The most commonly used effect sizes for dichotomous outcomes, for example, mortality, are the odds ratio and the relative risk. The results of a meta-analysis are usually presented in a complex figure, known as a forest plot, which shows both the individual studies and the summary statistics. Sensitivity analyses are performed to clarify the effect of the experimental design bias on the effect size. Clinical and statistical heterogeneity of the included studies are explored by the additional tools of fixed effect versus random effects models and subgroup analyses.

Can Factor V Leiden and prothrombin G20210A testing in women with recurrent pregnancy loss result in improved pregnancy outcomes?: Results from a targeted evidence-based review

Women with recurrent pregnancy loss are offered Factor V Leiden (F5) and/or prothrombin G20210A (F2) testing to identify candidates for anticoagulation to improve outcomes. A systematic literature review was performed to estimate test performance, effect sizes, and treatment effectiveness. Electronic searches were performed through April 2011, with review of references from included articles. English-language studies addressed analytic validity, clinical validity, and/or clinical utility and satisfied predefined inclusion criteria. Adequate evidence showed high analytic sensitivity and specificity for F5 and F2 testing. Evidence for clinical validity was adequate. The summary odds ratio for association of recurrent pregnancy loss with F5 in case-controlled studies was 2.02 (95% confidence interval, 1.60-2.55), with moderate heterogeneity and suggestion of publication bias. Longitudinal studies in women with recurrent pregnancy loss or unselected cohorts showed F5 carriers were more likely to have a subsequent loss than noncarriers (odds ratios: 1.93 and 2.03, respectively). Results for F2 testing were similar. For clinical utility, evidence was adequate that anticoagulation treatments were ineffective (except in antiphospholipid antibody syndrome) and had treatment-associated harms. The certainty of evidence is moderate (high, moderate, and low) that anticoagulation of women with recurrent pregnancy loss and F5/F2 variants would currently lead to net harms.

Genetic variants associated with breast-cancer risk: comprehensive research synopsis, meta-analysis, and epidemiological evidence

BACKGROUND

More than 1000 reports have been published in the past two decades on associations between variants in candidate genes and risk of breast cancer. Results have been generally inconsistent. We did a literature search and meta-analyses to provide a synopsis of the current understanding of the genetic architecture of breast-cancer risk.

METHODS

A systematic literature search for candidate-gene association studies of breast-cancer risk was done in two stages, using PubMed on or before Feb 28, 2010. A total of 24,500 publications were identified, of which 1059 were deemed eligible for inclusion. Meta-analyses were done for 279 genetic variants in 128 candidate genes or chromosomal loci that had at least three data sources. Variants with significant associations by meta-analysis were assessed using the Venice criteria and scored as having strong, moderate, or weak cumulative evidence for an association with breast-cancer risk.

FINDINGS

51 variants in 40 genes showed significant associations with breast-cancer risk. Cumulative epidemiological evidence of an association was graded as strong for ten variants in six genes (ATM, CASP8, CHEK2, CTLA4, NBN, and TP53), moderate for four variants in four genes (ATM, CYP19A1, TERT, and XRCC3), and weak for 37 variants. Additionally, in meta-analyses that included a minimum of 10,000 cases and 10,000 controls, convincing evidence of no association with breast-cancer risk was identified for 45 variants in 37 genes.

INTERPRETATION

Whereas most genetic variants assessed in previous candidate-gene studies showed no association with breast-cancer risk in meta-analyses, 14 variants in nine genes had moderate to strong evidence for an association. Further evaluation of these variants is warranted.

FUNDING

US National Cancer Institute.

Interactive effects of antioxidant genes and air pollution on respiratory function and airway disease: a HuGE review

Susceptibility to the respiratory effects of air pollution varies between individuals. Although some evidence suggests higher susceptibility for subjects carrying variants of antioxidant genes, findings from gene-pollution interaction studies conflict in terms of the presence and direction of interactions. The authors conducted a systematic review on antioxidant gene-pollution interactions which included 15 studies, with 12 supporting the presence of interactions. For the glutathione S-transferase M1 gene (GSTM1) (n=10 studies), only 1 study found interaction with the null genotype alone, although 5 observed interactions when GSTM1 was evaluated jointly with other genes (mainly NAD(P)H dehydrogenase [quinone] 1 (NQO1)). All studies on the glutathione S-transferase P1 (GSTP1) Ile105Val polymorphism (n=11) provided some evidence of interaction, but findings conflicted in terms of risk allele. Results were negative for glutathione S-transferase T1 (GSTT1) (n=3) and positive for heme oxygenase 1 (HMOX-1) (n=2). Meta-analysis could not be performed because there were insufficient data available for any specific gene-pollutant-outcome combination. Overall the evidence supports the presence of gene-pollution interactions, although which pollutant interacts with which gene is unclear. However, issues regarding multiple testing, selective reporting, and publication bias raise the possibility of false-positive findings. Larger studies with greater accuracy of pollution assessment and improved quality of conduct and reporting are required.

STin2 VNTR polymorphism in the serotonin transporter gene and migraine: pooled and meta-analyses

Data on the association between the SLC6A4 STin2 VNTR polymorphism and migraine are conflicting. To perform pooled and meta-analyses, we searched for studies published until September 2009 using electronic databases (MEDLINE, EMBASE, Science Citation Index) and reference lists of studies. Assessment for eligibility and extraction of data was performed by two independent investigators. We extracted allele and genotype frequencies for each study. We then calculated study-specific and pooled odds ratios (OR) and 95% confidence intervals (CI) assuming allele and genotype models. We also calculated pooled ORs and 95% CIs based on study-specific effect estimates for the allele model. We included five studies investigating the association between the STin2 VNTR polymorphism and migraine. Results from the allele model suggested a protective effect against migraine for the STin2.9 and STin2.10 alleles compared to the STin2.12 allele among populations of European descent, which however was not significant. Results from the genotype model indicated a significant ~25% reduced risk for migraine among carriers of the 10/12 genotype compared with carriers of the 12/12 genotype among all study populations (OR = 0.76, 95% CI 0.60–0.97) for any migraine, which was more pronounced among populations of European descent (OR = 0.68, 95% CI 0.53–0.87). Results for migraine with and without aura were of similar magnitude, but were not statistically significant. Our results suggest a protective effect of non-STin2.12 alleles compared to STin2.12 alleles, respectively, 10/12 and 10/10 genotypes compared to the 12/12 genotype against migraine among populations of European descent. Associations in non-European populations may differ.

Sex hormone receptor gene polymorphisms and migraine: a systematic review and meta-analysis

BACKGROUND

Data on the association between sex hormone receptor polymorphisms and migraine are conflicting.

METHODS

We performed a systematic review and meta-analysis on this topic searching for studies published until August 2009. For each study, we calculated odds ratios (ORs) and 95% confidence intervals (CIs) assuming additive, dominant, and recessive genetic models. We then calculated pooled ORs and 95% CIs.

RESULTS AND CONCLUSION

Among the seven genes targeted, four variants were investigated in multiple studies. Effect estimates from an additive model suggest that the ESR-1 594 G>A (pooled OR 1.37; 95% CI 1.02-1.83) and ESR-1 325 C>G (pooled OR 1.16; 95% CI 1.03-1.32) variants are associated with any migraine. This pattern does not differ between migraine with and without aura. In contrast, the ESR-1 Pvu II C>T and PGR PROGINS insert polymorphism do not appear to be associated with migraine. Results were driven by studies among Caucasians and may differ in other ethnic groups.

5-HTTLPR polymorphism in the serotonin transporter gene and migraine: a systematic review and meta-analysis

BACKGROUND AND METHODS

Data on the association between the SLC6A4 5-HTTLPR polymorphism and migraine are conflicting. We performed a systematic review and meta-analysis among studies published up to September 2009. For each study with genotype information, we calculated odds ratios (OR) and 95% confidence intervals (CI) assuming additive, dominant, and recessive genetic models. We then calculated pooled ORs and 95% CIs.

RESULTS

Among the ten studies identified there was no overall association between the polymorphism and any migraine for Europeans or Asians. However, European women carrying the S allele had an increased risk for any migraine (dominant model: pooled OR=2.02; 95% CI 1.24-3.28). Results among Europeans further suggested an increased risk for migraine with aura among carriers of the S/S genotype (recessive model: pooled OR=1.41; 95% CI 0.83-2.40).

CONCLUSIONS

While our results indicate no overall association between the SLC6A4 5-HTTLPR polymorphism and migraine among Europeans and Asians, gender and migraine aura status may have modifying roles among Europeans.

The association between the peroxisome proliferator-activated receptor-gamma2 (PPARG2) Pro12Ala gene variant and type 2 diabetes mellitus: a HuGE review and meta-analysis

The peroxisome proliferator-activated receptor-γ gene (PPARG) has been implicated in the etiology of type 2 diabetes mellitus and has been investigated in numerous epidemiologic studies. In this Human Genome Epidemiology review, the authors assessed this relation in an updated meta-analysis of 60 association studies. Electronic literature searches were conducted on September 14, 2009. Population-based cohort, case-control, cross-sectional, or genome-wide association studies reporting associations between the PPARG Pro12Ala gene variant (rs1801282) and type 2 diabetes were included. An updated literature-based meta-analysis involving 32,849 type 2 diabetes cases and 47,456 controls in relation to the PPARG Pro12Ala variant was conducted. The combined overall odds ratio, calculated by per-allele genetic model random-effects meta-analysis for type 2 diabetes and the Pro12Ala polymorphism, was 0.86 (95% confidence interval: 0.81, 0.90). The analysis indicated a moderate level of heterogeneity attributable to genuine variation in gene effect size (I² = 37%). This may reflect the variation observed between ethnic populations and/or differences in body mass index. Work on PPARG Pro12Ala should now focus on the observed heterogeneity in the magnitude of the association between populations. Further investigations into gene-gene and gene-environment interactions may prove enlightening.

Prioritizing GWAS results: A review of statistical methods and recommendations for their application

Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. A substantial number of recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. This review is written from the viewpoint that findings from the GWAS provide preliminary genetic information that is available for additional analysis by statistical procedures that accumulate evidence, and that these secondary analyses are very likely to provide valuable information that will help prioritize the strongest constellations of results. We review and discuss three analytic methods to combine preliminary GWAS statistics to identify genes, alleles, and pathways for deeper investigations. Meta-analysis seeks to pool information from multiple GWAS to increase the chances of finding true positives among the false positives and provides a way to combine associations across GWAS, even when the original data are unavailable. Testing for epistasis within a single GWAS study can identify the stronger results that are revealed when genes interact. Pathway analysis of GWAS results is used to prioritize genes and pathways within a biological context. Following a GWAS, association results can be assigned to pathways and tested in aggregate with computational tools and pathway databases. Reviews of published methods with recommendations for their application are provided within the framework for each approach.

MTHFR 677C>T and ACE D/I polymorphisms in migraine: a systematic review and meta-analysis

BACKGROUND

Data on the association between the MTHFR 677C>T and ACE D/I polymorphisms and migraine including aura status are conflicting.

OBJECTIVE

The objective of this study is to perform a systematic review and meta-analysis on this topic.

METHODS

We searched for studies published until March 2009 using electronic databases (MEDLINE, EMBASE, Science Citation Index) and reference lists of studies and reviews on the topic. Assessment for eligibility of studies and extraction of data was performed by 2 independent investigators. For each study we calculated the odds ratios (OR) and 95% confidence intervals (CI) assuming additive, dominant, and recessive genetic models. We then calculated pooled ORs and 95% CIs.

RESULTS

Thirteen studies investigated the association between the MTHFR 677C>T polymorphism and migraine. The TT genotype was associated with an increased risk for any migraine, which only appeared for migraine with aura (pooled OR = 1.48, 95% CI 1.02-2.13), but not for migraine without aura. Nine studies investigated the association of the ACE D/I polymorphism with migraine. The II genotype was associated with a reduced risk for migraine with aura (pooled OR = 0.71, 95% CI 0.55-0.93) and migraine without aura (pooled OR = 0.84, 95% CI 0.70-0.99). Results for both variants were driven by studies in non-Caucasian populations. Results among Caucasians did not suggest an association. Extractable data did not allow investigation of gene-gene interactions.

CONCLUSIONS

The MTHFR 677TT genotype is associated with an increased risk for migraine with aura, while the ACE II genotype is protective against both migraine with and without aura. Results for both variants appeared only among non-Caucasian populations. There was no association among Caucasians.

Credible genetic associations?

The proliferation in genetic association studies, and the recurring failure of initially promising findings to robustly replicate, demonstrates the need for stringent standards to ensure the identification of credible associations. The Human Genome Epidemiology Network has recently published intermin guideliness on evidential criteria for genetic association studies. These are reviewed, and their value and importance discussed, as well as the impact these guidelines will have on the conduct of genetic association studies.