Allele Comparison Research Articles

Association of GWAS-supported noncoding area loci rs404860, rs3117098, and rs7775228 with asthma in Chinese Zhuang population.

BackgroundAsthma is a complicated and polygenic inheritance disease, and its prevalence increases worldwide. Recent genome‐wide association studies (GWASs) identified a significant association of single nucleotide polymorphism with asthma in the Japanese population. This study aimed to examine the association of GWAS‐supported noncoding area loci, namely rs404860, rs3117098, and rs7775228, with asthma in Chinese Zhuang population.MethodsA case‐control study involving 223 individuals, comprising 123 patients with asthma and 100 healthy controls, was conducted. Genotypes were determined by polymerase chain reaction (PCR)/ligase detection reaction assay. The association between gene polymorphisms and asthma risk was calculated by logistic regression analysis using different genetic models through comparisons of alleles (A vs a), homozygote genotypes (AA vs aa), heterozygote genotypes (Aa vs aa), dominant models (AA+Aa vs aa), and recessive models (AA vs. Aa+aa).ResultsThe distribution of the genotype frequency of rs3117098 was statistically different between the case and control groups. For rs3117098, significant associations were observed through comparisons of alleles (OR: 1.832, 95% CI: 1.048‐3.204, P = .034) and dominant models (OR: 2.065, 95% CI: 1.001‐4.260, P = .050). The statistical analysis showed no significant difference for loci rs404860 and rs7775228 between patients with asthma and controls.Conclusionrs3117098 may be the risk factor for asthma in Chinese Zhuang population.

Vitamin D receptor ApaI (rs7975232), BsmI (rs1544410), Fok1 (rs2228570), and TaqI (rs731236) gene polymorphisms and susceptibility to pulmonary tuberculosis in an Iranian population: A systematic review and meta-analysis

Polymorphisms of vitamin D receptors (VDRs), ApaI, BsmI, FokI, and TaqI might affect susceptibility to tuberculosis (TB). In this systematic review and meta-analysis, all published articles which investigated the effects of these polymorphisms on the risk of TB in the Iranian population were retrieved. PubMed and Scopus were searched with no date or language restrictions. In this meta-analysis, the Comprehensive Meta-Analysis (CMA) version 2.0 and random effects model were applied. The association of polymorphisms with TB risk was assessed by measuring the odds ratio (ORs) at 95% CI. Heterogeneity was investigated based on Cochran Q-test and I2-index statistics. The significance level was set at 0.05. Also, Egger's regression intercept was determined to measure publication bias. A total of six articles on Iranian populations were included. TaqI (5/6 included studies) showed a significant association with the increased risk of TB based on ORs (allele comparison: 1.57 (1.0, 2.3), p-value: 0.02; additive model of tt/TT: 1.57 (0.9, 2.5), p-value: 0.05; recessive model (tt/Tt+TT): 1.99 (1.2, 3.2), p-value: 0.00; dominant model (tt+Tt/TT): 1.98 (1.1, 3.5), p-value: 0.01). BsmI showed a significant positive effect on TB risk only in its dominant genotype (bb+bB/BB) (1.44 (1.0, 1.9); p-value: 0.02). FokI and ApaI did not show any significant effects on TB development in Iranian populations. Findings showed the significant effect of TaqI polymorphism in all genetic models and the dominant model of BsmI on the increased risk of TB. However, the effects of TaqI and BsmI should be further investigated in a larger sample size.

Associations of six common functional polymorphisms in interleukins with tuberculosis: evidence from a meta-analysis

Associations of polymorphisms in interleukin-6 (IL-6), IL-8 and IL-10 with tuberculosis (TB) susceptibility were already reported by many publications. The aim of this meta-analysis was to more precisely clarify associations between polymorphisms in IL-6/IL-8/IL-10 and TB by combing the results of all relevant publications. Eligible publications were searched from PubMed, Embase, Web of Science and CNKI. We used Review Manager to combine the results of individual studies. A total of 47 publications were included in this study. IL-6 rs1800795 (1750 cases and 2335 controls, dominant, recessive and allele comparisons), IL-8 rs4073 (1125 cases and 1188 controls, dominant, recessive and allele comparisons), IL-10 rs1800871 (5528 cases and 7671 controls, dominant, recessive and allele comparisons), IL-10 rs1800872 (5269 cases and 7013 controls, dominant and allele comparisons) and IL-10 rs1800896 (7564 cases and 8952 controls, recessive comparison) polymorphisms were all significantly associated with TB in overall combined analyses. In subgroup analyses, we found that the positive results were mainly driven by the pulmonary tuberculosis and Asian subgroups. Collectively, this meta-analysis proved that IL-6 rs1800795, IL-8 rs4073, IL-10 rs1800871, IL-10 rs1800872 and IL-10 rs1800896 may confer susceptibility to TB.

How to avoid driving DNA caseworkers crazy: CaseSolver, an expert system to investigate complex crime scenes

DNA analyses can be used for both investigative (crime scene-focused), or evaluative (suspect-focused) reporting. Investigative, DNA-led exploration of serious crimes always involves the comparison of hundreds of biological samples submitted by the authorities for analysis. Crime stain comparisons include both evidence to evidence profiles and reference to evidence profiles. When many complex DNA results (mixtures, low template LT-DNA samples) are involved in the investigation of a crime, the manual comparison of DNA profiles is very time-consuming and prone to manual errors. In addition, if the person of interest is a minor contributor, the classical approach of performing searches of national DNA databases is problematic because it is realistically restricted to clear major contributors and the occurrence of masking and drop-out means that there will not be a definitive DNA profile to perform the search with.CaseSolver is an open source expert system that automates analysis of complex cases. It does this by three sequential steps: a) simple allele comparison b) likelihood ratio (LR) based on a qualitative model (forensim) c) LR based on a quantitative model (EuroForMix). The software generates a list of potential match candidates, ranked according to the LRs, which can be exported as a report. The software can also identify contributors from small or large databases (e.g., staff database or 1 mill. individuals). In addition, an informative graphical network plot is generated that easily identifies contributors in common to multiple stains. Here we describe recent improvements made to the software in version v1.5.0, made in response to user requirements during intensive casework usage.

Symbiotic incompatibility between soybean and Bradyrhizobium arises from one amino acid determinant in soybean Rj2 protein.

Cultivated soybean (Glycine max) carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. Here we found that the single isoleucine residue I490 in Rj2 is required for induction of symbiotic incompatibility. Furthermore, we investigated the geographical distribution of the Rj2-genotype soybean in a large set of germplasm by single nucleotide polymorphism (SNP) genotyping using a SNP marker for I490. By allelic comparison of 79 accessions in the Japanese soybean mini-core collection, we suggest substitution of a single amino acid residue (R490 to I490) in Rj2 induces symbiotic incompatibility with Bradyrhizobium diazoefficiens USDA 122. The importance of I490 was verified by complementation of rj2-soybean by the dominant allele encoding the Rj2 protein containing I490 residue. The Rj2 allele was also found in Glycine soja, the wild progenitor of G. max, and their single amino acid polymorphisms were associated with the Rj2-nodulation phenotype. By SNP genotyping against 1583 soybean accessions, we detected the Rj2-genotype in 5.4% of G. max and 7.7% of G. soja accessions. Distribution of the Rj2-genotype soybean plants was relatively concentrated in the temperate Asian region. These results provide important information about the mechanism of host genotype-specific symbiotic incompatibility mediated by host immunity and suggest that the Rj2 gene has been maintained by environmental conditions during the process of soybean domestication.

Genetic, morphological and chemical investigations reveal the genetic origin of Pompia (C. medica tuberosa Risso & Poiteau) – An old endemic Sardinian citrus fruit

Citrus fruits have been introduced to the Mediterranean area from Asia for centuries and spontaneous crosses have generated several hybrid forms, some of which have had agricultural or industrial success while others have remained niche food or ornamental products, or have disappeared. Pompia (C. medica tuberosa Risso & Poiteau) is an old endemic citrus fruit from Sardinia of unknown genetic origin. Initial phenotypic and molecular characterizations revealed a high degree of similarity with lemon (C. limon (L.) Burm.) and citron (C. medica L.). To identify the ancestors of Pompia, 70 citrus species of the Citrus genus were genotyped with 36 codominant molecular markers (SSR and InDel) of nuclear and cytoplasmic genomes. Diversity analysis and allelic comparisons between each citrus species at each locus indicated that Pompia resembles lemon and limonette of Marrakech, i.e. the result of a cross between sour orange (C. aurantium L.) and citron, where citron was the pollinator. Two Italian citron varieties were identified as potential male parents, i.e. Diamante and Common Poncire. However, we were unable to differentiate varieties of sour oranges because varietal diversification in this horticultural group resulted from DNA sequence variations that SSR or InDel markers could not reveal. Rhob el Arsa and Poncire de Collioure were found to be two synonyms of Pompia. Pompia appeared to be equally distinct from citron, lemon and sour orange based on the overall analysis of the fruit, leaf and seed phenotype, and juice chemical composition. At the leaf level, the Pompia essential oil (EO) composition is close to that of citron whereas the zest is much closer to that of sour orange.

A meta-analysis on associations of FTO, MTHFR and TCF7L2 polymorphisms with polycystic ovary syndrome

BackgroundWe aimed to better clarify the relationship between FTO/MTHFR/TCF7L2 polymorphisms and PCOS in a larger combined population by performing a meta-analysis. MethodsEligible articles were retrieved from Pubmed, Embase, Web of Science and CNKI. Review Manager Version was used to perform statistical analyses. ResultsForty-six studies were included for this meta-analysis. FTO rs9939609 polymorphism was found to be significantly associated with PCOS under dominant, recessive, over-dominant and allele comparisons, MTHFR rs1801131 polymorphism was found to be significantly associated with PCOS under recessive and allele comparisons, and MTHFR rs1801133 polymorphism was also found to be significantly associated with PCOS under dominant, recessive and allele comparisons in general population. In subgroup analyses, we found that positive results were mainly driven by the Asians. ConclusionsCollectively, this meta-analysis proved that FTO rs9939609, MTHFR rs1801131 and MTHFR rs1801133 polymorphisms may serve as predisposing factors of PCOS, especially for Asians.

Association between an indel polymorphism within the distal promoter of EGLN2 and cancer risk: An updated meta-analysis.

BackgroundThe association between a 4‐bp indel polymorphism (rs10680577) within the distal promoter of EGLN2 and cancer risk has been investigated by several case–control studies in recent years, but investigation results were inconsistent. Thus, a systematic assessment of the association was performed based on a literature review and pooled analysis.MethodsTwo investigators independently retrieved relevant studies from PubMed, Chinese National Knowledge Infrastructure (CNKI), Embase, and Google Scholar. The fixed or random effects model was selected to calculate odds ratios (ORs) with 95% confidence intervals (CIs) based on heterogeneity level. All analyses including heterogeneity assessment, subgroup analysis, sensitivity analysis, and publication bias assessment were performed using RevMan 5.3 software and Stata 12.0 software.ResultsA total of six relevant studies with 3,406 cases and 5,147 controls were included in the final analysis. The overall pooled analysis showed that EGLN2 rs10680577 polymorphism was significantly associated with cancer risk under all genetic models. However, subgroup analysis based on cancer type showed that the polymorphism was significantly associated with the risk of digestive system cancer under all genetic models, and with the risk of lung cancer under dominant model, heterozygote comparison model, and allele comparison model. Subgroup analysis based on population sources showed a significant association in Chinese population under all genetic models.ConclusionThe present result suggests that EGLN2 rs10680577 polymorphism is associated with cancer risk, and may act as a promising predictive biomarker for cancer risk, especially in Chinese population. However, further well‐designed studies are warranted to confirm these results.

Genetic variability and relationships in nine South African cattle breeds using microsatellite markers.

Genetic variability within and between breeds allows adaptation to a changing environment and consequently prepares producers for the future. Eleven bovine-specific microsatellite markers were used to genotype animals from each of nine South African cattle breeds: Afrikaner (N = 550), Angus (N = 550), Bonsmara (N = 550), Boran (N = 321), Brahman (N = 550), Drakensberger (N = 550), Nguni (N = 550), Simmental (N = 550), and Tuli (N = 311). These breeds were drawn from Bos taurus africanus, Bos taurus, and Bos indicus. Genetic variability estimates included unbiased heterozygosity, effective number of alleles, and inbreeding. Ranges of these parameters were 0.569-0.741, 8.818-11.455, and - 0.001-0.050, respectively. Breed private allele and breed pairwise comparison was also used to characterize the breeds. The analysis of population structure with K = 2 revealed clusters comprised of Sanga-indicine and taurine, while K = 3 included separate clusters of Sanga, indicine, and taurine, and with K = 9 showed the breeds arising from unique progenitor populations. This study broke new ground in molecular cattle genetic diversity by genotyping a large sample size per breed and using a larger number of breeds compared with similar studies that have been conducted in the recent past which have either used a smaller number of breeds or smaller sample sizes but with a larger number of marker loci. Thus, opportunities that arise to explore genetic diversity and relationships in both the livestock and wildlife industries in Southern Africa may capitalize on microsatellite marker databases which remain cost-effective and accessible due to their extensive use for parentage verification.

A meta-analysis on relationship between paraoxonase 1 polymorphisms and atherosclerotic cardiovascular diseases

BackgroundSome previous studies already explored associations between paraoxonase 1 (PON1) polymorphisms and atherosclerotic cardiovascular diseases (ASCVD), with conflicting findings. Here, we aimed to better analyze the relationship between PON1 polymorphisms and ASCVD in a larger combined population by performing a meta-analysis. MethodsWe searched Pubmed, Embase and Web of Science for related articles. We calculated odds ratio (OR) and 95% confidence interval (CI) to estimate whether there are genetic associations between PON1 polymorphisms and ASCVD. ResultsOne hundred and nine studies were included for this meta-analysis. The PON1 rs854560 (17,220 cases and 18,570 controls, recessive comparison: OR = 0.83, 95%CI 0.72–0.96) and rs662 (30,717 cases and 54,894 controls, dominant comparison: OR = 0.82, 95% CI 0.77–0.89; recessive comparison: OR = 1.17, 95% CI 1.07–1.28; allele comparison: OR = 0.85, 95% CI 0.81–0.90) polymorphisms were both found to be significantly associated with susceptibility to ASCVD in general population. Subgroup analyses by ethnicity revealed similar significant findings for rs854560 polymorphism only in East Asians, while similar positive findings for rs662 polymorphism were observed in Caucasians, East Asians and South Asians. Subgroup analyses by type of disease indicated that the significant findings for rs854560 polymorphism were mainly driven by the ischemic stroke (IS) subgroup, whereas the positive results for rs662 polymorphism were mainly driven by the coronary artery disease (CAD) subgroup. ConclusionsIn summary, this meta-analysis proved that PON1 rs854560 polymorphism could be used to identify individual with elevated susceptibility to IS, whereas rs662 polymorphism could be used to identify individual with elevated susceptibility to CAD.

HLA-G +3142 C>G polymorphism and cancer risk: Evidence from a meta-analysis and trial sequential analysis.

Human leukocyte antigen-G (HLA-G) plays an important role in the development of human cancers. Several published studies have investigated the relationship between the HLA-G +3142 C>G (rs1063320) polymorphism and cancer susceptibility in different populations. However, the results have yet to reach a consensus in different types of cancers. Therefore, we performed a meta-analysis to evaluate the effect of the HLA-G +3142 C>G polymorphism on cancer risk. A systematic literature search was performed in PubMed, Web of Science, CNKI, VIP, and Wanfang databases to acquire eligible studies up to February 20, 2019. The pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were used to assess the correlation between the HLA-G +3142 C>G polymorphism and cancer risk in a fixed-effects or random-effects model. Publication bias assessments, sensitivity analysis and stratified analyses were performed. To reduce the risk of type I error and assess whether the present evidence of the results was adequate and conclusive, trial sequential analysis (TSA) was also performed. Eight case-control studies comprising 1546 cases and 1595 controls were included in the present meta-analysis. The results revealed that the HLA-G +3142 C>G mutation significantly decreased the total cancer risk in recessive comparison model and allelic comparison model. Further stratified analyses showed that the HLA-G +3142 C>G mutation significantly decreases the risk of cancer in Asian populations. No similar relationship was found in other subgroups. No publication bias was identified in our present study. Omitting a single study at a time had no significant impact on the pooled OR of the sensitivity analysis assessing the association between the HLA-G +3142 C>G polymorphism and cancer risk, which demonstrates the stability of the current meta-analysis. TSA also identified our current findings. The results of our meta-analysis show that the HLA-G +3142 C>G polymorphism plays a protect role in the occurrence of human cancers, particularly in Asian populations. More case-control studies with different types of cancer in various ethnicities are needed to verify the findings.

Genetic variation in the HLA-G 3'UTR 14-bp insertion/deletion and the associated cancer risk: evidence from 25 case-control studies.

Human leucocyte antigen-G (HLA-G) plays an important role in the progression of human cancers. A growing number of published studies have investigated the correlation between the HLA-G 3′ untranslated region (3′UTR) 14-bp insertion/deletion (Ins/Del) polymorphism and the associated cancer risk in different populations. However, results from previous studies are inconclusive and inconsistent for the different type of cancers. Therefore, we undertook a meta-analysis to assess the effects of the HLA-G 14-bp Ins/Del polymorphism on cancer risk. A systematic literature search was conducted in PubMed, Web of Science, CNKI, VIP, and Wanfang databases to obtain relevant studies up to 28 January 2019. The pooled odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were used. Twenty-five published case–control studies comprising 4981 cases and 6391 controls were included in the current meta-analysis. The results of the overall analysis revealed that the HLA–G 14–bp Ins/Ins genotype and Ins allele were associated with the total cancer risk in the homozygote comparison model (Ins/Ins vs. Del/Del: OR = 0.80, CI = 0.64–1.00; P=0.049) and the allelic comparison model (Ins vs. Del: OR = 0.89, CI = 0.81–0.99; P=0.035), with a protective role. Further subgroup analyses indicated that the HLA–G 14–bp Ins/Del polymorphism was associated with the risk of breast cancer and oesophageal cancer (EC), and significant risk of cancer was also observed in Mixed populations and population-based (PB). The results of our meta-analysis show that the HLA–G 14-bp Ins/Del polymorphism plays an important role in cancer risk, particularly in breast cancer and esophageal cancer in Mixed populations. Additional case–control studies with different types of cancer spanning different ethnicities are needed to extend the present findings.

Vascular endothelial growth factor gene polymorphisms and hypertensive disorder of pregnancy: A meta-analysis

Whether vascular endothelial growth factor (VEGF) polymorphisms affect individual susceptibility to hypertensive disorder of pregnancy remain controversial. Therefore, we performed this meta-analysis to better evaluate associations between VEGF polymorphisms and hypertensive disorder of pregnancy in a larger pooled population. Pubmed, Web of Science, Embase and CNKI were searched for eligible studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Totally 24 studies were eligible for analyses. In overall analyses, a significant association with hypertensive disorder of pregnancy was observed for rs3025039 polymorphism in dominant (p = 0.01, OR = 0.66, 95%CI 0.48-0.91), recessive (p = 0.002, OR = 1.79, 95%CI 1.25-2.58), overdominant (p = 0.04, OR = 1.35, 95%CI 1.01-1.80) and allele (p = 0.01, OR = 0.72, 95%CI 0.56-0.93) comparisons. But we did not observe any significant associations with hypertensive disorder of pregnancy for other VEGF polymorphisms in overall analyses. Further subgroup analyses by ethnicity showed that rs2010963 polymorphism was significantly associated with hypertensive disorder of pregnancy in Caucasians (dominant and recessive models) and Africans (allele model), whereas rs3025039 polymorphism was significantly associated with hypertensive disorder of pregnancy in Asians (recessive model). In summary, our findings indicated that rs2010963 and rs3025039 polymorphisms were both significantly associated with the susceptibility to hypertensive disorder of pregnancy in certain populations.

Association of IL1RL1 rs3771180 and TSLP rs1837253 variants with asthma in the Guangxi Zhuang population in China.

ObjectiveIL‐1 receptor‐like 1 (IL1RL1) and thymic stromal lymphopoietin (TSLP) play important roles in asthma in various ways. IL1RL1 rs3771180 and TSLP rs1837253 single nucleotide polymorphisms (SNPs) are associated with asthma in some European nationals but not in Zhuang people. Accordingly, this study aimed to determine the associations of IL1RL1 rs3771180 and TSLP rs1837253 with asthma in Zhuang people.MethodsWe performed a case‐control study to observe the association between the two polymorphisms and asthma in a Guangxi Zhuang cohort consisting of 123 asthmatic patients and 100 healthy controls. These individuals were recruited from the Department of Respiration of the First Affiliated Hospital of Guangxi Medical University. Multiplex PCR assay was used to identify the genotype of rs3771180 and rs1837253. Data were analyzed with SPSS 22.0 and SHEsis.Resultsrs1837253 showed significant differences between asthmatic and control groups in allele comparison (OR = 2.15; 95% CI = 1.27‐3.63; P = 0.004), as well as in the homozygote (OR = 4.83; 95% CI = 1.47‐16.47; P = 0.012), heterozygote (OR = 2.69; 95% CI = 1.20‐6.00; P = 0.016), and dominant (OR = 3.01; 95% CI = 1.39‐6.52; P = 0.005) genetic models. However, the genotype frequencies of rs3771180 did not obviously differ.Conclusionrs1837253 is associated with asthma susceptibility and may increase the risk of asthma in Zhuang people in Guangxi.

CCDN1 rs603965 polymorphism may serve as a genetic biomarker of brain tumor: A meta-analysis of 5,769 subjects.

IntroductionSome studies already tried to assess the associations between cyclin D1 (CCND1) polymorphisms and brain tumor. However, the results of these studies were not consistent. Thus, we performed the present meta‐analysis to explore the relationship between CCND1 polymorphisms and brain tumor in a larger pooled population.MethodsPubMed, Web of Science, Embase, and CNKI were searched for related articles. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the potential associations.ResultsTotally nine studies with 5,769 subjects were analyzed. A significant association with brain tumor susceptibility was observed for the rs603965 polymorphism in GG versus GA + AA (dominant comparison, p = 0.003, OR = 0.72, 95% CI 0.57–0.89, I 2 = 64%), AA versus GG + GA (recessive comparison, p = 0.004, OR = 1.46, 95% CI 1.13–1.88, I 2 = 67%), and G versus A (allele comparison, p = 0.0004, OR = 0.77, 95% CI 0.66–0.89, I 2 = 66%) in overall population. Further subgroup analyses by ethnicity yielded similar positive results in both Asians and Caucasians. Moreover, in stratified analyses by type of disease, we noticed that the rs603965 polymorphism was significantly associated with the susceptibility to glioma, but such positive results were not detected in pituitary adenoma or meningioma. Additionally, a significant association with tumor grade was also observed for the rs603965 polymorphism in G versus A (allele comparison, p = 0.02, OR = 0.74, 95% CI 0.59–0.95, I 2 = 26%).ConclusionsOur findings suggested that CCND1 rs603965 polymorphism may serve as a potential genetic biomarker of brain tumor, especially for glioma.

Association of ADH1B Arg47His polymorphism with the risk of cancer: a meta-analysis.

Alcohol consumption has been established to be a major factor in the development and progress of cancer. Genetic polymorphisms of alcohol-metabolism genes result in differences between individuals in exposure to acetaldehyde, leading to possible carcinogenic effects. Arg47His (rs1229984 G > A) in ADH1B have been frequently studied for its potential effect on carcinogenesis. However, the findings are as yet inconclusive. To gain a more precise estimate of this potential association, we conducted a meta-analysis including 66 studies from 64 articles with 31999 cases and 50964 controls. The pooled results indicated that ADH1B Arg47His polymorphism is significantly associated with the decreased risk of overall cancer (homozygous model, odds ratio (OR) = 0.62, 95% confidence interval (CI) = 0.49–0.77; heterozygous model, OR = 0.71, 95% CI = 0.60–0.84; recessive model, OR = 0.83, 95% CI = 0.76–0.91; dominant model, OR = 0.62, 95% CI = 0.53–0.72; and allele comparison, OR = 0.82, 95% CI = 0.75–0.89). Stratified analysis by cancer type and ethnicity showed that a decreased risk was associated with esophageal cancer and head and neck cancer amongst Asians. In conclusion, our meta-analysis suggested that ADH1B Arg47His polymorphism was significantly associated with decreased overall cancer risk. These findings need further validation in large multicenter investigations.

CaseSolver: An investigative open source expert system based on EuroForMix

For very serious crimes, reporting scientists often have to contend with complex cases where literally hundreds of items are submitted by investigators for analysis. In order to efficiently expedite the challenge of comparing reference profiles to evidence profiles, many of which are mixtures, we have developed an investigative open source expert system CaseSolver. We have analysed a real case based on GlobalFiler involving 119 evidence profiles and 3 reference profiles. To provide a demonstration of the power of the system we also added the three references to a fictive large database of 1 million individuals in order to test subsequent recovery of the presumed true contributors. CaseSolver was used on a Fusion 6C validation study involving 25 two- to four-person mixture profiles based on 14 reference profiles. The sequential use of simple allele comparison, the qualitative model (forensim) and the quantitative model (EuroForMix) makes the analysis very fast and accurate – and finally, the software generates a list of potential match candidates which can be exported as a report. From these two studies we found that the resolution of match candidates from CaseSolver was the same as that reported by a scientist who worked manually through the samples, except that CaseSolver highlighted two manual errors. For the validation study we found low template DNA samples giving negative results, which demonstrate the limitations of the tool; but overall our assessment shows that CaseSolver will benefit all analyses involving mixture interpretation and screening. Importantly, CaseSolver removes the very time-consuming aspect of manual comparison and gives improved quality by preventing manual errors.

Association between interleukin 8-receptor gene (CXCR1 and CXCR2) polymorphisms and urinary tract infection: Evidence from 4097 subjects.

The aim of this study was to determine whether a correlation exists between interleukin-8 receptor polymorphisms and urinary tract infection (UTI) susceptibility. We systematically searched electronic databases including PubMed, Embase, China National Knowledge Infrastructure, and Web of Science up to 5 November 2017 to select appropriate studies that focused on C-X-C chemokine receptor type 1 and/or 2 (CXCR1, CXCR2) polymorphisms with susceptibility to UTI. Eight case-control studies including 2085 patients with UTI and 2012 controls were enrolled in this study. Seven studies of CXCR1 rs2234671 and two studies of rs3138086 were included in the meta-analyses. Pooled odds ratio (OR) and corresponding 95% confidence interval (CI) were synthesized using fixed-effects or random-effects model according to heterogeneity. No significant correlations were found between CXCR1 rs2234671 and rs3138086 polymorphisms and UTI susceptibility. However, subgroup analysis showed that rs2234671 was associated with an increased risk of UTI under allelic comparisons (C vs. G, OR = 1.95, 95% CI = 1.07-3.55), heterozygous model (GC vs. GG, OR = 1.93, 95% CI = 1.06-3.50), and dominant model (GC + CC vs. GG, OR = 1.98, 95% CI = 1.07-3.69) in children, especially in paediatric patients with acute pyelonephritis (allelic, OR = 2.43, 95% CI = 1.28-4.60; heterozygous, OR = 2.40, 95% CI = 1.24-4.62; dominant, OR = 2.48, 95% CI = 1.26-4.88). Furthermore, these results remained the same after eliminating paediatric patients with vesicoureteral reflux. CXCR1 rs2234671 polymorphism might be associated with an increased risk of UTI in children.

Correlation between PNPLA3 rs738409 polymorphism and hepatocellular carcinoma: a meta-analysis of 10,330 subjects.

The correlation between patatin-like phospholipase domain-containing protein 3 (PNPLA3) rs738409 polymorphism and hepatocellular carcinoma was investigated by several pilot studies, but the results of these studies were controversial. Therefore, we performed this study to better assess the relationship between PNPLA3 rs738409 polymorphism and the likelihood of hepatocellular carcinoma. Eligible studies were searched in PubMed, Medline, EMBASE, and Web of Science. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the relationship between PNPLA3 rs738409 polymorphism and hepatocellular carcinoma. A total of 17 studies with 10,330 participants were analyzed. A significant association with the likelihood of hepatocellular carcinoma was detected for the PNPLA3 rs738409 polymorphism in dominant (P = 0.0001; OR 0.66; 95% CI 0.53, 0.82), recessive (P < 0.0001; OR 2.32; 95% CI 1.76, 3.06) and allele (P < 0.0001; OR 0.64; 95% CI 0.53, 0.77) comparisons. Further subgroup analyses revealed that the PNPLA3 rs738409 polymorphism was significantly associated with the likelihood of hepatocellular carcinoma in Caucasians (dominant model: P < 0.0001, OR 0.57, 95% CI 0.45, 0.71; recessive model: P < 0.0001, OR 2.74, 95% CI 2.02, 3.71; allele model: P < 0.0001, OR 0.56, 95% CI 0.46, 0.67). However, no positive results were detected in Asians. Our findings indicated that the PNPLA3 rs738409 polymorphism may serve as a potential biological marker of hepatocellular carcinoma in Caucasians.

Correlation between MTHFR polymorphisms and glaucoma: A meta-analysis.

BackgroundWhether methylenetetrahydrofolate reductase (MTHFR) polymorphisms are implicated in glaucoma remains controversial. Therefore, we performed this study to better assess the relationship between MTHFR polymorphisms and the likelihood of glaucoma.MethodsA systematic research of PubMed, Medline, and Embase was performed to retrieve relevant articles. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated.ResultsA total of 18 studies with 7,168 participants were analyzed. In overall analyses, a significant association with the likelihood of glaucoma was detected for the rs1801133 polymorphism in dominant (p = 0.04, OR = 0.90, 95%CI 0.81–1.00) and allele (p = 0.02, OR = 0.91, 95%CI 0.84–0.98) comparisons. Further, subgroup analyses by ethnicity revealed that both rs1801131 and rs1801133 polymorphisms were significantly associated with the likelihood of glaucoma in West Asians. However, no positive results were detected for two investigated polymorphisms in East Asians and Caucasians.ConclusionOur findings indicated that rs1801131 and rs1801133 polymorphisms may serve as genetic biomarkers of glaucoma in West Asians.