Permutation – based statistical tests for multiple hypotheses

<p>Abstract</p> <p>Background</p> <p>Genomics and proteomics analyses regularly involve the simultaneous test of hundreds of hypotheses, either on numerical or categorical data. To correct for the occurrence of false positives, validation tests based on multiple testing correction, such as Bonferroni and Benjamini and Hochberg, and re-sampling, such as permutation tests, are frequently used. Despite the known power of permutation-based tests, most available tools offer such tests for either <it>t</it>-test or ANOVA only. Less attention has been given to tests for categorical data, such as the Chi-square. This project takes a first step by developing an open-source software tool, Ptest, that addresses the need to offer public software tools incorporating these and other statistical tests with options for correcting for multiple hypotheses.</p> <p>Results</p> <p>This study developed a public-domain, user-friendly software whose purpose was twofold: first, to estimate test statistics for categorical and numerical data; and second, to validate the significance of the test statistics via Bonferroni, Benjamini and Hochberg, and a permutation test of numerical and categorical data. The tool allows the calculation of Chi-square test for categorical data, and ANOVA test, Bartlett's test and t-test for paired and unpaired data. Once a test statistic is calculated, Bonferroni, Benjamini and Hochberg, and a permutation tests are implemented, independently, to control for Type I errors. An evaluation of the software using different public data sets is reported, which illustrates the power of permutation tests for multiple hypotheses assessment and for controlling the rate of Type I errors.</p> <p>Conclusion</p> <p>The analytical options offered by the software can be applied to support a significant spectrum of hypothesis testing tasks in functional genomics, using both numerical and categorical data.</p

Sex moderates the association between the COMT Val158Met single-nucleotide polymorphism and disorderliness facet of novelty seeking

Previous studies have shown inconsistent results regarding the effect of the Val158Met polymorphism of the catechol-O-methyltransferase (COMT) gene on personality and cognition. Here, nonclinical Caucasian university students of Italian origin were administered the Temperament and Character Inventory-Revised, Tellegen Absorption Scale, Differential Attentional Processes Inventory, and Waterloo-Stanford Group Scale of Hypnotic Susceptibility. We found that the COMT Val158Met polymorphism was significantly associated with the disorderliness facet of novelty seeking (NS4) and that sex was a moderator of this association. Females with the Met/Met genotype showed higher NS4 scores compared to those with the Val/Met and Val/Val genotypes. No significant genotype effect was found for males. Additionally, we failed to find a significant effect of the COMT gene on attention and hypnotic suggestibility measures. These results provide further evidence for a sex-specific influence on the gene-behaviour associations. Polymorphisms in dopamine system genes are reported to play a crucial role in influencing various aspects of plays a crucial role in influencing various aspects of personality traits and cognitive performance; however, previous studies have shown inconsistent results on the involvment of the functional Val158Met polymorphism of the catechol-O-methyltransferase (COMT) gene. In the present study, nonclinical Caucasian university students of Italian origin were administered the Temperament and Character Inventory-Revised, Tellegen Absorption Scale, Differential Attentional Processes Inventory, and Waterloo-Stanford Group Scale of Hypnotic Susceptibility. We found that the COMT Val158Met polymorphism was significantly associated with the disorderliness facet of novelty seeking (NS4) and that sex was a moderator of this association. Females with the Met/Met genotype showed higher NS4 scores compared to those with the Val/Met and Val/Val genotypes. In contrast, no significant genotype effect was found for males. Additionally, we failed to find a significant association of COMT enzyme activity with attention and hypnotic suggestibility measures. These results provide further evidence of a sex-specific influence on the gene-behaviour association

Association analysis of ACE and ACTN3 in Elite Caucasian and East Asian Swimmers

PURPOSE: Polymorphic variation in the angiotensin-converting enzyme (ACE) and alpha-actinin-3 (ACTN3) genes has been reported to be associated with endurance and/or power-related human performance. Our aim was to investigate whether polymorphisms in ACE and ACTN3 are associated with elite swimmer status in Caucasian and East Asian populations. METHODS: ACE I/D and ACTN3 R577X genotyping was carried out for 200 elite Caucasian swimmers from European, Commonwealth, Russian and American cohorts (short and middle distance, SMD &le; 400 m, n = 130; long distance, LD&nbsp;greater than&nbsp;400 m, n = 70) and 326 elite Japanese and Taiwanese swimmers (short distance, SD &le; 100 m, n = 166; middle distance, MD: 200 - 400 m, n = 160). Genetic associations were evaluated by logistic regression and other tests accommodating multiple testing adjustment. RESULTS: ACE I/D was associated with swimmer status in Caucasians, with the D-allele being overrepresented in SMD swimmers under both additive and I-allele dominant models (permutation test p = 0.003 and p = 0.0005, respectively). ACE I/D was also associated with swimmer status in East Asians. In this group, however, the I-allele was overrepresented in the SD swimmer group (permutation test p = 0.041 and p = 0.0098 under the additive and the D-allele-dominant models, respectively). ACTN3 R577X was not significantly associated with swimmer status in either Caucasians or East Asians. CONCLUSIONS: ACE I/D associations were observed in these elite swimmer cohorts, with different risk alleles responsible for the associations in swimmers of different ethnicities. The functional ACTN3 R577X polymorphism did not show any significant association with elite swimmer status, despite numerous previous reports of associations with 'power/sprint' performance in other sports.Additional co-authors: Jason Gulbin, Viktor A. Rogozkin, Ildus I. Ahmetov, Nan Yang, Kathryn N. North, Saraslanidis Ploutarhos, Hugh E. Montgomery, Mark E.S. Bailey, and Yannis P. Pitsiladi

Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota.

Daily PrEP is highly effective at preventing HIV-1 acquisition, but risks of long-term tenofovir disoproxil fumarate plus emtricitabine (TDF-FTC) include renal decline and bone mineral density decrease in addition to initial gastrointestinal side effects. We investigated the impact of TDF-FTC on the enteric microbiome using rectal swabs collected from healthy MSM before PrEP initiation and after 48 to 72 weeks of adherent PrEP use. The V4 region of the 16S ribosomal RNA gene sequencing showed that Streptococcus was significantly reduced from 12.0% to 1.2% (p = 0.036) and Erysipelotrichaceae family was significantly increased from 0.79% to 3.3% (p = 0.028) after 48-72 weeks of daily PrEP. Catenibacterium mitsuokai, Holdemanella biformis and Turicibacter sanguinis were increased within the Erysipelotrichaceae family and Streptococcus agalactiae, Streptococcus oralis, Streptococcus mitis were reduced. These changes were not associated with host factors including PrEP duration, age, race, tenofovir diphosphate blood level, any drug use and drug abuse, suggesting that the observed microbiome shifts were likely induced by daily PrEP use. Long-term PrEP resulted in increases of Catenibacterium mitsuokai and Holdemanella biformis, which have been associated with gut microbiome dysbiosis. Our observations can aid in characterizing PrEP's side effects, which is likely to improve PrEP adherence, and thus HIV-1 prevention

A multi-dimensional and integrative approach to examining the high-risk and ultra-high-risk stages of bipolar disorder

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Resting-state hyperconnectivity of the anticorrelated intrinsic networks in schizophrenic patients and their unaffected siblings

Abnormal connectivity of the intrinsic anticorrelated networks, the task-negative network (TNN) and task-positive network (TPN), is implicated in schizophrenia. Comparisons between schizophrenic patients and their unaffected siblings offer an opportunity to further understand illness susceptibility and pathophysiology. We hypothesized that schizophrenic patients would demonstrate hyperconnectivity in the intrinsic networks and that similar, but less pronounced, hyperconnectivity would be evident in the networks of the unaffected siblings. Resting-state functional magnetic resonance images were obtained from schizophrenic patients (n=25), their unaffected siblings (n=25), and healthy controls (n=25). The posterior cingulate cortex/precuneus (PCC/PCu) and right dorsolateral prefrontal cortex (DLPFC) were used as seed regions to identify the TNN and TPN. Interregional connectivity strengths were analyzed using overlapped intrinsic networks composed of regions common to the intrinsic networks of the three subject groups. In the TNN, schizophrenic patients alone demonstrated hyperconnectivity between the PCC/PCu and left inferior temporal gyrus and between the ventral medial prefrontal cortex and the right lateral parietal cortex. Both schizophrenic patients and their unaffected siblings showed increased connectivity in the TNN between the bilateral inferior temporal gyri. In the TPN, schizophrenic patients showed hyperconnectivity between the left DLPFC and right inferior frontal gyrus relative to unaffected siblings, though this trend only approached statistical significance in comparison to healthy controls. Resting-state hyperconnectivity of the intrinsic networks may underlie the pathophysiology of schizophrenia by disrupting network coordination. Similar, though milder, hyperconnectivity in unaffected siblings of schizophrenic patients may contribute to their cognitive deficits and increased risk to develop schizophrenia

Brain structure can mediate or moderate the relationship of behavior to brain function and transcriptome. A preliminary study

Abnormalities in motor-control behavior, which have been with concussion and head acceleration events (HAE), can be quantified using virtual reality (VR) technologies. Motor-control behavior has been consistently mapped to the brain's somatomotor network (SM) using both structural (sMRI) and functional MRI (fMRI). However, no studies habe integrated HAE, motor-control behavior, sMRI and fMRI measures. Here, brain networks important for motor-control were hypothesized to show changes in tractography-based diffusion weighted imaging [difference in fractional anisotropy (dFA)] and resting-state fMRI (rs-fMRI) measures in collegiate American football players across the season, and that these measures would relate to VR-based motor-control. We firther tested if nine inflammation-related miRNAs were associated with behavior-structure-function variables. Using permutation-based mediation and moderation methods, we found that across-season dFA from the SM structural connectome (SM-dFA) mediated the relationship between across-season VR-based Sensory-motor Reactivity (dSR) and rs-fMRI SM fingerprint similarity (p = 0.007 and Teff = 47%). The interaction between dSR and SM-dFA also predicted (pF = 0.036, pbeta3 = 0.058) across-season levels of dmiRNA-30d through permutation-based moderation analysis. These results suggest (1) that motor-control is in a feedback relationship with brain structure and function, (2) behavior-structure-function can be connected to HAE, and (3) behavior-structure might predict molecular biology measures.Comment: 62 pages, 4 figures, 2 table