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  • 1
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    A survey of tools for variant analysis of next-generation genome sequencing data (2014)
    Oxford University Press
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    Publication Date: 2014-03-18
    Description: Recent advances in genome sequencing technologies provide unprecedented opportunities to characterize individual genomic landscapes and identify mutations relevant for diagnosis and therapy. Specifically, whole-exome sequencing using next-generation sequencing (NGS) technologies is gaining popularity in the human genetics community due to the moderate costs, manageable data amounts and straightforward interpretation of analysis results. While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting specific parts of the analysis workflow or providing a complete solution. Here, we surveyed 205 tools for whole-genome/whole-exome sequencing data analysis supporting five distinct analytical steps: quality assessment, alignment, variant identification, variant annotation and visualization. We report an overview of the functionality, features and specific requirements of the individual tools. We then selected 32 programs for variant identification, variant annotation and visualization, which were subjected to hands-on evaluation using four data sets: one set of exome data from two patients with a rare disease for testing identification of germline mutations, two cancer data sets for testing variant callers for somatic mutations, copy number variations and structural variations, and one semi-synthetic data set for testing identification of copy number variations. Our comprehensive survey and evaluation of NGS tools provides a valuable guideline for human geneticists working on Mendelian disorders, complex diseases and cancers.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 2
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    Non-invasive mapping of organ perfusion and blood flow by CT and MRI highlighted by a case of pulmonary artery stenosis (2014)
    Oxford University Press
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    Publication Date: 2014-04-09
    Print ISSN: 1525-2167
    Electronic ISSN: 1532-2114
    Topics: Medicine
    Published by Oxford University Press
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  • 3
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    The mass-radius relationship for very low mass stars: four new discoveries from the HATSouth Survey (2013)
    Oxford University Press
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    Publication Date: 2013-12-23
    Description: We report the discovery of four transiting F-M binary systems with companions between 0.1 and 0.2 M in mass by the HATSouth survey. These systems have been characterized via a global analysis of the HATSouth discovery data, combined with high-resolution radial velocities and accurate transit photometry observations. We determined the masses and radii of the component stars using a combination of two methods: isochrone fitting of spectroscopic primary star parameters and equating spectroscopic primary star rotation velocity with spin–orbit synchronization. These new very low mass companions are HATS550-016B ( $0.110_{-0.006}^{+0.005}\,\mathrm{M}_{\odot }$ , $0.147_{-0.004}^{+0.003}\,\mathrm{R}_{\odot }$ ), HATS551-019B ( $0.17_{-0.01}^{+0.01}\,\mathrm{M}_{\odot }$ , $0.18_{-0.01}^{+0.01}\,\mathrm{R}_{\odot }$ ), HATS551-021B ( $0.132_{-0.005}^{+0.014}\,\mathrm{M}_{\odot }$ , $0.154_{-0.008}^{+0.006}\,\mathrm{R}_{\odot }$ ) and HATS553-001B ( $0.20_{-0.02}^{+0.01}\,\mathrm{M}_{\odot }$ , $0.22_{-0.01}^{+0.01}\,\mathrm{R}_{\odot }$ ). We examine our sample in the context of the radius anomaly for fully convective low-mass stars. Combining our sample with the 13 other well-studied very low mass stars, we find a tentative 5 per cent systematic deviation between the measured radii and theoretical isochrone models.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Integration of TP53, DREAM, MMB-FOXM1 and RB-E2F target gene analyses identifies cell cycle gene regulatory networks (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Cell cycle (CC) and TP53 regulatory networks are frequently deregulated in cancer. While numerous genome-wide studies of TP53 and CC-regulated genes have been performed, significant variation between studies has made it difficult to assess regulation of any given gene of interest. To overcome the limitation of individual studies, we developed a meta-analysis approach to identify high confidence target genes that reflect their frequency of identification in independent datasets. Gene regulatory networks were generated by comparing differential expression of TP53 and CC-regulated genes with chromatin immunoprecipitation studies for TP53, RB1, E2F, DREAM, B-MYB, FOXM1 and MuvB. RNA-seq data from p21-null cells revealed that gene downregulation by TP53 generally requires p21 (CDKN1A). Genes downregulated by TP53 were also identified as CC genes bound by the DREAM complex. The transcription factors RB, E2F1 and E2F7 bind to a subset of DREAM target genes that function in G1/S of the CC while B-MYB, FOXM1 and MuvB control G2/M gene expression. Our approach yields high confidence ranked target gene maps for TP53, DREAM, MMB-FOXM1 and RB-E2F and enables prediction and distinction of CC regulation. A web-based atlas at www.targetgenereg.org enables assessing the regulation of any human gene of interest.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification (2016)
    Oxford University Press
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    Publication Date: 2016-03-26
    Description: Motivation: Isobaric labelling techniques such as iTRAQ and TMT are popular methods for relative protein abundance estimation in proteomic studies. However, measurements are assessed at the peptide spectrum level and exhibit substantial heterogeneity per protein. Hence, clever summarization strategies are required to infer protein ratios. So far, current methods rely exclusively on quantitative values, while additional information on peptides is available, yet it is not considered in these methods. Methods: We present iPQF ( i sobaric P rotein Q uantification based on F eatures) as a novel peptide-to-protein summarization method, which integrates peptide spectra characteristics as well as quantitative values for protein ratio estimation. We investigate diverse features characterizing spectra reliability and reveal significant correlations to ratio accuracy in spectra. As a result, we developed a feature-based weighting of peptide spectra. Results: A performance evaluation of iPQF in comparison to nine different protein ratio inference methods is conducted on five published MS2 and MS3 datasets with predefined ground truth. We demonstrate the benefit of using peptide feature information to improve protein ratio estimation. Compared to purely quantitative approaches, our proposed strategy achieves increased accuracy by addressing peptide spectra reliability. Availability and implementation: The iPQF algorithm is available within the established R/Bioconductor package MSnbase (version ≥ 1.17.8). Contact: renardB@rki.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 6
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    Low p14ARF expression in neuroblastoma cells is associated with repressed histone mark status, and enforced expression induces growth arrest and apoptosis (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: The TP53 tumor suppressor pathway is abrogated by TP53 mutations in the majority of human cancers. Increased levels of wild-type TP53 in aggressive neuroblastomas appear paradox but are tolerated by tumor cells due to co-activation of the TP53 ubiquitin ligase, MDM2. The role of the MDM2 antagonist, p14 ARF , in controlling the TP53-MDM2 balance in neuroblastoma is unresolved. In the present study, we show that conditional p14 ARF expression substantially suppresses viability, clonogenicity and anchorage-independent growth in p14 ARF -deficient or MYCN -amplified neuroblastoma cell lines. Furthermore, ectopic 14 ARF expression induced accumulation of cells in the G1 phase and apoptosis, which was paralleled by accumulation of TP53 and its targets. Comparative genomic hybridization analysis of 193 primary neuroblastomas detected one homozygous deletion of CDKN2A (encoding both p14 ARF and p16 INK4A ) and heterozygous loss of CDKN2A in 22% of tumors. Co-expression analysis of p14 ARF and its transactivator, E2F1, in a set of 68 primary tumors revealed only a weak correlation, suggesting that further regulatory mechanisms govern p14 ARF expression in neuroblastomas. Intriguingly, analyses utilizing chromatin immunoprecipitation revealed different histone mark-defined epigenetic activity states of p14 ARF in neuroblastoma cell lines that correlated with endogenous p14 ARF expression but not with episomal p14 ARF promoter reporter activity, indicating that the native chromatin context serves to epigenetically repress p14 ARF in neuroblastoma cells. Collectively, the data pinpoint p14 ARF as a critical factor for efficient TP53 response in neuroblastoma cells and assign p14 ARF as a neuroblastoma suppressor candidate that is impaired by genomic loss and epigenetic repression.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 7
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    Validity and Concordance Between Self-Reported and Clinical Diagnosis of Hypertension Among Elderly Residents in Northeastern Brazil (2013)
    Oxford University Press
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    Publication Date: 2013-12-24
    Description: BACKGROUND Self-reported information has been used as an easy and quick method to estimate the prevalence of systemic hypertension in populations. However, verification of whether self-reports of the disease are consistent with clinical diagnosis is essential for proper use of this information. This study aimed to verify the validity and concordance between self-reported and clinical diagnosis of hypertension in the elderly population of a city in northeastern Brazil. METHODS This was a cross-sectional and population-based study. The prevalence of diagnosed and self-reported hypertension and the validity and concordance between self-reported and clinical diagnosis and their distribution according to demographic and socioeconomic variables were assessed. The validity of self-reported hypertension was determined by sensitivity, specificity, and positive and negative predictive value. RESULTS Overall, 795 elderly patients were evaluated (69.1% women). There was a high prevalence of hypertension among the elderly (diagnosed: 75.1%, 95% confidence interval (CI) = 71.1%–77.9%; self-reported: 59.7%, 95% CI = 56.3%–63.1%). For self-reported hypertension, sensitivity was substantial (77.1%), specificity was excellent (93.4%), positive predictive value was excellent (97.3%), and negative predictive value was moderate (57.2%). There was a moderate concordance between self-reported and clinical diagnosis of hypertension (kappa = 0.59; P 〈 0.001). CONCLUSIONS Reasonable validity and moderate concordance of self-reported information on hypertension was observed, which reinforces the idea that this information can be used as strategy for detecting the disease prevalence in this population. However, because of nonachievement of excellence in the validity and reliability of the measured blood pressure, this information should be carefully considered for the strategic planning of health services.
    Print ISSN: 0895-7061
    Electronic ISSN: 1879-1905
    Topics: Medicine
    Published by Oxford University Press
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  • 8
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    Higher plasma CXCL12 levels predict incident myocardial infarction and death in chronic kidney disease: findings from the Chronic Renal Insufficiency Cohort study (2014)
    Oxford University Press
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    Publication Date: 2014-08-15
    Description: Aims Genome-wide association studies revealed an association between a locus at 10q11, downstream from CXCL12, and myocardial infarction (MI). However, the relationship among plasma CXCL12, cardiovascular disease (CVD) risk factors, incident MI, and death is unknown. Methods and results We analysed study-entry plasma CXCL12 levels in 3687 participants of the Chronic Renal Insufficiency Cohort (CRIC) Study, a prospective study of cardiovascular and kidney outcomes in chronic kidney disease (CKD) patients. Mean follow-up was 6 years for incident MI or death. Plasma CXCL12 levels were positively associated with several cardiovascular risk factors (age, hypertension, diabetes, hypercholesterolaemia), lower estimated glomerular filtration rate (eGFR), and higher inflammatory cytokine levels ( P 〈 0.05). In fully adjusted models, higher study-entry CXCL12 was associated with increased odds of prevalent CVD (OR 1.23; 95% confidence interval 1.14, 1.33, P 〈 0.001) for one standard deviation (SD) increase in CXCL12. Similarly, one SD higher CXCL12 increased the hazard of incident MI (1.26; 1.09,1.45, P 〈 0.001), death (1.20; 1.09,1.33, P 〈 0.001), and combined MI/death (1.23; 1.13–1.34, P 〈 0.001) adjusting for demographic factors, known CVD risk factors, and inflammatory markers and remained significant for MI (1.19; 1.03,1.39, P = 0.01) and the combined MI/death (1.13; 1.03,1.24, P = 0.01) after further controlling for eGFR and urinary albumin:creatinine ratio. Conclusions In CKD, higher plasma CXCL12 was associated with CVD risk factors and prevalent CVD as well as the hazard of incident MI and death. Further studies are required to establish if plasma CXCL12 reflect causal actions at the vessel wall and is a tool for genomic and therapeutic trials.
    Print ISSN: 0195-668X
    Electronic ISSN: 1522-9645
    Topics: Medicine
    Published by Oxford University Press
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  • 9
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    The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes (2012)
    Oxford University Press
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    Publication Date: 2012-02-28
    Description: Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like cyclin B, CDC2 and CDC25C are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in G 0 /G 1 . It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and human cyclin B2 promoters in G 0 . Association of DREAM and cell cycle-dependent regulation is abrogated when the CHR is mutated. Although E2f4 is part of the complex, a CDE is not essential but can enhance binding of DREAM. We show that the CHR element is not only necessary for repression of gene transcription in G 0 /G 1 , but also for activation in S, G 2 and M phases. In proliferating cells, the B-myb-containing MMB complex binds the CHR of both promoters independently of the CDE. Bioinformatic analyses identify many genes which contain conserved CHR elements in promoters binding the DREAM complex. With Ube2c as an example from that screen, we show that inverse CHR sites are functional promoter elements that can bind DREAM and MMB. Our findings indicate that the CHR is central to DREAM/MMB-dependent transcriptional control during the cell cycle.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Evaluation for West Nile Virus (WNV) RNA in Urine of Patients Within 5 Months of WNV Infection (2012)
    Oxford University Press
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    Publication Date: 2012-04-16
    Print ISSN: 0022-1899
    Electronic ISSN: 1537-6613
    Topics: Medicine
    Published by Oxford University Press on behalf of The Infectious Diseases Society of America (IDSA).
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