Filtering, FDR and power

Background: In high-dimensional data analysis such as differential gene expression analysis, people often use filtering methods like fold-change or variance filters in an attempt to reduce the multiple testing penalty and improve power. However, filtering may introduce a bias on the multiple testing correction. The precise amount of bias depends on many quantities, such as fraction of probes filtered out, filter statistic and test statistic used.Results: We show that a biased multiple testing correction results if non-differentially expressed probes are not filtered out with equal probability from the entire range of p-values. We illustrate our results using both a simulation study and an experimental dataset, where the FDR is shown to be biased mostly by filters that are associated with the hypothesis being tested, such as the fold change. Filters that induce little bias on the FDR yield less additional power of detecting differentially expressed genes. Finally, we propose a statistical test that can be used in practice to determine whether any chosen filter introduces bias on the FDR estimate used, given a general experimental setup.Conclusions: Filtering out of probes must be used with care as it may bias the multiple testing correction. Researchers can use our test for FDR bias to guide their choice of filter and amount of filtering in practice

Integrating copy number data of 64 iAMP21 BCP-ALL patients narrows the common region of amplification to 1.57 Mb

Background and purposeIntrachromosomal amplification of chromosome 21 (iAMP21) is a rare subtype of B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). It is unknown how iAMP21 contributes to leukaemia. The currently known commonly amplified region is 5.1 Mb.MethodsWe aimed to narrow down the common region of amplification by using high resolution techniques. Array comparative genomic hybridization (aCGH) was used to determine copy number aberrations, Affymetrix U133 Plus2 expression arrays were used to determine gene expression. Genome-wide expression correlations were evaluated using Globaltest.ResultsWe narrowed down the common region of amplification by combining copy number data from 12 iAMP21 cases with 52 cases from literature. The combined common region of amplification was 1.57 Mb, located from 36.07 to 37.64 Mb (GRCh38). This region is located telomeric from, but not including, RUNX1, which is the locus commonly used to diagnose iAMP21. This narrow region, which falls inside the Down Syndrome critical region, includes 13 genes of which the expression of eight genes was significantly upregulated compared with 143 non-iAMP21 B-other cases. Among these, transcriptional repressor RIPPLY3 (also known as DSCR6) was the highest overexpressed gene (fold change = 4.2, FDR DiscussionThe more precise definition of the common region of amplification could be beneficial in the diagnosis of iAMP21 based on copy number analysis from DNA sequencing or arrays as well as stimulate functional research into the role of the included genes in iAMP21 biology.</p

GeneHopper: a web-based search engine to link gene-expression platforms through GenBank accession numbers

Global gene-expression analysis is carried out using different technologies that are either array- or sequence-tag-based. To compare experiments that are performed on these different platforms, array probes and sequence tags need to be linked. An additional challenge is cross-referencing between species, to compare human profiles with those obtained in a mouse model, for example. We have developed the web-based search engine GeneHopper to link different expression resources based on UniGene clusters and HomoloGene orthologs databases of the National Center for Biotechnology Information (NCBI)

Human Papillomavirus Deregulates the Response of a Cellular Network Comprising of Chemotactic and Proinflammatory Genes

Despite the presence of intracellular pathogen recognition receptors that allow infected cells to attract the immune system, undifferentiated keratinocytes (KCs) are the main targets for latent infection with high-risk human papilloma viruses (hrHPVs). HPV infections are transient but on average last for more than one year suggesting that HPV has developed means to evade host immunity. To understand how HPV persists, we studied the innate immune response of undifferentiated human KCs harboring episomal copies of HPV16 and 18 by genome-wide expression profiling. Our data showed that the expression of the different virus-sensing receptors was not affected by the presence of HPV. Poly(I:C) stimulation of the viral RNA receptors TLR3, PKR, MDA5 and RIG-I, the latter of which indirectly senses viral DNA through non-self RNA polymerase III transcripts, showed dampening in downstream signalling of these receptors by HPVs. Many of the genes downregulated in HPV-positive KCs involved components of the antigen presenting pathway, the inflammasome, the production of antivirals, pro-inflammatory and chemotactic cytokines, and components downstream of activated pathogen receptors. Notably, gene and/or protein interaction analysis revealed the downregulation of a network of genes that was strongly interconnected by IL-1β, a crucial cytokine to activate adaptive immunity. In summary, our comprehensive expression profiling approach revealed that HPV16 and 18 coordinate a broad deregulation of the keratinocyte's inflammatory response, and contributes to the understanding of virus persistence

Diagnostic accuracy of depression questionnaires in adult patients with diabetes: a systematic review and meta-analysis

Importance Comorbid depression is common among patients with diabetes and has severe health consequences, but often remains unrecognized. Several questionnaires are used to screen for depression. A systematic review and meta-analysis regarding the diagnostic accuracy of depression questionnaires in adults with diabetes is unavailable. Objective To conduct a systematic review and meta-analysis to evaluate the diagnostic accuracy of depression questionnaires in adults with type 1 or type 2 diabetes. Data sources PubMed, Embase and PsycINFO were searched from inception to 28 February 2018. Study selection Studies were included when the diagnostic accuracy of depression questionnaires was assessed in a diabetes population and the reference standard was a clinical interview. Data extraction and synthesis Data extraction was performed by one reviewer and checked by another. Two reviewers independently conducted the quality assessment (QUADAS-2). Diagnostic accuracy was pooled in bivariate random effects models. This study is reported according to PRISMA-DTA and is registered with PROSPERO (CRD42018092950). Main Outcome(s) and measure(s) Diagnostic accuracy, expressed as sensitivity and specificity, of depression questionnaires in an adult diabetes population. Results A total 6,097 peer-reviewed articles were screened. Twenty-one studies (N= 5,703 patients) met the inclusion criteria for the systematic review. Twelve different depression questionnaires were identified, of which the CES-D (n=6 studies) and PHQ-9 (n=7 studies) were the most frequently evaluated. Risk of bias was unclear for multiple domains in the majority of studies. In the meta-analyses, five (N= 1,228) studies of the CES-D (≥16), five (N= 1,642) of the PHQ-9 (≥10) and four (N=822) of the algorithm of the PHQ-9 were included in the pooled analysis. The CES-D (≥16) had a pooled sensitivity of 85.0% (95%CI, 71.3-92.8%) and a specificity of 71.6% (95%CI, 62.5-79.2%); the PHQ-9 (≥10) had a sensitivity of 81.5% (95%CI, 57.1-93.5%) and a specificity of 79.7% (95%CI, 62.1-90.4%). The algorithm for the PHQ-9 had a sensitivity of 60.9% (95%CI, 52.3-50 90.8%) and a specificity of 64.0% (95%CI, 53.0-93.9%). Conclusions and relevance This review indicates that the CES-D had the highest sensitivity, whereas the PHQ-9 had the highest specificity, although confidence intervals were wide and overlapping. The algorithm for the PHQ-9 had the lowest sensitivity and specificity. Given the variance in results and suboptimal reporting of studies, further high quality studies are needed to confirm the diagnostic accuracy of these depression questionnaires in patients with diabetes

The homeobox gene MEIS1 is methylated in BRAFp.V600E mutated colon tumors

Development of colorectal cancer (CRC) can occur both via gene mutations in tumor suppressor genes and oncogenes, as well as via epigenetic changes, including DNA methylation. Site-specific methylation in CRC regulates expression of tumor-associated genes. Right-sided colon tumors more frequently have BRAFp.V600E mutations and have higher methylation grades when compared to left-sided malignancies. The aim of this study was to identify DNA methylation changes associated with BRAFp.V600E mutation status. We performed methylation profiling of colon tumor DNA, isolated from frozen sections enriched for epithelial cells by macro-dissection, and from paired healthy tissue. Single gene analyses comparing BRAFp.V600E with BRAF wild type revealed MEIS1 as the most significant differentially methylated gene (log2 fold change: 0.89, false discovery rate-adjusted P-value 2.8*10-9). This finding was validated by methylation-specific PCR that was concordant with the microarray data. Additionally, validation in an independent cohort (n=228) showed a significant association between BRAF p.V600E and MEIS1 methylation (OR: 13.0, 95% CI: 5.2 - 33.0, P<0.0001). MEIS1 methylation was associated with decreased MEIS1 gene expression in both patient samples and CRC cell lines. The same was true for gene expression of a truncated form of MEIS1, MEIS1D27, which misses exon 8 and has a proposed tumor suppression function. To trace the origin of MEIS1 promoter methylation, 14 colorectal tumors were flow-sorted. Four out of eight BRAFp.V600E tumor epithelial fractions (50%) showed MEIS1 promoter methylation, as well as three out of eight BRAFp.V600E stromal fractions (38%). Only one out of six BRAF wild type showed MEIS1 promoter methylation in both the epithelial tumor and stromal fractions (17%). In conclusion, BRAFp.V600E colon tumors showed significant MEIS1 promoter methylation, which was associated with decreased MEIS1 gene expression. Copyright

Ambient ultrafine particles and asthma onset until age 20: The PIAMA birth cohort

Rationale: Evidence regarding the role of long-term exposure to ultrafine particles (<0.1 μm, UFP) in asthma onset is scarce. Objectives: We examined the association between exposure to UFP and asthma development in the Dutch PIAMA (Prevention and Incidence of Asthma and Mite Allergy) birth cohort and assessed whether there is an association with UFP, independent of other air pollutants. Methods: Data from birth up to age 20 years from 3687 participants were included. Annual average exposure to UFP at the residential addresses was estimated with a land-use regression model. Overall and age-specific associations of exposure at the birth address and current address at the time of follow-up with asthma incidence were assessed using discrete-time hazard models adjusting for potential confounders. We investigated both single- and two-pollutant models accounting for co-exposure to other air pollutants (PM2.5 and PM10 mass concentrations, nitrogen dioxide, and PM2.5 absorbance). Measurements and main results: A total of 812 incident asthma cases were identified. Overall, we found that higher UFP exposure was associated with higher asthma incidence (adjusted odds ratio (95% confidence interval) 1.08 (1.02,1.14) and 1.06 (1.00, 1.12) per interquartile range increase in exposure at the birth address and current address at the time of follow-up, respectively). Age-specific associations were not consistent. The association was no longer significant after adjustment for other traffic-related pollutants (nitrogen dioxide and PM2.5 absorbance). Conclusions: Our findings support the importance of traffic-related air pollutants for asthma development through childhood and adolescence, but provide little support for an independent effect of UFP