Explore the vast range of titles available.

Background Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packages can generate a Manhattan plot, but they are all limited in the extent to which they can annotate gene-names, allele frequencies, and variants having high impact on gene function or provide any other added information or flexibility. Furthermore, in a conventional Manhattan plot, there is no way of distinguishing a locus identified due to a single variant with very significant p -value from a locus with multiple variants which appear to be in a haplotype block having very similar p -values. Results Here we present a software tool written in R, which generates a transposed Manhattan plot along with additional features like variant consequence and minor allele frequency to annotate the plot and addresses these limitations. The software also gives flexibility on how and where the user wants to display the annotations. The software can be downloaded from CRAN repository and also from the GitHub project page. Conclusions We present a major step up to the existing conventional Manhattan plot generation tools. We hope this form of display along with the added annotations will bring more insight to the reader from this new Manhattan++ plot.

CADM2 has been associated with a range of behavioural and metabolic traits, including physical activity, risk-taking, educational attainment, alcohol and cannabis use and obesity. Here, we set out to determine whether CADM2 contributes to mechanisms shared between mental and physical health disorders. We assessed genetic variants in the CADM2 locus for association with phenotypes in the UK Biobank, IMPROVE, PROCARDIS and SCARFSHEEP studies, before performing meta-analyses. A wide range of metabolic phenotypes were meta-analysed. Psychological phenotypes analysed in UK Biobank only were major depressive disorder, generalised anxiety disorder, bipolar disorder, neuroticism, mood instability and risk-taking behaviour. In UK Biobank, four, 88 and 172 genetic variants were significantly (p < 1 × 10 −5 ) associated with neuroticism, mood instability and risk-taking respectively. In meta-analyses of 4 cohorts, we identified 362, 63 and 11 genetic variants significantly (p < 1 × 10 −5 ) associated with BMI, SBP and CRP respectively. Genetic effects on BMI, CRP and risk-taking were all positively correlated, and were consistently inversely correlated with genetic effects on SBP, mood instability and neuroticism. Conditional analyses suggested an overlap in the signals for physical and psychological traits. Many significant variants had genotype-specific effects on CADM2 expression levels in adult brain and adipose tissues. CADM2 variants influence a wide range of both psychological and metabolic traits, suggesting common biological mechanisms across phenotypes via regulation of CADM2 expression levels in adipose tissue. Functional studies of CADM2 are required to fully understand mechanisms connecting mental and physical health conditions.

Several genome-wide association studies have recently linked a group of single nucleotide polymorphisms in the 9p21 region with cardiovascular disease. The molecular mechanisms of this link are not fully understood. We investigated five different expression microarray datasets in order to determine if the genotype had effect on expression of any gene transcript in aorta, mammary artery, carotid plaque and lymphoblastoid cells. After multiple testing correction, no genes were found to have relation to the rs2891168 risk genotype, either on a genome-wide scale or on a regional (8 MB) scale. The neighbouring ANRIL gene was found to have eight novel transcript variants not previously known from literature and these varied by tissue type. We therefore performed a detailed probe-level analysis and found small stretches of significant relation to genotype but no consistent associations. In all investigated tissues we found an inverse correlation between ANRIL and the MTAP gene and a positive correlation between ANRIL and CDKN2A and CDKN2B. Investigation of relation of the risk genotype to gene expression is complicated by the transcript complexity of the locus. With our investigation of a range of relevant tissue we wish to underscore the need for careful attention to the complexity of the alternative splicing issues in the region and its implications to the design of future gene expression studies.

Progress in mapping loci associated with common complex diseases or quantitative inherited traits has been expedited by large-scale meta-analyses combining information across multiple studies, assembled through collaborative networks of researchers. Participating studies will usually have been independently designed and implemented in unique settings that are potential sources of phenotype, ancestry or other variability that could introduce between-study heterogeneity into a meta-analysis. Heterogeneity tests based on individual genetic variants (e.g. Q, I2) are not suited to identifying locus-specific from more systematic multi-locus or genome-wide patterns of heterogeneity. We have developed and evaluated an aggregate heterogeneity M statistic that combines between-study heterogeneity information across multiple genetic variants, to reveal systematic patterns of heterogeneity that elude conventional single variant analysis. Application to a GWAS meta-analysis of coronary disease with 48 contributing studies uncovered substantial systematic between-study heterogeneity, which could be partly explained by age-of-disease onset, family-history of disease and ancestry. Future meta-analyses of diseases and traits with multiple known genetic associations can use this approach to identify outlier studies and thereby optimize power to detect novel genetic associations.

Kaposi’s sarcoma (KS) is a cancer that often affects individuals with human immunodeficiency virus, acquired immunodeficiency syndrome (AIDS), those who have received an organ transplant, or others who are immunocompromised. KS is a vascular tumor that most often presents in cutaneous sites, including the lower extremities, oral mucosa, and genitalia. Literature regarding KS with ocular involvement is scarce. We present a rare case in which a patient diagnosed with AIDS-associated KS exhibited ocular and diffuse manifestations. The lesions of cutaneous KS are frequently mistaken for an alternative diagnoses; therefore, the clinician should have a high index of suspicion for this vascular tumor in AIDS patients.

Epidemiological studies suggest a positive association between coronary artery disease (CAD) and late-onset Alzheimer’s disease (LOAD). This large-scale genetic study brings together ‘big data’ resources to examine the causal impact of genetic determinants of CAD on risk of LOAD. A two-sample Mendelian randomization approach was adopted to estimate the causal effect of CAD on risk of LOAD using summary data from 60,801 CAD cases from CARDIoGRAM plus C4D and 17,008 LOAD cases from the IGAP Consortium. Additional analyses assessed the independent relevance of genetic associations at the APOE locus for both CAD and LOAD. Higher genetically determined risk of CAD was associated with a slightly higher risk of LOAD (Odds Ratio (OR) per log-odds unit of CAD [95% CI]: 1.07 [1.01–1.15]; p = 0.027). However, after exclusion of the APOE locus, the estimate of the causal effect of CAD for LOAD was attenuated and no longer significant (OR 0.94 [0.88–1.01]; p = 0.072). This Mendelian randomization study indicates that the APOE locus is the chief determinant of shared genetic architecture between CAD and LOAD, and suggests a lack of causal relevance of CAD for risk of LOAD after exclusion of APOE .

Chronic otitis media with effusion (COME) is the most common cause of hearing loss in children, and known to have high heritability. Mutant mouse models have identified Fbxo11 , Evi1 , Tgif1 , and Nisch as potential risk loci. We recruited children aged 10 and under undergoing surgical treatment for COME from 35 hospitals in the UK, and their nuclear family. We performed association testing with the loci FBXO11 , EVI1 , TGIF1 and NISCH and sought to replicate significant results in a case-control cohort from Finland. We tested 1296 families (3828 individuals), and found strength of association with the T allele at rs881835 (p = 0.006, OR 1.39) and the G allele at rs1962914 (p = 0.007, OR 1.58) at TGIF1 , and the A allele at rs10490302 (p = 0.016, OR 1.17) and the G allele at rs2537742 (p = 0.038, OR 1.16) at FBXO11 . Results were not replicated. This study supports smaller studies that have also suggested association of otitis media with polymorphism at FBX011 , but this is the first study to report association with the locus TGIF1 . Both FBX011 and TGIF1 are involved in TGF-β signalling, suggesting this pathway may be important in the transition from acute to chronic middle ear inflammation, and a potential molecular target.

Gastrointestinal stromal tumors (GISTs) are rare gastrointestinal (GI) tumors, representing a small portion of soft tissue tumors of the abdominal cavity. Extraintestinal gastrointestinal stromal tumors (EGISTs) are uncommon forms of GISTs that present outside the GI tract. There have only been a rare number of reported cases of EGIST presenting above the diaphragm. We present the case of a 50-year-old female with shortness of breath, and found to have bilateral pleural effusions and left-sided lung mass. The initial lung mass aspiration was negative for malignancy; yet, pleural fluid was suggestive of malignancy, and repeat biopsy and immunohistochemical stain were diagnostic for GIST. Ultimately, the patient underwent video-assisted thoracoscopic surgery, pleurodesis with doxycycline, and adjuvant therapy with imatinib. This is a report of primary EGIST presenting as an isolated lung lesion with no involvement of the GI tract. In patients with suspected malignancy, it is of paramount importance to obtain a detailed history, including remote signs and symptoms, while performing a thorough work-up. Especially in the lung where initial biopsies can be skewed due to inflammation and atelectasis, repeat biopsies may be necessary to obtain an accurate diagnosis.

Variants at the interleukin 6 receptor (IL6R) gene regulate inflammation and are associated with risk of coronary heart disease (CHD). The aim of the present study was to investigate the effects of IL6R haplotypes on circulating levels of inflammatory biomarkers and risk of CHD. We performed a discovery analysis in SHEEP, a myocardial infarction (MI) case control study (n = 2,774) and replicated our results in two large, independent European populations, PROCARDIS, a CHD case control study (n = 7,998), and IMPROVE (n = 3,711) a prospective cardiovascular cohort study. Two major haplotype blocks (rs12083537A/G and rs4075015A/T--block 1; and rs8192282G/A, rs4553185T/C, rs8192284A/C, rs4240872T/C and rs7514452T/C--block 2) were identified in the IL6R gene. IL6R haplotype associations with C-reactive protein (CRP), fibrinogen, IL6, soluble IL6R (sIL6R), IL6, IL8 and TNF-α in SHEEP, CRP and fibrinogen in PROCARDIS and CRP in IMPROVE as well as association with risk of MI and CHD, were analyzed by THESIAS. Haplotypes in block 1 were associated neither with circulating inflammatory biomarkers nor with the MI/CHD risk. Haplotypes in block 2 were associated with circulating levels of CRP, in all three study populations, with fibrinogen in SHEEP and PROCARDIS, with IL8 and sIL6Rin SHEEP and with a modest, non significant, increase (7%) in MI/CHD risk in the three populations studied. Our results indicate that IL6R haplotypes regulate the circulating levels of inflammatory biomarkers. Lack of association with the risk of CHD may be explained by the combined effect of SNPs with opposite effect on the CHD risk, the sample size as well as by structural changes affecting sIL6R stability in the circulation.

The moth flame optimization (MFO) method has been introduced as a means to approximate single–input–single–output (SISO) complex high-order linear time-invariant systems (CHOLTIS). Initially, the unknown parameters within the denominator and numerator of the reduced-order linear time-invariant system (ROLTIS) are determined through balanced truncation. This process establishes the initial values of the parameters for MFO. To confine the exploration space of MFO around the coefficients derived from the balanced truncated model, a strategic constant is employed. This constant defines the lower and upper bounds, effectively constraining the search area of MFO. Consequently, MFO can focus its optimization efforts within a targeted range, improving efficiency and efficacy. The optimization process with MFO is then applied to fine-tune the unknown parameters of the ROLTIS. Through iterative optimization, MFO adjusts these parameters to minimize the error between the step response of CHOLTIS and the desired ROLTIS. This iterative process ensures that the resulting reduced-order system closely approximates the original high-order system. Moreover, to enhance the accuracy of the approximation, a gain adjustment factor is introduced after the optimization process. This factor enables the ROLTIS to match the steady-state response with that of the CHOLTIS. By fine-tuning the gain, the methodology ensures that the reduced-order system maintains consistent behavior with the original system under steady-state conditions. The efficacy of the proposed methodology is validated by applying it to four distinct high-order systems sourced from the literature. These systems encompass various configurations, including those with only real poles, real and imaginary poles, and repeated poles. Through testing on variety of systems, the proposed methodology consistently produces optimal and stable reduced-order systems with the lowest error indices, demonstrating its versatility and reliability across different system types and complexities.