scholarly journals Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ben D. Fulcher ◽  
Aurina Arnatkeviciute ◽  
Alex Fornito
Keyword(s):  
False Positive ◽  
False Positive Rate ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Brain Atlas ◽  
Positive Bias ◽  
Spatially Resolved ◽  
Brain Structure And Function ◽  
And Function ◽  
Gene Category

AbstractTranscriptomic atlases have improved our understanding of the correlations between gene-expression patterns and spatially varying properties of brain structure and function. Gene-category enrichment analysis (GCEA) is a common method to identify functional gene categories that drive these associations, using gene-to-category annotation systems like the Gene Ontology (GO). Here, we show that applying standard GCEA methodology to spatial transcriptomic data is affected by substantial false-positive bias, with GO categories displaying an over 500-fold average inflation of false-positive associations with random neural phenotypes in mouse and human. The estimated false-positive rate of a GO category is associated with its rate of being reported as significantly enriched in the literature, suggesting that published reports are affected by this false-positive bias. We show that within-category gene–gene coexpression and spatial autocorrelation are key drivers of the false-positive bias and introduce flexible ensemble-based null models that can account for these effects, made available as a software toolbox.

scholarly journals A practical guide to linking brain-wide gene expression and neuroimaging data

2018 ◽  
Author(s):  
Aurina Arnatkevičiūtė ◽  
Ben D. Fulcher ◽  
Alex Fornito
Keyword(s):  
Gene Expression ◽  
Brain Atlas ◽  
Expression Data ◽  
Analysis Pipeline ◽  
Atlas Data ◽  
Processing Pipeline ◽  
Neuroimaging Data ◽  
Brain Structure And Function ◽  
Expression Atlas ◽  
And Function

AbstractThe recent availability of comprehensive, brain-wide gene expression atlases such as the Allen Human Brain Atlas (AHBA) has opened new opportunities for understanding how spatial variations on the molecular scale relate to the macroscopic neuroimaging phenotypes. A rapidly growing body of literature is demonstrating relationships between gene expression and diverse properties of brain structure and function, but approaches for combining expression atlas data with neuroimaging are highly inconsistent, with substantial variations in how the expression data are processed. The degree to which these methodological variations affect findings is unclear. Here, we outline a seven-step analysis pipeline for relating brain-wide transcriptomic and neuroimaging data and compare how different processing choices influence the resulting data. We suggest that studies using AHBA should work towards a unified data processing pipeline to ensure consistent and reproducible results in this burgeoning field.

scholarly journals Desikan-Killiany-Tourville Atlas Compatible Version of M-CRIB Neonatal Parcellated Whole Brain Atlas: The M-CRIB 2.0

2018 ◽  
Author(s):  
Bonnie Alexander ◽  
Wai Yen Loh ◽  
Lillian G. Matthews ◽  
Andrea L. Murray ◽  
Chris Adamson ◽  
...  
Keyword(s):  
Brain Regions ◽  
Brain Atlas ◽  
Whole Brain ◽  
Brain Structure And Function ◽  
Postmenstrual Age ◽  
Mri Scans ◽  
Subcortical Regions ◽  
Cortical Regions ◽  
And Function ◽  
Ventral Diencephalon

AbstractOur recently published M-CRIB atlas comprises 100 neonatal brain regions including 68 compatible with the widely-used Desikan-Killiany adult cortical atlas. A successor to the Desikan-Killiany atlas is the Desikan-Killiany-Tourville atlas, in which some regions with unclear boundaries were removed, and many existing boundaries were revised to conform to clearer landmarks in sulcal fundi. Our first aim here was to modify cortical M-CRIB regions to comply with the Desikan-Killiany-Tourville protocol, in order to offer: a) compatibility with this adult cortical atlas, b) greater labelling accuracy due to clearer landmarks, and c) optimisation of cortical regions for integration with surface-based infant parcellation pipelines. Secondly, we aimed to update subcortical regions in order to offer greater compatibility with subcortical segmentations produced in FreeSurfer. Data utilized were the T2-weighted MRI scans in our M-CRIB atlas, for ten healthy neonates (postmenstrual age at MRI 40-43 weeks, 4 female), and corresponding parcellated images. Edits were performed on the parcellated images in volume space using ITK-SNAP. Cortical updates included deletion of frontal and temporal poles and ‘Banks STS’, and modification of boundaries of many other regions. Changes to subcortical regions included the addition of ‘ventral diencephalon’, and deletion of ‘subcortical matter’ labels. A detailed updated parcellation protocol was produced. The resulting whole-brain M-CRIB 2.0 atlas comprises 94 regions altogether. This atlas provides comparability with adult Desikan-Killiany-Tourville-labelled cortical data and FreeSurfer-labelled subcortical data, and is more readily adaptable for incorporation into surface-based neonatal parcellation pipelines. As such, it offers the ability to help facilitate a broad range of investigations into brain structure and function both at the neonatal time point and developmentally across the lifespan.

scholarly journals Overcoming bias in gene-set enrichment analyses of brain-wide transcriptomic data

2020 ◽  
Author(s):  
Ben D. Fulcher ◽  
Aurina Arnatkevičiūtė ◽  
Alex Fornito
Keyword(s):  
Gene Expression ◽  
Brain Structure ◽  
False Positive ◽  
Structure And Function ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Enrichment ◽  
Gene Set ◽  
Transcriptomic Data ◽  
Brain Structure And Function ◽  
And Function

The recent availability of whole-brain atlases of gene expression, which quantify the transcriptional activity of thousands of genes across many different brain regions, has opened new opportunities to understand how gene-expression patterns relate to spatially varying properties of brain structure and function. To aid interpretation of a given neural phenotype, gene-set enrichment analysis (GSEA) has become a standard statistical methodology to identify functionally related groups of genes, annotated using systems such as the Gene Ontology (GO), that are associated with a given phenotype. While GSEA has identified groups of genes related to diverse aspects of brain structure and function in mouse and human, here we show that these results are affected by substantial statistical biases. Quantifying the falsepositive rates of individual GO categories across an ensemble of random phenotypic maps, we found an average 875-fold inflation of significant findings relative to expectation in mouse, and a 582-fold inflation in human, with some categories being judged as significant for over 20% of random phenotypes. Concerningly, the probability of a GO category being reported as significant in the extant literature increases with its estimated false-positive rate, suggesting that published reports are strongly affected by the reporting of false-positive bias. We show that the bias is primarily driven by within-category gene–gene coexpression and spatial autocorrelation, which are not accounted for in conventional GSEA nulls, and we introduce flexible ensemble-based null models that can account for these effects. Testing a range of structural connectivity and cell density phenotypes in mouse and human, we demonstrate that many GO categories that would conventionally be judged as highly significant are in fact consistent with ensembles of random phenotypes. Our results highlight major pitfalls with applying standard GSEA to brain-wide transcriptomic data and outline solutions to this pervasive problem, which is made available as an open toolbox.

Improving diagnosis of acute appendicitis with atypical findings by Tc-99m HMPAO leukocyte scan

2002 ◽  
Vol 41 (01) ◽  
pp. 37-41 ◽  
Author(s):  
S. Shung-Shung ◽  
S. Yu-Chien ◽  
Y. Mei-Due ◽  
W. Hwei-Chung ◽  
A. Kao
Keyword(s):  
Acute Appendicitis ◽  
False Positive ◽  
False Positive Rate ◽  
Accurate Method ◽  
Clinical Findings ◽  
Pathological Findings ◽  
Lower Quadrant ◽  
Predictive Values ◽  
Positive Rate

Summary Aim: Even with careful observation, the overall false-positive rate of laparotomy remains 10-15% when acute appendicitis was suspected. Therefore, the clinical efficacy of Tc-99m HMPAO labeled leukocyte (TC-WBC) scan for the diagnosis of acute appendicitis in patients presenting with atypical clinical findings is assessed. Patients and Methods: Eighty patients presenting with acute abdominal pain and possible acute appendicitis but atypical findings were included in this study. After intravenous injection of TC-WBC, serial anterior abdominal/pelvic images at 30, 60, 120 and 240 min with 800k counts were obtained with a gamma camera. Any abnormal localization of radioactivity in the right lower quadrant of the abdomen, equal to or greater than bone marrow activity, was considered as a positive scan. Results: 36 out of 49 patients showing positive TC-WBC scans received appendectomy. They all proved to have positive pathological findings. Five positive TC-WBC were not related to acute appendicitis, because of other pathological lesions. Eight patients were not operated and clinical follow-up after one month revealed no acute abdominal condition. Three of 31 patients with negative TC-WBC scans received appendectomy. They also presented positive pathological findings. The remaining 28 patients did not receive operations and revealed no evidence of appendicitis after at least one month of follow-up. The overall sensitivity, specificity, accuracy, positive and negative predictive values for TC-WBC scan to diagnose acute appendicitis were 92, 78, 86, 82, and 90%, respectively. Conclusion: TC-WBC scan provides a rapid and highly accurate method for the diagnosis of acute appendicitis in patients with equivocal clinical examination. It proved useful in reducing the false-positive rate of laparotomy and shortens the time necessary for clinical observation.

Predicting Fetal Chromosome Anomalies in the First Trimester Using Pregnancy Associated Plasma Protein-A: A Comparison of Statistical Methods

1993 ◽  
Vol 32 (02) ◽  
pp. 175-179 ◽  
Author(s):  
B. Brambati ◽  
T. Chard ◽  
J. G. Grudzinskas ◽  
M. C. M. Macintosh
Keyword(s):  
Logistic Regression ◽  
General Population ◽  
Likelihood Ratio ◽  
False Positive ◽  
False Positive Rate ◽  
Ratio Method ◽  
Detection Rates ◽  
Gaussian Distributions ◽  
Positive Rate ◽  
Likelihood Ratio Method

Abstract:The analysis of the clinical efficiency of a biochemical parameter in the prediction of chromosome anomalies is described, using a database of 475 cases including 30 abnormalities. A comparison was made of two different approaches to the statistical analysis: the use of Gaussian frequency distributions and likelihood ratios, and logistic regression. Both methods computed that for a 5% false-positive rate approximately 60% of anomalies are detected on the basis of maternal age and serum PAPP-A. The logistic regression analysis is appropriate where the outcome variable (chromosome anomaly) is binary and the detection rates refer to the original data only. The likelihood ratio method is used to predict the outcome in the general population. The latter method depends on the data or some transformation of the data fitting a known frequency distribution (Gaussian in this case). The precision of the predicted detection rates is limited by the small sample of abnormals (30 cases). Varying the means and standard deviations (to the limits of their 95% confidence intervals) of the fitted log Gaussian distributions resulted in a detection rate varying between 42% and 79% for a 5% false-positive rate. Thus, although the likelihood ratio method is potentially the better method in determining the usefulness of a test in the general population, larger numbers of abnormal cases are required to stabilise the means and standard deviations of the fitted log Gaussian distributions.

Identification of and Correction for Publication Bias: Comment

2019 ◽  
Author(s):  
Amanda Kvarven ◽  
Eirik Strømland ◽  
Magnus Johannesson
Keyword(s):  
Publication Bias ◽  
False Positive ◽  
Large Scale ◽  
Meta Analysis ◽  
False Positive Rate ◽  
Effect Sizes ◽  
Replication Studies ◽  
Moderate Reduction ◽  
Positive Rate ◽  
Meta Analyses

Andrews & Kasy (2019) propose an approach for adjusting effect sizes in meta-analysis for publication bias. We use the Andrews-Kasy estimator to adjust the result of 15 meta-analyses and compare the adjusted results to 15 large-scale multiple labs replication studies estimating the same effects. The pre-registered replications provide precisely estimated effect sizes, which do not suffer from publication bias. The Andrews-Kasy approach leads to a moderate reduction of the inflated effect sizes in the meta-analyses. However, the approach still overestimates effect sizes by a factor of about two or more and has an estimated false positive rate of between 57% and 100%.

The ENIGMA Brain Injury Working Group: Approach, Challenges, and Potential Benefits

2019 ◽  
Author(s):  
Elisabeth A. Wilde ◽  
Emily L. Dennis ◽  
David F Tate
Keyword(s):  
Brain Injury ◽  
Working Group ◽  
Meta Analysis ◽  
Special Issue ◽  
Group Approach ◽  
Challenges And Opportunities ◽  
Brain Structure And Function ◽  
Potential Benefits ◽  
And Function ◽  
Neuroimaging Genetics

The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) consortium brings together researchers from around the world to try to identify the genetic underpinnings of brain structure and function, along with robust, generalizable effects of neurological and psychiatric disorders. The recently-formed ENIGMA Brain Injury working group includes 8 subgroups, based largely on injury mechanism and patient population. This introduction to the special issue summarizes the history, organization, and objectives of ENIGMA Brain Injury, and includes a discussion of strategies, challenges, opportunities and goals common across 6 of the subgroups under the umbrella of ENIGMA Brain Injury. The following articles in this special issue, including 6 articles from different subgroups, will detail the challenges and opportunities specific to each subgroup.

Characteristics of false-positive alerts on transcranial motor evoked potential monitoring during pediatric scoliosis and adult spinal deformity surgery: an “anesthetic fade” phenomenon

2020 ◽  
Vol 32 (3) ◽  
pp. 423-431 ◽  
Author(s):  
Hiroki Ushirozako ◽  
Go Yoshida ◽  
Tomohiko Hasegawa ◽  
Yu Yamato ◽  
Tatsuya Yasuda ◽  
...  
Keyword(s):  
Spinal Deformity ◽  
False Positive ◽  
Adult Spinal Deformity ◽  
False Positive Rate ◽  
Multivariate Logistic Regression Analysis ◽  
Motor Evoked Potential ◽  
Scoliosis Surgery ◽  
True Negative ◽  
Duration Of Surgery ◽  
Spinal Deformity Surgery

OBJECTIVETranscranial motor evoked potential (TcMEP) monitoring may be valuable for predicting postoperative neurological complications with a high sensitivity and specificity, but one of the most frequent problems is the high false-positive rate. The purpose of this study was to clarify the differences in the risk factors for false-positive TcMEP alerts seen when performing surgery in patients with pediatric scoliosis and adult spinal deformity and to identify a method to reduce the false-positive rate.METHODSThe authors retrospectively analyzed 393 patients (282 adult and 111 pediatric patients) who underwent TcMEP monitoring while under total intravenous anesthesia during spinal deformity surgery. They defined their cutoff (alert) point as a final TcMEP amplitude of ≤ 30% of the baseline amplitude. Patients with false-positive alerts were classified into one of two groups: a group with pediatric scoliosis and a group with adult spinal deformity.RESULTSThere were 14 cases of false-positive alerts (13%) during pediatric scoliosis surgery and 62 cases of false-positive alerts (22%) during adult spinal deformity surgery. Compared to the true-negative cases during adult spinal deformity surgery, the false-positive cases had a significantly longer duration of surgery and greater estimated blood loss (both p < 0.001). Compared to the true-negative cases during pediatric scoliosis surgery, the false-positive cases had received a significantly higher total fentanyl dose and a higher mean propofol dose (0.75 ± 0.32 mg vs 0.51 ± 0.18 mg [p = 0.014] and 5.6 ± 0.8 mg/kg/hr vs 5.0 ± 0.7 mg/kg/hr [p = 0.009], respectively). A multivariate logistic regression analysis revealed that the duration of surgery (1-hour difference: OR 1.701; 95% CI 1.364–2.120; p < 0.001) was independently associated with false-positive alerts during adult spinal deformity surgery. A multivariate logistic regression analysis revealed that the mean propofol dose (1-mg/kg/hr difference: OR 3.117; 95% CI 1.196–8.123; p = 0.020), the total fentanyl dose (0.05-mg difference; OR 1.270; 95% CI 1.078–1.497; p = 0.004), and the duration of surgery (1-hour difference: OR 2.685; 95% CI 1.131–6.377; p = 0.025) were independently associated with false-positive alerts during pediatric scoliosis surgery.CONCLUSIONSLonger duration of surgery and greater blood loss are more likely to result in false-positive alerts during adult spinal deformity surgery. In particular, anesthetic doses were associated with false-positive TcMEP alerts during pediatric scoliosis surgery. The authors believe that false-positive alerts during pediatric scoliosis surgery, in particular, are caused by “anesthetic fade.”

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