Assessment of cumulative evidence on genetic associations: interim guidelines

Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant

Lumbar disc degeneration (LDD) is associated with both genetic and environmental factors and affects many people worldwide. A hallmark of LDD is loss of proteoglycan and water content in the nucleus pulposus of intervertebral discs. While some genetic determinants have been reported, the etiology of LDD is largely unknown. Here we report the findings from linkage and association studies on a total of 32,642 subjects consisting of 4,043 LDD cases and 28,599 control subjects. We identified carbohydrate sulfotransferase 3 (CHST3), an enzyme that catalyzes proteoglycan sulfation, as a susceptibility gene for LDD. The strongest genome-wide linkage peak encompassed CHST3 from a Southern Chinese family–based data set, while a genome-wide association was observed at rs4148941 in the gene in a meta-analysis using multiethnic population cohorts. rs4148941 lies within a potential microRNA-513a-5p (miR-513a-5p) binding site. Interaction between miR-513a-5p and mRNA transcribed from the susceptibility allele (A allele) of rs4148941 was enhanced in vitro compared with transcripts from other alleles. Additionally, expression of CHST3 mRNA was significantly reduced in the intervertebral disc cells of human subjects carrying the A allele of rs4148941. Together, our data provide new insights into the etiology of LDD, implicating an interplay between genetic risk factors and miRNA.

NBN Gene Polymorphisms and Cancer Susceptibility: A Systemic Review

The relationship between DNA repair failure and cancer is well established as in the case of rare, high penetrant genes in high cancer risk families. Beside this, in the last two decades, several studies have investigated a possible association between low penetrant polymorphic variants in genes devoted to DNA repair pathways and risk for developing cancer. This relationship would be also supported by the observation that DNA repair processes may be modulated by sequence variants in DNA repair genes, leading to susceptibility to environmental carcinogens. In this framework, the aim of this review is to provide the reader with the state of the art on the association between common genetic variants and cancer risk, limiting the attention to single nucleotide polymorphisms (SNPs) of the NBN gene and providing the various odd ratios (ORs). In this respect, the NBN protein, together with MRE11 and RAD50, is part of the MRN complex which is a central player in the very early steps of sensing and processing of DNA double-strand breaks (DSBs), in telomere maintenance, in cell cycle control, and in genomic integrity in general. So far, many papers were devoted to ascertain possible association between common synonymous and non-synonymous NBN gene polymorphisms and increased cancer risk. However, the results still remain inconsistent and inconclusive also in meta-analysis studies for the most investigated E185Q NBN miscoding variant.

The interleukin 10 -819C/T polymorphism and cancer risk: a HuGE review and meta-analysis of 73 studies including 15,942 cases and 22,336 controls

The aim of the present work was to perform a meta-analysis to evaluate the association between the interleukin 10 (IL-10) -819C/T (rs1800871) polymorphism and cancer risk. A total of 73 studies, including 15,942 cancer cases and 22,336 controls, were identified in this meta-analysis. The odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using the random-effects model. Overall, no significant association was identified between the IL-10 -819C/T polymorphism and cancer risk. In the subgroup analyses, the T allele and TT genotype were associated with a moderately reduced cancer risk in the Asian population (T allele vs. C allele: OR=0.93, 95%CI: 0.87, 0.99; TT vs. CC: OR=0.86, 95%CI: 0.76, 0.98; TT vs. CT/CC: OR=0.90, 95%CI: 0.82, 0.98). Individuals who were homozygous for the T allele (TT) were found to be associated with significantly reduced gastric cancer risk in the Asian population. The heterozygous variant (CT) and the dominant model (TT/CT vs. CC) were associated with an increased risk for cervical and ovarian cancer. However, the IL-10 -819C/T polymorphism was not significantly associated with breast cancer, colorectal cancer, lung cancer, hepatocellular carcinoma, prostate cancer, lymphoma, or melanoma. The depressed cancer risk of the TT genotype occurred in the studies of hospital-based case-control studies and the studies recruited less than 500 subjects, but no statistically significant results were found in the stratified analyses using genotyping method. The results suggest that the IL-10 -819TT genotype may be a protective factor for cancer in Asians, especially gastric cancer. In contrast, the CT genotype and the dominant model could be risk factors for cervical and ovarian cancer. The importance of stratifying by ethnicity, cancer type, study design, and sample size needs to be standardized in future studies, together with considering the association between the IL-10 -819C/T polymorphism and cancer risk. Furthermore, the linkage of -819C/T with other polymorphisms of the IL-10 gene may help explain the variability in findings.

Association of XRCC1 Arg399Gln polymorphism with bladder cancer susceptibility: a meta-analysis

Genetic variations in DNA repair genes are thought to modify DNA repair capacity and may to be related to cancer susceptibility. However, epidemiological study results have been inconsistent. In this meta-analysis, we assessed 24 case-control studies of association between the X-ray repair cross complementing group 1 (XRCC1) Arg399Gln polymorphism and bladder cancer susceptibility in the general population and in Asian and non-Asian subgroups. A moderately significant association with bladder cancer risk was found for AG vs GG (OR=1.110, 95% CI=1.018-1.210). No significant associations with bladder cancer risk were found for AA vs GG (OR=0.942, 95% CI=0.823-1.077), the dominant model AA/AG vs GG (OR=1.075, 95% CI=0.990-1.167) and the recessive model AA vs AG/GG(OR=0.890, 95% CI=0.788-1.005). In subgroup analysis, a moderately significant association was also found for AG vs GG (OR=1.091, 95% CI=1.008-1.180) in non-Asian subgroup. The analysis suggests that the XRCC1 Arg399Gln polymorphism might be a moderate risk factor for bladder cancer, especially in non-Asian population.

Cervical spondylotic myelopathy: methodological approaches to evaluate the literature and establish best evidence

STUDY DESIGN

Review of methods.

OBJECTIVE

To provide a detailed description of the methods undertaken in the articles in this focus issue pertaining to cervical spondylotic myelopathy (CSM) and ossification of the posterior longitudinal ligament (OPLL) and to describe the process used to develop summary statements and clinical recommendations regarding factors associated with the mechanisms, diagnosis, progression, and treatment of CSM and OPLL.

SUMMARY OF BACKGROUND DATA

We present methods used in conducting the systematic, evidence-based reviews and development of expert panel summary statements and clinical recommendations of the mechanisms, diagnosis, progression, and treatment of CSM and OPLL. Our intent is that clinicians will combine the information from these systematic reviews, narrative reviews, and primary research studies with an understanding of their own capacities and experience to better manage patients with CSM or OPLL and consider future research for the diagnosis and treatment of these diseases.

METHODS

For the systematic reviews, which make up the bulk of the studies in this focus issue, a systematic search and critical review of the English language literature was undertaken for articles published on the mechanisms, diagnosis, progression, and treatment of CSM and OPLL. Articles were screened for relevance using a priori criteria and relevant articles were critically reviewed. Whether an article was included for review depended on whether the study question was descriptive, one of therapy, or one of prognosis. The strength of evidence for the overall body of literature in each topic area was determined by 2 independent reviewers considering risk of bias, consistency, directness, and precision of results using a modification of the Grading of Recommendation Assessment, Development and Evaluation criteria. Disagreements were resolved by consensus. Findings from articles meeting inclusion criteria were summarized. From these summaries, summary statements or clinical recommendations were formulated among subject experts through a modified Delphi process using the Grading of Recommendation Assessment, Development and Evaluation approach. Methods for the 2 primary research studies and the narrative reviews are also reviewed.

RESULTS

Because of the nature of questions that needed to be addressed, not all studies in this focus issue were amenable to systematic review. As a result, this focus issue consists of several different article types, including 1 research protocol, 2 primary research studies, 2 narrative literature reviews, 7 systematic reviews, and 3 articles that combine a systematic review component with either a narrative section (n = 2) or a provider survey (n = 1). In general, the strength of evidence ratings ranged from insufficient to moderate. Summary statements or clinical recommendations were made according to available evidence and study type: 16 summary statements were made across 8 articles, and 17 clinical recommendations were made across 9 articles. Three articles had both summary statements and clinical recommendations, 5 had summary statements only, 6 had clinical recommendations only, and 1 (the research protocol) was not amenable to either.

CONCLUSION

Systematic reviews, narrative reviews, and primary research studies were undertaken to understand the mechanisms, diagnosis, progression, and treatment of CSM and OPLL and to provide summary statements and clinical recommendations. This article reports the methods used in the studies in this focus issue. SUMMARY STATEMENTS: The objectives of this focus issue were met using a variety of article and study designs, each of which has some unique methodological aspects associated with it. The reader should refer to the full article in this issue for additional details specific to that topic. The methods for systematic review follow accepted standards for rigor and, together with the application of Grading of Recommendation Assessment, Development and Evaluation, are intended to allow for transparency in the process for creating the clinical recommendation.

Genetics and heritability of cervical spondylotic myelopathy and ossification of the posterior longitudinal ligament: results of a systematic review

STUDY DESIGN

Systematic review.

OBJECTIVE

To answer the following 3 clinical questions: (1) What is the evidence supporting a heritable predisposition for cervical spondylotic myelopathy (CSM) and ossification of the posterior longitudinal ligament (OPLL)? (2) What specific genetic polymorphisms have been associated with CSM and OPLL? (3) What is the evidence supporting a genetic basis for predicting postoperative outcomes for patients with CSM and OPLL?

SUMMARY OF BACKGROUND DATA

OPLL and CSM are thought to be multifactorial conditions resulting from a combination of environmental and genetic factors.

METHODS

A systematic review of the English language literature was undertaken for articles published between 1980 and November 7, 2012. The strength of evidence was determined by 2 independent reviewers using the Grading of Recommendation Assessment, Development and Evaluation (GRADE) criteria for studies addressing the first question of heritability and using the criteria set forth by the HuGENet Working Group in the Venice Interim Guidelines to address the last 2 questions of genetic association.

RESULTS

Of the 118 citations identified through the initial literature search, a total of 23 articles remained after application of inclusion/exclusion criteria. The 3 family association studies related to question 1 supported the principle of an inherited predisposition to CSM and OPLL; however, the strength of evidence supporting these findings was low. Within the 19 case-control studies related to question 2, 2 single nucleotide polymorphisms (COL6A1/Intron 32(-29) and COL11A2/Intron 6(-4)) were observed at higher frequencies in OPLL cases than in controls in more than 1 study and may be associated with its development. There was insufficient evidence to support an association between CSM and any specific single nucleotide polymorphism or haplotype or to support the association of specific gene alleles with postoperative CSM outcomes.

CONCLUSION

Existing family studies provide support for the principle of an inherited predisposition to CSM and OPLL. Multiple studies support the association of 2 collagen gene related single nucleotide polymorphisms with OPLL; however, there is insufficient evidence to support the association between CSM and any genetic polymorphism or to support a genetic predictor of surgical outcome. SUMMARY STATEMENTS: STATEMENT 1: Existing family studies provide support for the principle of an inherited predisposition to CSM and OPLL. STATEMENT 2: Two SNPs related to the collagen 6A1 gene (COL6A1/Intron 32(-29)) and the collagen 11A2 gene (COL11A2/Intron 6(-4)) have been associated with OPLL in multiple studies and may be associated with its development. STATEMENT 3: No statement can be made from the literature regarding the association of specific SNPs or haplotypes with CSM. STATEMENT 4: No statement can be made from the literature regarding genetic predictors of surgical outcome in the context of OPLL or CSM.

Genetic polymorphisms of XRCC3 Thr241Met (C18067T, rs861539) and bladder cancer risk: a meta-analysis of 18 research studies

The relationship of bladder cancer with the presence of X-ray cross-complementing group 3(XRCC3) genetic polymorphism Thr241Met has been reported with inconsistent results. The objective of this study was to quantitatively evaluate the association between this polymorphism and bladder cancer susceptibility. A comprehensive research was conducted through PubMed, Medline, Embase, and Web of Science databases up to Aug. 20, 2013. Pooled odds ratio and 95 % confidence interval were calculated using a fixed or random effects model. Statistical analysis was performed with Stata 12.0 software. Of the 18 case-control studies selected for this meta-analysis, a total of 5,667 bladder cancer cases and 7,609 controls were included. The combined results based on all studies suggested that XRCC3 Thr241Met was associated with bladder cancer risk under homozygote and recessive models. When stratifying for ethnicity, significant association was found in Caucasians under homozygote and recessive models. This meta-analysis suggests that XRCC3 Thr241Met polymorphism is a risk factor for bladder cancer risk. However, further well-designed studies are required to confirm our findings.

Quantitative assessment of the association between XPG Asp1104His polymorphism and bladder cancer risk

Published data regarding the association between XPG Asp1104His polymorphism and bladder cancer risk remained controversial. This meta-analysis of literatures was performed to draw a more precise estimation of the relationship. We systematically searched PubMed, Embase, and Web of Science with a time limit of June 22, 2013. Summary odds ratios (ORs) with 95 % CIs were used to assess the strength of the association between XPG Asp1104His polymorphism and bladder cancer risk using random effects model. A total of eight case-control studies including 2,613 cases and 2,934 controls were included for analysis. Overall, no significant association was found between XPG Asp1104His polymorphism and bladder cancer susceptibility for CC vs. GG (OR = 1.12, 95 % CI = 0.74-1.69), GC vs. GG (OR = 1.12, 95 % CI = 0.86-1.46), the dominant model CC + GC vs. GG (OR = 1.08, 95 % CI = 0.85-1.38), and the recessive model CC vs. GC + GG (OR = 0.92, 95 % CI = 0.66-1.29). In the subgroup analysis, no significant associations were found in either Asian or non-Asian population. This meta-analysis suggested that XPG Asp1104His polymorphism was not associated with bladder cancer risk.

Lack of association of apolipoprotein E (Apo E) ε2/ε3/ε4 polymorphisms with primary open-angle glaucoma: a meta-analysis from 1916 cases and 1756 controls

Background

A number of case-control studies were conducted to investigate the association of apolipoprotein E (Apo E) polymorphisms with primary open angle glaucoma (POAG). But the results remain controversial. This meta-analysis aims to comprehensively evaluate the relationship between a common ε2/ε3/ε4 polymorphism in Apo E gene on the risk of POAG.

Method

A comprehensive literature search for studies published up to April 2013 was performed. Summary odds ratios (ORs) and 95% confidence intervals (CI) were calculated employing random-effects models irrespective of between-study heterogeneity. Publication bias of literatures was evaluated using funnel plots and Egger's test.

Results

A total of 12 studies including 1916 cases and 1756 controls meeting the predefined criteria were involved in this meta-analysis. Overall, the Apo E ε2 allele and ε4 allele were not associated with POAG, compared with those carrying ε3 allele, with ORs of 0.98 (95% CI, 0.79 to 1.23; P = 0.872) and 1.05 (95% CI, 0.78 to 1.41; P = 0.743), respectively. Genotypic analysis also found no significant association between the ε4 carriers (ε3/ε4+ε4/ε4), ε2 carriers (ε2/ε3+ε2/ε2) and POAG, compared with participants with Apo E ε3/3, with ORs of 0.91 (95% CI, 0.66 to 1.25; P = 0.543) and 1.08 (95% CI, 0.74 to 1.57; P = 0.694), respectively. In the subgroup analysis by ethnicity, source of controls, genotyping methods, Hardy-Weinberg equilibrium or not, or type of the POAG, still no obvious associations were found.

Conclusions

This meta-analysis suggests that Apo E ε2/ε3/ε4 polymorphisms may not be associated with the risk of POAG. However, well-designed studies with larger sample size and more ethnic groups are required to further validate the results.

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.

Association between XRCC1 and XRCC3 polymorphisms with lung cancer risk: a meta-analysis from case-control studies

Many studies have reported the association of X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln, Arg194Trp, Arg280His, −77T>C, and X-ray repair cross-complementing group 3 (XRCC3) T241M polymorphisms with lung cancer risk, but the results remained controversial. Hence, we performed a meta-analysis to investigate the association between lung cancer risk and XRCC1 Arg399Gln (14,156 cases and 16,667 controls from 41 studies), Arg194Trp (7,426 cases and 9,603 controls from 23 studies), Arg280His (6,211 cases and 6,763 controls from 16 studies), −77T>C (2,487 cases and 2,576 controls from 5 studies), and XRCC3 T241M (8,560 cases and 11,557 controls from 19 studies) in different inheritance models. We found that −77T>C polymorphism was associated with increased lung cancer risk (dominant model: odds ration [OR] = 1.45, 95% confidence interval [CI] = 1.27–1.66, recessive model: OR = 1.73, 95% CI = 1.14–2.62, additive model: OR = 1.91, 95% CI = 1.24–1.94) when all the eligible studies were pooled into the meta-analysis. In the stratified and sensitive analyses, significantly decreased lung cancer risk was observed in overall analysis (dominant model: OR = 0.83, 95% CI = 0.78–0.89; recessive model: OR = 0.90, 95% CI = 0.81–1.00; additive model: OR = 0.82, 95% CI = 0.74–0.92), Caucasians (dominant model: OR = 0.82, 95% CI = 0.76–0.87; recessive model: OR = 0.89, 95% CI = 0.80–0.99; additive model: OR = 0.81, 95% CI = 0.73–0.91), and hospital-based controls (dominant model: OR = 0.81, 95% CI = 0.76–0.88; recessive model: OR = 0.89, 95% CI = 0.79–1.00; additive model: OR = 0.80, 95% CI = 0.71–0.90) for XRCC3 T241M. In conclusion, this meta-analysis indicates that XRCC1 −77T>C shows an increased lung cancer risk and XRCC3 T241M polymorphism is associated with decreased lung cancer risk, especially in Caucasians.

SMAD7 rs12953717 polymorphism contributes to increased risk of colorectal cancer

Mothers against decapentaplegic homolog 7 (SMAD7) rs12953717 polymorphism has been implicated to alter the risk of colorectal cancer (CRC), but the results are controversial. The objective of this study was to quantitatively evaluate the association between SMAD7 rs12953717 polymorphism and CRC susceptibility. A comprehensive search was conducted to identify all eligible studies of SMAD7 rs12953717 polymorphism and CRC risk. Pooled odds ratio and 95% confidence interval were calculated using a fixed or random effects model. Statistical analysis was performed with Review Manager 5.0 and Stata 11. A total of 11 case-control studies, including 12,058 cases and 11,444 controls, were identified. The combined results based on all studies suggested that rs12953717 was associated with CRC risk under all genetic models. When stratifying for race, the data showed that the rs12953717 was associated with a significantly increased CRC risk under all genetic models in Caucasians. Statistically significant association was found in all genetic models except in recessive model comparison in the subgroup of Asians. After stratifying the studies by study design, there was a significant association between rs12953717 polymorphism and CRC risk under all genetic models in the subgroup of population-based studies. Our study suggests that rs12953717 polymorphism is associated with an increased CRC risk.

Novel insights into etiologies of leukemia: a HuGE review and meta-analysis of CYP1A1 polymorphisms and leukemia risk

We conducted a meta-analysis to investigate the association of 2 single nucleotide polymorphisms in the cytochrome P450, family 1, subfamily 1A1 gene (CYP1A1), CYP1A1*2A and CYP1A1*2C, with the risk of developing different subtypes of leukemia in adults and children. A total of 26 studies published between 1999 and 2011 were identified by searching the PubMed, EMBASE, Medline, and Web of Science databases. The odds ratios for the CYP1A1 polymorphisms and leukemia risk were calculated. The cumulative evidence in genetic associations was graded by using the Venice criteria of the Human Genome Epidemiology Network (Atlanta, Georgia). The results showed that the cumulative evidence was moderate for the association of the CYP1A1*2A variant with leukemia in Caucasians and with childhood acute lymphoid leukemia in Caucasians. In addition, there was moderate evidence that children who carry both the CYP1A1*2A variant and the glutathione S-transferase M1 null genotype have an increased risk of acute lymphoid leukemia. For the CYP1A1*2C polymorphism, the cumulative evidence of an association with leukemia risk was moderate for adults and weak for children. Logistic regression analysis demonstrated an interaction between the CYP1A1*2C polymorphism and age. This meta-analysis showed that the CYP1A1*2A and CYP1A1*2C polymorphisms were associated with an increased risk of leukemia, and that the associations might vary by ethnicity, gene-gene interactions, age, and leukemia subtype.

Association between the Thr241Met polymorphism of X-ray repair cross-complementing group 3 gene and glioma risk: evidence from a meta-analysis based on 4,136 cases and 5,233 controls

Genetic polymorphism of X-ray repair cross-complementing group 3 (XRCC3) Thr241Met has been implicated to alter the risk of glioma, but the results are controversial. Medline, PubMed, Embase, and Cochrane Library databases were independently searched by two investigators up to 13 July 2013. Summary odds ratios (OR) and 95% confidence interval (CI) for Thr241Met polymorphism and prostate cancer were calculated. Statistical analysis was performed with the software program Stata 12.0. A total of 10 independent studies, including 4,136 cases and 5,233 controls, were identified. Our analysis suggested that Thr241Met was not associated with glioma risk in overall population. In the subgroup analysis, we detected no significant association between Thr241Met polymorphism and glioma risk in different descent populations. Subgroup analysis was held by source of controls, significant association was found between this polymorphism and glioma risk for population-based studies (homozygote model: OR = 1.747, 95% CI = 1.123-2.717, Ph = 0.059, I(2) = 59.7%; recessive model, OR = 1.455, 95% CI = 1.179-1.795, Ph = 0.111, I(2) = 50.1%; allele model, OR = 1.258, 95% CI = 1.010-1.566, Ph = 0.011, I(2) = 72.9%). This meta-analysis showed the evidence that XRCC3 Thr241Met polymorphism was associated with a low risk of glioma development.

Pharmacogenomics of opioids and perioperative pain management

Inadequate pain relief and adverse effects from analgesics remain common in children and adults during the perioperative period. Opioids are the most commonly used analgesics in children and adults to treat perioperative pain. Narrow therapeutic index and a large interpatient variability in response to opioids are clinically significant, with inadequate pain relief at one end of the spectrum and serious side effects, such as respiratory depression and excessive sedation due to relative overdosing, at the other end. Personalizing analgesia during the perioperative period attempts to maximize pain relief while minimizing adverse events from therapy. While various factors influence response to treatment among surgical patients, age, sex, race and pharmacogenetic differences appear to play major roles in predicting outcome. Genetic factors include a subset of genes that modulate the proteins involved in pain perception, pain pathway, analgesic metabolism (pharmacokinetics), transport and receptor signaling (pharmacodynamics). While results from adult genetic studies can provide direction for pediatric studies, they have limited direct applicability, as children's genetic predispositions to analgesic response may be influenced by developmental and behavioral components, altered sensitivity to analgesics and variation in gene-expression patterns. We have reviewed the available evidence on improving and personalizing pain management with opioids and the significance of individualizing analgesia, in order to maximize analgesic effect with minimal adverse effects with opioids. While the early evidence on individual genotype associations with pain, analgesia and opioid adverse outcome are promising, the large amount of conflicting data in the literature suggests that there is a need for larger and more robust studies with appropriate population stratification and consideration of nongenetic and other genetic risk factors. Although the clinical evidence and the prospect of being able to provide point-of-care genotyping to enable clinicians to deliver personalized analgesia for individual patients is still not available, positioning our research to identify all possible major genetic and nongenetic risk factors of an individual patient, advancing less expensive point-of-care genotyping technology and developing easy-to-use personalized clinical decision algorithms will help us to improve current clinical and economic outcomes associated with pain and opioid pain management.

A systematic review of cancer GWAS and candidate gene meta-analyses reveals limited overlap but similar effect sizes

Candidate gene and genome-wide association studies (GWAS) represent two complementary approaches to uncovering genetic contributions to common diseases. We systematically reviewed the contributions of these approaches to our knowledge of genetic associations with cancer risk by analyzing the data in the Cancer Genome-wide Association and Meta Analyses database (Cancer GAMAdb). The database catalogs studies published since January 1, 2000, by study and cancer type. In all, we found that meta-analyses and pooled analyses of candidate genes reported 349 statistically significant associations and GWAS reported 269, for a total of 577 unique associations. Only 41 (7.1%) associations were reported in both candidate gene meta-analyses and GWAS, usually with similar effect sizes. When considering only noteworthy associations (defined as those with false-positive report probabilities≤0.2) and accounting for indirect overlap, we found 202 associations, with 27 of those appearing in both meta-analyses and GWAS. Our findings suggest that meta-analyses of well-conducted candidate gene studies may continue to add to our understanding of the genetic associations in the post-GWAS era.

The association between the PPARγ2 Pro12Ala polymorphism and nephropathy susceptibility in type 2 diabetes: a meta-analysis based on 9,176 subjects

Background

The polymorphism Pro12Ala in peroxisome proliferator-activated receptor­γ2 gene (PPARγ2) has been reported to be associated with diabetic nephropathy (DN) in some studies, though the results remain inconclusive. To explore this relationship between PPARγ2 Pro12Ala polymorphism and the susceptibility for DN, a cumulative meta-analysis was performed in this study.

Method

PubMed, Medline, Embase and Web of Science databases have been systematically searched to identify relevant studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated.

Results

18 studies were included in this meta-analysis, involving 3,361 cases and 5,815 controls. The PPARγ2 Ala12 allele was significantly associated with decreased risk of DN based on dominant model (OR=0.778; 95%CI=0.618–0.981; P_{heterogeneity}=0.008; P=0.034). In the stratified analysis by ethnicity, significantly decreased risks were found among Caucasians for dominant model (OR=0.674; 95%CI=0.500–0.909; P_{heterogeneity}=0.079; P=0.010), while there was no significant association was found in Asians.

Conclusions

The results from the present meta-analysis indicated that the Pro12Ala polymorphism in PPARγ2 gene is not a risk factor for DN in type 2 diabetes (T2D). Further large and well-designed studies are needed to confirm this conclusion.

Virtual slides

The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/7491348341027320.

Identification of a KCNQ1 polymorphism acting as a protective modifier against arrhythmic risk in long-QT syndrome

BACKGROUND

Long-QT syndrome (LQTS) is characterized by such striking clinical heterogeneity that, even among family members carrying the same mutation, clinical outcome can range between sudden death and no symptoms. We investigated the role of genetic variants as modifiers of risk for cardiac events in patients with LQTS.

METHODS AND RESULTS

In a matched case-control study including 112 patient duos with LQTS from France, Italy, and Japan, 25 polymorphisms were genotyped based on either their association with QTc duration in healthy populations or on their role in adrenergic responses. The duos were composed of 2 relatives harboring the same heterozygous KCNQ1 or KCNH2 mutation: 1 with cardiac events and 1 asymptomatic and untreated. The findings were then validated in 2 independent founder populations totaling 174 symptomatic and 162 asymptomatic patients with LQTS, and a meta-analysis was performed. The KCNQ1 rs2074238 T-allele was significantly associated with a decreased risk of symptoms 0.34 (0.19-0.61; P<0.0002) and with shorter QTc (P<0.0001) in the combined discovery and replication cohorts.

CONCLUSIONS

We provide evidence that the KCNQ1 rs2074238 polymorphism is an independent risk modifier with the minor T-allele conferring protection against cardiac events in patients with LQTS. This finding is a step toward a novel approach for risk stratification in patients with LQTS.

Genetics of disc-related disorders: current findings and lessons from other complex diseases

Disc-related disorders are highly genetic conditions with heritability estimates of up to 75 % and yet, few genomic locations have been moderately associated with the disorders. Candidate gene studies have shown possible disease associations on loci and genes of 1p21.1 (COL11A1), 6q27 (THBS2), 9q22.31 (ASPN), 10p12.31 (SKT), 20q11.2 (GDF5) and 20q13.12 (MMP9). More recently, in 2012, the first genome-wide association study revealed variants on loci and genes of 3p26.2, 6p21.32 (HLA region) and 6q26 (PARK2) that associate with disc-related disorders. In many other complex diseases, large meta-analyses of hundreds of thousands of study subjects and loci have revealed remarkable pathways. As methodology is evolving rapidly, we have already stepped into the era of routinely sequencing all bases in all human exons and we are approaching the era of sequencing the entire genome of study subjects with common diseases. The past decade has taught us that the common variants seen throughout populations seem to have low effects in many common diseases, explain relatively little of the overall heritability of the diseases and demand thousands of study subjects to identify associations. It seems that familial rare variants play an important role in many common diseases leading us back to valuing studies with large families and isolated populations. Moreover, careful characterization of environmental conditions are needed to explore and determine gene-environment interactions as genes that increase disease risk in one context may not do so under another context.

The geometric increase in meta-analyses from China in the genomic era

Meta-analyses are increasingly popular. It is unknown whether this popularity is driven by specific countries and specific meta-analyses types. PubMed was used to identify meta-analyses since 1995 (last update 9/1/2012) and catalogue their types and country of origin. We focused more on meta-analyses from China (the current top producer of meta-analyses) versus the USA (top producer until recently). The annual number of meta-analyses from China increased 40-fold between 2003 and 2011 versus 2.4-fold for the USA. The growth of Chinese meta-analyses was driven by genetics (110-fold increase in 2011 versus 2003). The HuGE Navigator identified 612 meta-analyses of genetic association studies published in 2012 from China versus only 109 from the USA. We compared in-depth 50 genetic association meta-analyses from China versus 50 from USA in 2012. Meta-analyses from China almost always used only literature-based data (92%), and focused on one or two genes (94%) and variants (78%) identified with candidate gene approaches (88%), while many USA meta-analyses used genome-wide approaches and raw data. Both groups usually concluded favorably for the presence of genetic associations (80% versus 74%), but nominal significance (P<0.05) typically sufficed in the China group. Meta-analyses from China typically neglected genome-wide data, and often included candidate gene studies published in Chinese-language journals. Overall, there is an impressive rise of meta-analyses from China, particularly on genetic associations. Since most claimed candidate gene associations are likely false-positives, there is an urgent global need to incorporate genome-wide data and state-of-the art statistical inferences to avoid a flood of false-positive genetic meta-analyses.

Credibility analysis of putative disease-causing genes using bioinformatics

Background

Genetic studies are challenging in many complex diseases, particularly those with limited diagnostic certainty, low prevalence or of old age. The result is that genes may be reported as disease-causing with varying levels of evidence, and in some cases, the data may be so limited as to be indistinguishable from chance findings. When there are large numbers of such genes, an objective method for ranking the evidence is useful. Using the neurodegenerative and complex disease amyotrophic lateral sclerosis (ALS) as a model, and the disease-specific database ALSoD, the objective is to develop a method using publicly available data to generate a credibility score for putative disease-causing genes.

Methods

Genes with at least one publication suggesting involvement in adult onset familial ALS were collated following an exhaustive literature search. SQL was used to generate a score by extracting information from the publications and combined with a pathogenicity analysis using bioinformatics tools. The resulting score allowed us to rank genes in order of credibility. To validate the method, we compared the objective ranking with a rank generated by ALS genetics experts. Spearman's Rho was used to compare rankings generated by the different methods.

Results

The automated method ranked ALS genes in the following order: SOD1, TARDBP, FUS, ANG, SPG11, NEFH, OPTN, ALS2, SETX, FIG4, VAPB, DCTN1, TAF15, VCP, DAO. This compared very well to the ranking of ALS genetics experts, with Spearman's Rho of 0.69 (P = 0.009).

Conclusion

We have presented an automated method for scoring the level of evidence for a gene being disease-causing. In developing the method we have used the model disease ALS, but it could equally be applied to any disease in which there is genotypic uncertainty.

APC polymorphisms and the risk of colorectal neoplasia: a HuGE review and meta-analysis

Adenomatous polyposis coli gene (APC) polymorphisms may influence the risk for colorectal neoplasia. However, results thus far have been inconclusive. We performed a systematic literature search of the Medline, Embase, Cochrane Collaboration, and HuGE databases and reviewed the references of pertinent articles through May 2012. Odds ratios with 95% confidence intervals were used to estimate the association between 3 APC polymorphisms (D1822V, E1317Q, and I1307K) and colorectal neoplasia. In total, 40 studies from 1997 to 2010 were included in this meta-analysis, and individuals with the D1822V variant homozygote VV genotype had a slight decrease in the risk for colorectal neoplasia compared with the wild-type homozygote DD genotype (pooled odds ratio = 0.87, 95% confidence interval: 0.77, 0.99). There was a small association between the APC E1317Q polymorphism and a risk for colorectal neoplasia (variant vs. wild-type: pooled odds ratio = 1.41, 95% confidence interval: 1.14, 1.76), particularly for colorectal adenomas (variant vs. wild-type: odds ratio = 2.89, 95% confidence interval: 1.83, 4.56). Compared with those who carried the wild-type I1307K, Ashkenazi Jews who carried the I1307K variant were at a significantly increased risk for colorectal neoplasia, with a pooled odds ratio of 2.17 (95% confidence interval: 1.64, 2.86). Our study suggests that APC is a candidate gene for colorectal neoplasia susceptibility.

Association between insulin receptor substrate 1 Gly972Arg polymorphism and cancer risk

Epidemiological studies investigating the association between the insulin receptor substrate 1 (IRS1) gene Gly972Arg (rs1801278) polymorphism and various carcinomas risk reported conflicting results. Thus, a systemic review and meta-analysis of published studies were performed to assess the possible association. A comprehensive search was conducted to identify all eligible studies of IRS1 Gly972Arg polymorphism and cancer risk. Odds ratios (ORs) and 95 % confidence intervals (CIs) were used to assess the strength of the associations. A total of 16 independent studies, including 11,776 cases and 11,654 controls, were identified. When all studies were pooled, we found a significant association between IRS1 Gly972Arg polymorphism and increased cancer risk under dominant model (OR = 1.16, 95 %CI = 1.04-1.30, P = 0.007) and allelic model (OR = 1.16, 95 %CI = 1.02-1.30, P = 0.02). In subgroup analysis based on cancer type, increased cancer risk was found in ovarian cancer (dominant: OR = 1.55, 95 %CI = 1.17-2.05, P = 0.002; allelic: OR = 1.55, 95 %CI = 1.19-2.01, P = 0.001), breast cancer (allelic: OR = 1.12, 95 %CI = 1.00-1.26, P = 0.05), and other cancers (allelic: OR = 1.31, 95 %CI = 1.00-1.71, P = 0.05). When stratified by study types, significant associations were observed in both cohort studies (dominant: OR = 1.25, 95 %CI = 1.06-1.47, P = 0.007; allelic: OR = 1.25, 95 %CI = 1.07-1.46, P = 0.005) and case-control studies (dominant: OR = 1.15, 95 %CI = 1.01-1.31, P = 0.04). In the subgroup analyses by ethnicity, significantly increased cancer risk was suggested among both Caucasians (dominant: OR = 1.13, 95 %CI = 1.02-1.26, P = 0.02; allelic: OR = 1.13, 95 %CI = 1.03-1.25, P = 0.01) and mixed population (dominant: OR = 1.22, 95 %CI = 1.01-1.46, P = 0.04). Our investigations demonstrate that IRS1 Gly972Arg polymorphism was associated with an increased risk of cancer, and additional well-designed studies are warranted to validate these findings.

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.

Use of genomic panels to determine risk of developing type 2 diabetes in the general population: a targeted evidence-based review

This evidence review addresses whether type 2 diabetes genomic risk panels improve health outcomes (e.g., reduce rates of developing type 2 diabetes) in low- or high-risk adults; two clinical scenarios promulgated by commercial companies offering such testing. Evidence for the analytic validity of available genomic profiles was inadequate. Clinical validity ranged from inadequate to convincing for 30 variants identified on five type 2 diabetes genomic panels and by genome-wide association studies. Eight common variants were identified for general population use; evidence credibility based on published criteria was strong for two variants, moderate for two variants, and weak for four variants. TCF7L2 had the largest per-allele odds ratio of 1.39 (95% confidence interval 1.33-1.46). Models combining the best four, best eight, and all 30 variants used summary effect sizes, reported genotype frequencies, and assumed independent effects. Areas under the curve were 0.547, 0.551, and 0.570, respectively. In high-risk populations, per-allele odds ratios for TCF7L2 alone were similar to those of the general population. TCF7L2, in combination with other variants, yielded minimal improvement in risk reclassification. Evidence on TCF7L2 clinical validity was adequate. Three studies addressed the clinical utility of intervention effectiveness, stratified by TCF7L2 genotype; none found significant interactions. Clinical utility evidence was inadequate. In addition to analytic validity and clinical utility knowledge gaps, additional gaps were identified regarding how to inform, produce, and evaluate models combining multiple variants.

Recommendations from the EGAPP Working Group: does genomic profiling to assess type 2 diabetes risk improve health outcomes?

SUMMARY OF RECOMMENDATIONS

The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group (EWG) found insufficient evidence to recommend testing for predictive variants in 28 variants (listed in Table 1) to assess risk for type 2 diabetes in the general population, on the basis of studies in populations of northern European descent. The EWG found that the magnitude of net health benefit from the use of any of these tests alone or in combination is close to zero. The EWG discourages clinical use unless further evidence supports improved clinical outcomes.The EWG found insufficient evidence to recommend testing for the TCF7L2 gene to assess risk for type 2 diabetes in high-risk individuals. The EWG found that the magnitude of net health benefit from the use of this test is close to zero. The EWG discourages clinical use unless further evidence supports improved clinical outcomes.On the basis of the available evidence for both the scenarios, the overall certainty of net health benefit is deemed "low."

RATIONALE

It has been suggested that genomic profiling in the general population or in high-risk populations for type 2 diabetes might lead to management changes (e.g., earlier initiation or higher rates of medical interventions, or targeted recommendations for behavioral change) that improve type 2 diabetes outcomes or prevent type 2 diabetes. The EWG found no direct evidence to support this possibility; therefore, this review sought indirect evidence aimed at documenting the extent to which genomic profiling alters type 2 diabetes risk estimation, alone and in combination with traditional risk factors, and the extent to which risk classification improves health outcomes.

ANALYTIC VALIDITY

Assay-related evidence on available genomic profiling tests was deemed inadequate. However, on the basis of existing technologies that have been or may be used, the analytic sensitivity and specificity of tests for individual gene variants might be at least satisfactory.

CLINICAL VALIDITY

Twenty-eight candidate markers were evaluated in the general population. Evidence on clinical validity was rated inadequate for 24 of these associations (86%) and adequate for 4 (14%). Inadequate grades were based on limited evidence, poor replication, existence of possible biases, or combinations of these factors. Type 2 diabetes genomic profiling provided areas under the receiver operator characteristics curve of 55%-57%, with 4, 8, and 28 genes. Only TCF7L2 had convincing evidence of an association with type 2 diabetes with an odds ratio of 1.39 (95% confidence interval: 1.33-1.46).TCF7L2 was evaluated for high-risk populations, and the overall odds ratio was 1.66 (95% confidence interval: 1.22-2.27) for association with progression to type 2 diabetes.

CLINICAL UTILITY

No studies were available to provide direct evidence on the balance of benefits and harms for genetic profiling for type 2 diabetes alone or in addition to traditional risk factors in the general population.Evidence for high-risk populations and TCF7L2 was inadequate on the basis of two identified studies. These studies found close to zero additional benefit with the addition of genomic markers to traditional risk factors (diet, body mass index, and glucose tolerance).

CONTEXTUAL ISSUES

Prevention of type 2 diabetes is a public health priority. Improvements in the outcomes associated with genomic profiling could have important impacts. Traditional risk factors (e.g., body mass index, weight, fat mass, and exercise) have an advantage in clinical screening and risk assessment strategies because they measure the actual targets for therapy (e.g., fasting plasma glucose and medical interventions). To be useful in predicting disease risk, genomic testing should improve the predictive value of these traditional risk factors. Some issues important for clinical utility remain unknown, such as the level of risk that changes intervention, whether long-term disease outcomes will improve, how individuals being tested will understand/respond to test results and interact with the health-care system, and whether testing will motivate behavior change or amplify potential harms.

C677T polymorphism of methylenetetrahydrofolate reductase may contribute to cervical cancer risk in complete over-dominant model

PURPOSE

Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in the metabolism of folate. The single nucleotide polymorphism (SNP), C677T (Ala>Val, rs1801133), has been confirmed to decrease the enzyme activity. The association between C677T and cervical cancer susceptibility has been widely studied. However, the results were inconsistent. In order to elucidate the role of this SNP in cervical cancer, a meta-analysis was conducted.

METHODS

The literature search was performed using the following databases: PubMed, Embase and ISI Web of Science up to December 2012. The effect of association was indicated as crude odds ratio (OR) with the corresponding 95% confidence interval (CI).

RESULTS

Six studies including 1431 cases and 1915 controls explored C677T genotypes were involved in this meta-analysis. Overall meta-analysis showed that C677T polymorphism increased cervical cancer risk in the complete over-dominant model (random-effect OR=1.33, 95% CI: 1.00-1.77, I(2)=69%). After excluding one study which showed apparent heterogeneity, the heterogeneity disappeared. The meta-analysis of five studies including 1231 cases and 1715 controls showed the fixed-effect OR reached 1.20 (95% CI: 1.03-1.40, I(2)=0) as (TT+CC) in the complete over-dominant model.

CONCLUSIONS

C677T polymorphism of MTHFR gene may increase the risk of cervical cancer in the complete over-dominant model. The association merits replicating and validating in further studies.

Association of SMAD7 rs12953717 polymorphism with cancer: a meta-analysis

BACKGROUND

Accumulating evidence has suggested that Mothers against decapentaplegic homolog 7 (SMAD7) rs12953717 polymorphism might be related to cancer risk. However, epidemiologic findings have been inconsistent. We therefore performed a meta-analysis to clarify the association between the SMAD7 rs12953717 polymorphism and cancer risk.

METHODS

A comprehensive search was conducted to identify all eligible studies of SMAD7 rs12953717 polymorphism and cancer risk. We used odds ratios (ORs) to assess the strength of the association, and 95% confidence intervals (CIs) to give a sense of the precision of the estimate. Heterogeneity, publication bias, and sensitivity analysis were also explored.

RESULTS

A total of 14 case-control studies, including 16928 cases and 14781 controls, were included in the present meta-analysis. The overall results showed that the variant genotypes were associated with a significantly increased risk of all cancer types (homozygote comparison, OR = 1.23, 95%CI = 1.10-1.38, P<0.01; heterozygote comparison, OR = 1.12, 95%CI = 1.02-1.22, P = 0.02; recessive model, OR = 1.17, 95%CI = 1.07-1.29, P<0.01; dominant model, OR = 1.15, 95%CI = 1.06-1.25, P<0.01; allelic model, OR = 1.12, 95%CI = 1.06-1.18, P<0.01). Further sensitivity analysis confirmed the significant association. In the subgroup analysis by ethnicity, SMAD7 rs12953717 polymorphism was significantly associated with cancer risk in both Caucasians and Asians. In the subgroup analysis by cancer types, SMAD7 rs12953717 polymorphism was significantly associated with colorectal cancer.

CONCLUSIONS

Our investigations demonstrate that rs12953717 polymorphism is associated with the susceptibility of cancer. Large-scale and well-designed case-control studies are necessary to validate the risk identified in the present meta-analysis.

A family-based association analysis and meta-analysis of the reading disabilities candidate gene DYX1C1

Reading disabilities (RD) have a significant genetic basis and have shown linkage to multiple regions including chromosome 15q. Dyslexia susceptibility 1 candidate gene 1 (DYX1C1) on chromosome 15q21 was originally proposed as a candidate gene with two potentially functional polymorphisms at the -3G/A and 1249G/T positions showing association with RD. However, subsequent studies have yielded mixed results. We performed a literature review and meta-analysis of the -3G/A and 1249G/T polymorphisms, including new unpublished data from two family-based samples. Ten markers in DYX1C1 were genotyped in the two independently ascertained samples. Single marker and -3G/A:1249G/T haplotype analyses were performed for RD in both samples, and quantitative trait analyses using standardized reading-related measures was performed in one of the samples. For the meta-analysis, we used a random-effects model to summarize studies that tested for association between -3G/A or 1249G/T and RD. No significant association was found between the DYX1C1 SNPs and RD or any of the reading-related measures tested after correction for the number of tests performed. The previously reported risk haplotype (-3A:1249T) was not biased in transmission. A total of 9 and 10 study samples were included in the meta-analysis of the -3G/A and 1249G/T polymorphisms, respectively. Neither polymorphism reached statistical significance, but the heterogeneity for the 1249G/T polymorphism was high. The results of this study do not provide evidence for association between the putatively functional SNPs -3G/A and 1249G/T and RD.

Neurocarta: aggregating and sharing disease-gene relations for the neurosciences

BACKGROUND

Understanding the genetic basis of diseases is key to the development of better diagnoses and treatments. Unfortunately, only a small fraction of the existing data linking genes to phenotypes is available through online public resources and, when available, it is scattered across multiple access tools.

DESCRIPTION

Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 7,000 genes to 2,000 different phenotypes.

CONCLUSIONS

Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Functional regulation of Alu element of human angiotensin-converting enzyme gene in neuron cells

The angiotensin-converting enzyme (ACE) insertion/deletion (I/D) genotype and its protein activity have been widely implicated to be associated with Alzheimer's disease (AD). However, whether the insertion sequence, Alu element, in intron 16 of the human ACE gene plays a functional role remains uncertain. To investigate the influence of the I/D polymorphism on ACE promoter, we recombined the I and D form fragments with the human ACE promoter sequence before the reporter gene in pSEAP-Basic2 vector. The effect of the Alu element on regulating the transcriptional activity of ACE promoter was examined using transient transfection in SH-SY5Y cells. We found that the I form fragment upregulated the transcriptional activity of ACE promoter by approximately 70% but that the D form fragment did not. Our study first reveals that Alu sequence in human ACE gene possesses a regulatory function on the ACE promoter activity in neuron. This novel finding bridges the gap between the association of ACE I/D genotype with AD, and suggests that Alu sequence is not merely a "junk" DNA in human ACE gene.

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.

GSTT1 null genotype is associated with an increased risk of prostate cancer in caucasians: a meta-analysis

BACKGROUND

Many studies have investigated the association between glutathione S-transferase T1 (GSTT1) null genotype and the risk of prostate cancer (PCa), but the impact of GSTT1 null genotype on PCa risk in Caucasians is still unclear owing to the inconsistency of such studies. The present study aimed to quantify the strength of association between GSTT1 null genotype and the risk of PCa in Caucasians.

METHODS

We searched the PubMed, Embase and Web of Science databases for studies assessing the association between GSTT1 null genotype and the risk of PCa in Caucasians. We estimated the summary odds ratio (OR) with the corresponding 95% confidence interval (95% CI) to assess the association.

RESULTS

16 case-control studies with 11,648 subjects were included in this meta-analysis. Meta-analysis of a total of 16 studies showed GSTT1 null genotype was significantly associated with an increased risk of PCa in Caucasians (random-effects OR 1.30, 95% CI 1.10-1.53, p = 0.002). After adjustment for heterogeneity, GSTT1 null genotype was still associated with an increased risk of PCa in Caucasians (fixed-effects OR 1.33, 95% CI 1.17-1.52, p < 0.001). The cumulative meta-analyses of all 16 studies showed a trend of more obvious association as information accumulated by year.

CONCLUSIONS

Meta-analysis of available data suggests the GSTT1 null genotype is significantly associated with an increased risk of PCa in Caucasians.

A serotonin transporter gene (SLC6A4) polymorphism is associated with reduced risk of irritable bowel syndrome in American and Asian population: a meta-analysis

AIM

Association studies of serotonin transporter gene SLC6A4 I/S polymorphism and irritable bowel syndrome (IBS) have shown inconsistent and contradictory results among different populations. In the present study, meta-analysis was performed to evaluate the association between SLC6A4 I/S polymorphism and IBS susceptibility.

METHODOLOGY

Systemic assessment was performed for the published studies based on the association of SLC6A4 I/S polymorphism and IBS risk from PubMed (Medline), EMBASE search. A meta-analysis was done to appraise the said association. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated for allele contrast, homozygous, heterozygous, dominant and recessive genetic model.

RESULTS

A total of twelve studies comprising 2068 IBS cases and 2076 controls were included in this meta-analysis. Overall, no significant results were obtained for S allele carrier (S vs. I: p=0.488; OR=1.073, 95% CI=0.879 to 1.311) Co-dominant (SS vs. II; p=0.587; OR=1.112, 95% CI=0.758 to 1.631), (IS vs. II; p=0.361; OR=0.878, 95% CI=0.665 to 1.160). Similarly, dominant (SS+IS vs. II: p=0.853; OR=0.974, 95% CI=0.736 to 1.288) and recessive (SS vs. II+IS: p=0.267; OR=1.172, 95% CI=0.886 to 1.522) genetic models did not demonstrate risk. In the subgroup population based analysis, reduced risks were found in American (IS vs. II: p=0.009; OR=0.685, 95% CI=0.516 to 0.908) and Asian (SS+IS vs. II; p=0.001; OR=0.116, 95% CI=0.068 to 0.197) population. However, no risk was observed in European population.

CONCLUSIONS

This investigation clearly demonstrates that SLC6A4 (Ins/Del) polymorphism is associated with reduced risk of IBS in American and Asian population. However, future well-designed studies with stratified case control and biological characterization will be needed to validate this finding.

Pro variant of TP53 Arg72Pro contributes to gastric cancer risk in Asians: evidence from a meta-analysis

BACKGROUND

Previous studies investigating the association between TP53 Arg72Pro polymorphism and gastric cancer (GC) risk in Asian population have reported controversial results. Thus, a meta-analysis was performed.

METHODS

A comprehensive literature search was conducted and 17 case-control studies were finally included, involving a total of 5,990 GC cases and 6,812 controls. Subgroup analyses were performed by the sample size.

RESULTS

Meta-analysis of all 17 studies showed variant genotypes of TP53 Arg72Pro to be associated with an elevated GC risk in three genetic comparison models (OR(Pro vs. Arg)=1.13, 95%CI 1.03-1.25, P(OR)=0.01; OR(Homozygote comparison model)=1.33, 95%CI 1.07-1.64, P(OR)=0.009; OR(Dominant genetic model)=1.13, 95%CI 1.05-1.22, P(OR)=0.002). Besides, a more obvious association was observed after the heterogeneity was decreased (all P values less than 0.001). This association was further identified by both subgroup and sensitivity analyses.

CONCLUSIONS

This meta-analysis suggests the Pro variant of TP53 Arg72Pro contributes to gastric cancer risk in Asians.

Genetic association studies in lumbar disc degeneration: a systematic review

Objective

Low back pain is associated with lumbar disc degeneration, which is mainly due to genetic predisposition. The objective of this study was to perform a systematic review to evaluate genetic association studies in lumbar disc degeneration as defined on magnetic resonance imaging (MRI) in humans.

Methods

A systematic literature search was conducted in MEDLINE, MEDLINE In-Process, SCOPUS, ISI Web of Science, The Genetic Association Database and The Human Genome Epidemiology Network for information published between 1990–2011 addressing genes and lumbar disc degeneration. Two investigators independently identified studies to determine inclusion, after which they performed data extraction and analysis. The level of cumulative genetic association evidence was analyzed according to The HuGENet Working Group guidelines.

Results

Fifty-two studies were included for review. Forty-eight studies reported at least one positive association between a genetic marker and lumbar disc degeneration. The phenotype definition of lumbar disc degeneration was highly variable between the studies and replications were inconsistent. Most of the associations presented with a weak level of evidence. The level of evidence was moderate for ASPN (D-repeat), COL11A1 (rs1676486), GDF5 (rs143383), SKT (rs16924573), THBS2 (rs9406328) and MMP9 (rs17576).

Conclusions

Based on this first extensive systematic review on the topic, the credibility of reported genetic associations is mostly weak. Clear definition of lumbar disc degeneration phenotypes and large population-based cohorts are needed. An international consortium is needed to standardize genetic association studies in relation to disc degeneration.

Knowledge integration in cancer: current landscape and future prospects

Knowledge integration includes knowledge management, synthesis, and translation processes. It aims to maximize the use of collected scientific information and accelerate translation of discoveries into individual and population health benefits. Accumulated evidence in cancer epidemiology constitutes a large share of the 2.7 million articles on cancer in PubMed. We examine the landscape of knowledge integration in cancer epidemiology. Past approaches have mostly used retrospective efforts of knowledge management and traditional systematic reviews and meta-analyses. Systematic searches identify 2,332 meta-analyses, about half of which are on genetics and epigenetics. Meta-analyses represent 1:89-1:1162 of published articles in various cancer subfields. Recently, there are more collaborative meta-analyses with individual-level data, including those with prospective collection of measurements [e.g., genotypes in genome-wide association studies (GWAS)]; this may help increase the reliability of inferences in the field. However, most meta-analyses are still done retrospectively with published information. There is also a flurry of candidate gene meta-analyses with spuriously prevalent "positive" results. Prospective design of large research agendas, registration of datasets, and public availability of data and analyses may improve our ability to identify knowledge gaps, maximize and accelerate translational progress or-at a minimum-recognize dead ends in a more timely fashion.

Significant association between GSTT1 null genotype and risk of asthma during childhood in Caucasians

Asthma is a complex multifactorial disorder and its management requires a better understanding of its various pathogenesis and mechanisms. Previous studies assessing the association between glutathione S-transferase T1 (GSTT1) null genotype and asthma risk during childhood reported conflicting results. To get a more precise estimation of the association between GSTT1 null genotype and risk of asthma during childhood, we performed a meta-analysis of 16 studies with a total of 18,558 subjects. Subgroup analyses were performed by ethnicity. The pooled odds ratio (OR) with corresponding 95 % confidence interval (95 %CI) was used to assess the association. Overall, there was a significant association between GSTT1 null genotype and increased risk of children asthma (OR = 1.25, 95 % CI, 1.02-1.54; P = 0.032). Subgroup analyses showed GSTT1 null genotype was associated with increased risk of children asthma in Caucasians (OR = 1.46, 95 % CI, 1.04-2.03; P = 0.027), but not in Asians (OR = 1.03, 95 % CI, 0.55-1.94; P = 0.928) and Africans (OR = 1.33, 95 % CI, 0.92-1.91; P = 0.127). There was no evidence of publication bias in the subgroup analysis of Caucasians. In conclusion, there is a significant association between GSTT1 null genotype and risk of asthma during childhood in Caucasians. More well-designed epidemiological studies are needed to further assess this association in Asians and Africans.

Association between the OGG1 Ser326Cys and APEX1 Asp148Glu polymorphisms and lung cancer risk: a meta-analysis

The previous published data on the association between the 8-oxo-guanine glycosylase-1 (OGG1) and apurinic/apyrimidinic-endonuclease-1 (APEX1/APE1) polymorphisms and lung cancer risk remained controversial. Several polymorphisms in the OGG1 and APEX1 gene have been described, including the commonly occurring Ser326Cys in OGG1 and Asp148Glu in APEX1. This meta-analysis of literatures was performed to derive a more precise estimation of the relationship. A total of 37 studies were identified to the meta-analysis, including 9,203 cases and 10,994 controls for OGG1 Ser326Cys (from 25 studies) and 3,491 cases and 4,708 controls for APEX1 Asp148Glu (from 12 studies). When all the eligible studies were pooled into the meta-analysis of OGG1 Ser326Cys polymorphism, significantly increased lung cancer risk was observed in recessive model (OR = 1.17, 95 % CI = 1.03-1.33) and in additive model (OR = 1.21, 95 % CI = 1.03-1.42). In the stratified analysis, significantly increased risk of lung cancer was also observed on the population-based studies (recessive model: OR = 1.26, 95 % CI = 1.08-1.46, additive model: OR = 1.42, 95 % CI = 1.06-1.73) and non-smokers (dominant model: OR = 1.20, 95 % CI = 1.02-1.42, recessive model: OR = 1.20, 95 % CI = 1.02-1.40, additive model: OR = 1.35, 95 % CI = 1.08-1.68). Additionally, when one study was deleted in the sensitive analysis, the results of OGG1 Ser326Cys were changed in Asians (recessive model: OR = 1.16, 95 % CI = 1.06-1.27, additive model: OR = 1.23, 95 % CI = 1.09-1.38). When all the eligible studies were pooled into the meta-analysis of APEX1 Asp148Glu polymorphism, there was no evidence of significant association between lung cancer risk and APEX1 Asp148Glu polymorphism in any genetic model. In the stratified analysis, significantly decreased lung adenocarcinoma risk was observed in recessive model (OR = 0.68, 95 % CI = 0.48-0.97, P (h) = 0.475, I(2) = 0.0 %). Additionally, when one study was deleted in the sensitive analysis, the results of APEX1 Asp148Glu were changed in Asians (recessive model: OR = 1.21, 95 % CI = 1.03-1.43) and smokers (dominant model: OR = 1.62, 95 % CI = 1.08-2.44, additive model: OR = 1.37, 95 % CI = 1.02-1.84). In summary, this meta-analysis indicates that OGG1 Ser326Cys show an increased lung cancer risk in Asians and non-smokers, APEX1 Asp148Glu polymorphism may be associated with decreased lung adenocarcinoma risk, and APEX1 Asp148Glu polymorphism show an increased lung cancer risk in Asians and smokers. However, a study with the larger sample size is needed to further evaluated gene-environment interaction on OGG1 Ser326Cys and APEX1 Asp148Glu polymorphisms and lung cancer risk.

Three polymorphisms in the IL-10 gene and the risk of HCV infection: a meta-analysis plus a Chinese Association Study involving 1140 subjects

The influence of an immunosuppressive cytokine, interleukin-10 (IL-10), on the outcome of hepatitis C virus (HCV) infection has been increasingly reported recently. A number of polymorphisms appear to control the level of IL-10 production. Among them, −592C/A, −819C/T and −1082G/A in the IL-10 gene are three most studied single nucleotide polymorphisms. To provide a more definitive conclusion about their association with the risk of HCV infection, a meta-analysis was performed by combining and summarizing a total of 17 studies. A biological justification for the choice of genetic model was provided. The results indicated no significant association between these IL-10 polymorphisms and the susceptibility to HCV infection [–592C/A: odds ratio (OR) 0·99, 95% confidence interval (CI) 0·78–1·25; –819C/T: OR 0·90, 95% CI 0·69–1·18; –1082G/A: OR 1·34, 95% CI 0·90–2·00]. However, this analysis did not account for the possible risk modifications by other factors, such as ethnicity and virus persistence. Therefore, the effects of ethnicity and virus persistence were investigated using Bayesian meta-regression and subgroup analysis. Finally, an extended case-control association study was conducted in a Chinese population involving 1140 subjects. Both serum level and genotype data of IL-10 −1082G/A were determined. As a result, a low prevalence of G allele was observed. Significantly higher IL-10 production was observed in HCV patients, especially patients with the GG genotype.

Association between common polymorphism near the MC4R gene and obesity risk: a systematic review and meta-analysis

BACKGROUND

Genome-wide association studies on Europeans have shown that two polymorphisms (rs17782313, rs12970134) near the melanocortin 4 receptor (MC4R) gene were associated with increased risk of obesity. Subsequently studies among different ethnic populations have shown mixed results with some confirming and others showing inconsistent results, especially among East Asians and Africans. We performed a comprehensive meta-analysis of various studies from different ethnic populations to assess the association of the MC4R polymorphism with obesity risk.

METHODS

We retrieved all published literature that investigated association of MC4R variants with obesity from PubMed and Embase. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated using fixed- or random-effects model.

RESULTS

A total of 61 studies (80,957 cases/220,223 controls) for rs17782313 polymorphism (or proxy) were included in the meta-analysis. The results suggested that rs17782313 polymorphism was significantly associated with obesity risk (OR=1.18, 95%CI=1.15-1.21, p<0.001). Similar trends were observed among subgroups of Europeans and East Asians, adults and children, studies with high quality score, and for each five MC4R polymorphisms independently.

CONCLUSIONS

The present meta-analysis confirms the significant association of MC4R polymorphism with risk of obesity. Further studies should be conducted to identify the causal variant and the underlying mechanisms of the identified association.

Hemochromatosis gene (HFE) polymorphisms and risk of type 2 diabetes mellitus: a meta-analysis

The hemochromatosis gene (HFE) has been involved in the etiology of type 2 diabetes mellitus and investigated in numerous epidemiologic studies. The current meta-analysis was conducted to evaluate the gene-disease association in relevant studies. Electronic literature search was performed on June 18, 2011, from databases of PubMed/MEDLINE, EMBASE, and HuGE Navigator. Articles were inspected by 2 authors independently, and data were extracted by identical extraction form. A total of 5,528 type 2 diabetes cases and 6,920 controls in relation to HFE polymorphisms (a cysteine to tyrosine substitution at amino acid position 282 (C282Y) and a histidine to aspartate substitution at amino acid position 63 (H63D)) were included in the meta-analysis (1997-2011). A fixed- or random-effect model was used to calculate the pooled odds ratios based on the results from the heterogeneity tests. An increased odds ratio for type 2 diabetes mellitus was observed in persons carrying a D allele at the H63D polymorphism compared with those with an H allele (odds ratio (OR) = 1.21, 95% confidence interval (CI): 1.03, 1.41; P = 0.02). Moreover, carriers of a D allele had a modestly increased risk compared with persons with the wild genotype (OR = 1.12, 95% CI: 1.00, 1.25; P = 0.04). The C282Y variant was not significantly associated with diabetes risk. In summary, persons with a D allele may have a moderately increased risk of type 2 diabetes mellitus.

The effect of XPD/ERCC2 polymorphisms on gastric cancer risk among different ethnicities: a systematic review and meta-analysis

Background

Potential xeroderma pigmentosum group D (XPD), also called excision repair cross-complimentary group two (ERCC2), Lys751Gln and Asp312Asn polymorphisms have been implicated in gastric cancer risk among different ethnicities.

Methods

We aimed to explore the effect of XPD Lys751Gln and Asp312Asn polymorphisms on the susceptibility to gastric cancer among different ethnicities through a systematic review and meta-analysis. Each initially included article was scored for quality appraisal. Desirable data were extracted and registered into databases. 13 studies were ultimately eligible for the meta-analysis of Lys751Gln polymorphism and 9 studies for the meta-analysis of Asp312Asn polymorphism. We adopted the most probably appropriate genetic model (recessive model) for both Lys751Gln and Asp312Asn polymorphisms. Potential sources of heterogeneity were sought out via subgroup and sensitivity analyses, and publication biases were estimated.

Results

Statistically significant findings were apparently noted in Asians but not in Caucasians for both XPD Lys751Gln and XPD Asp312Asn polymorphisms. A statistically significant finding could be seen in noncardia-type gastric cancer for XPD Lys751Gln polymorphism. A statistically significant finding could also be seen in high quality subgroup, small-and-moderate sample size subgroup, articles published after 2007, or PCR-RFLP genotyping subgroup for XPD Asp312Asn polymorphism.

Conclusions

Our meta-analysis indicates that XPD Gln751Gln (CC) genotype and Asn312Asn (AA) genotype may seem to be more susceptible to gastric cancer in Asian populations but not in Caucasian populations, suggesting that the two genotypes may be important biomarkers of gastric cancer susceptibility for Asian populations, the assumption that needs to be further confirmed in well-designed studies among different ethnicities. Gln751Gln (CC) genotype may also be associated with noncardia-type gastric cancer risk, which should also be confirmed among different ethnicities in the future.