Journal of clinical bioinformatics最新文献

{"title":"TRANSFoRm Query Workbench","authors":"Theodoros N. Arvanitis, W. Kuchinke","doi":"10.1186/2043-9113-5-S1-S16","DOIUrl":"https://doi.org/10.1186/2043-9113-5-S1-S16","url":null,"abstract":"","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2043-9113-5-S1-S16","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65701530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MOLGENIS catalogue","authors":"M. Swertz, David van Enckevort, Chao Pang","doi":"10.1186/2043-9113-5-S1-S8","DOIUrl":"https://doi.org/10.1186/2043-9113-5-S1-S8","url":null,"abstract":"","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2043-9113-5-S1-S8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65701891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative efficacy and acceptability of five anti-tubercular drugs in treatment of multidrug resistant tuberculosis: a network meta-analysis.","authors":"Huaidong Wang,&nbsp;Xiaotian Zhang,&nbsp;Yuanxiang Bai,&nbsp;Zipeng Duan,&nbsp;Yan Lin,&nbsp;Guoqing Wang,&nbsp;Fan Li","doi":"10.1186/s13336-015-0020-x","DOIUrl":"https://doi.org/10.1186/s13336-015-0020-x","url":null,"abstract":"<p><p>Multidrug resistant tuberculosis (MDR-TB) is a serious form of tuberculosis (TB). There is no recognized effective treatment for MDR-TB, although there are a number of publications that have reported positive results for MDR-TB. We performed a network meta-analysis to assess the efficacy and acceptability of potential antitubercular drugs. We conducted a network meta-analysis of randomized controlled clinical trials to compare the efficacy and acceptability of five antitubercular drugs, bedaquiline, delamanid, levofloxacin, metronidazole and moxifloxacin in the treatment of MDR-TB. We included eleven suitable trials from nine journal articles and six clinical trials from ClinicalTrials.gov, with data for 1472 participants. Bedaquiline (odds ratio [OR] 2.69, 95% CI 1.02-7.43), delamanid (OR 2.45, 95% CI 1.36-4.89) and moxifloxacin (OR 2.47, 95% CI 1.01, 7.31) were significantly more effective than placebo. For efficacy, the results indicated no statistical significance between each antitubercular drug. For acceptability, the results indicated no statistically significant difference between each compared intervention. There is insufficient evidence to suggest that any one of the five antitubercular drugs (bedaquiline, delamanid, levofloxacin, metronidazole and moxifloxacin) has superior efficacy compared to the others. </p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-015-0020-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33272121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine.","authors":"Christian Castaneda,&nbsp;Kip Nalley,&nbsp;Ciaran Mannion,&nbsp;Pritish Bhattacharyya,&nbsp;Patrick Blake,&nbsp;Andrew Pecora,&nbsp;Andre Goy,&nbsp;K Stephen Suh","doi":"10.1186/s13336-015-0019-3","DOIUrl":"https://doi.org/10.1186/s13336-015-0019-3","url":null,"abstract":"<p><p>As research laboratories and clinics collaborate to achieve precision medicine, both communities are required to understand mandated electronic health/medical record (EHR/EMR) initiatives that will be fully implemented in all clinics in the United States by 2015. Stakeholders will need to evaluate current record keeping practices and optimize and standardize methodologies to capture nearly all information in digital format. Collaborative efforts from academic and industry sectors are crucial to achieving higher efficacy in patient care while minimizing costs. Currently existing digitized data and information are present in multiple formats and are largely unstructured. In the absence of a universally accepted management system, departments and institutions continue to generate silos of information. As a result, invaluable and newly discovered knowledge is difficult to access. To accelerate biomedical research and reduce healthcare costs, clinical and bioinformatics systems must employ common data elements to create structured annotation forms enabling laboratories and clinics to capture sharable data in real time. Conversion of these datasets to knowable information should be a routine institutionalized process. New scientific knowledge and clinical discoveries can be shared via integrated knowledge environments defined by flexible data models and extensive use of standards, ontologies, vocabularies, and thesauri. In the clinical setting, aggregated knowledge must be displayed in user-friendly formats so that physicians, non-technical laboratory personnel, nurses, data/research coordinators, and end-users can enter data, access information, and understand the output. The effort to connect astronomical numbers of data points, including '-omics'-based molecular data, individual genome sequences, experimental data, patient clinical phenotypes, and follow-up data is a monumental task. Roadblocks to this vision of integration and interoperability include ethical, legal, and logistical concerns. Ensuring data security and protection of patient rights while simultaneously facilitating standardization is paramount to maintaining public support. The capabilities of supercomputing need to be applied strategically. A standardized, methodological implementation must be applied to developed artificial intelligence systems with the ability to integrate data and information into clinically relevant knowledge. Ultimately, the integration of bioinformatics and clinical data in a clinical decision support system promises precision medicine and cost effective and personalized patient care. </p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-015-0019-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33183093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomics and partial least square discriminant analysis to predict history of myocardial infarction of self-claimed healthy subjects: validity and feasibility for clinical practice.","authors":"Nornazliya Mohamad,&nbsp;Rose Iszati Ismet,&nbsp;MohdSalleh Rofiee,&nbsp;Zakaria Bannur,&nbsp;Thomas Hennessy,&nbsp;Manikandan Selvaraj,&nbsp;Aminuddin Ahmad,&nbsp;FadzilahMohd Nor,&nbsp;ThuhairahHasrah Abdul Rahman,&nbsp;Kamarudzaman Md Isa,&nbsp;AdzroolIdzwan Ismail,&nbsp;Lay Kek Teh,&nbsp;Mohd Zaki Salleh","doi":"10.1186/s13336-015-0018-4","DOIUrl":"https://doi.org/10.1186/s13336-015-0018-4","url":null,"abstract":"<p><strong>Background: </strong>The dynamics of metabolomics in establishing a prediction model using partial least square discriminant analysis have enabled better disease diagnosis; with emphasis on early detection of diseases. We attempted to translate the metabolomics model to predict the health status of the Orang Asli community whom we have little information. The metabolite expressions of the healthy vs. diseased patients (cardiovascular) were compared. A metabotype model was developed and validated using partial least square discriminant analysis (PLSDA). Cardiovascular risks of the Orang Asli were predicted and confirmed by biochemistry profiles conducted concurrently.</p><p><strong>Results: </strong>Fourteen (14) metabolites were determined as potential biomarkers for cardiovascular risks with receiver operating characteristic of more than 0.7. They include 15S-HETE (AUC = 0.997) and phosphorylcholine (AUC = 0.995). Seven Orang Asli were clustered with the patients' group and may have ongoing cardiovascular risks and problems. This is supported by biochemistry tests results that showed abnormalities in cholesterol, triglyceride, HDL and LDL levels.</p><p><strong>Conclusions: </strong>The disease prediction model based on metabolites is a useful diagnostic alternative as compared to the current single biomarker assays. The former is believed to be more cost effective since a single sample run is able to provide a more comprehensive disease profile, whilst the latter require different types of sampling tubes and blood volumes.</p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-015-0018-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33157684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variations in genome-wide RNAi screens: lessons from influenza research.","authors":"Yu-Chi Chou,&nbsp;Michael Mc Lai,&nbsp;Yi-Chen Wu,&nbsp;Nai-Chi Hsu,&nbsp;King-Song Jeng,&nbsp;Wen-Chi Su","doi":"10.1186/s13336-015-0017-5","DOIUrl":"https://doi.org/10.1186/s13336-015-0017-5","url":null,"abstract":"<p><p>Genome-wide RNA interference (RNAi) screening is an emerging and powerful technique for genetic screens, which can be divided into arrayed RNAi screen and pooled RNAi screen/selection based on different screening strategies. To date, several genome-wide RNAi screens have been successfully performed to identify host factors essential for influenza virus replication. However, the host factors identified by different research groups are not always consistent. Taking influenza virus screens as an example, we found that a number of screening parameters may directly or indirectly influence the primary hits identified by the screens. This review highlights the differences among the published genome-wide screening approaches and offers recommendations for performing a good pooled shRNA screen/selection. </p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-015-0017-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33107135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.","authors":"Arnold I Emerson,&nbsp;Simeon Andrews,&nbsp;Ikhlak Ahmed,&nbsp;Thasni Ka Azis,&nbsp;Joel A Malek","doi":"10.1186/s13336-015-0016-6","DOIUrl":"https://doi.org/10.1186/s13336-015-0016-6","url":null,"abstract":"<p><strong>Background: </strong>Network biology currently focuses primarily on metabolic pathways, gene regulatory, and protein-protein interaction networks. While these approaches have yielded critical information, alternative methods to network analysis will offer new perspectives on biological information. A little explored area is the interactions between domains that can be captured using domain co-occurrence networks (DCN). A DCN can be used to study the function and interaction of proteins by representing protein domains and their co-existence in genes and by mapping cancer mutations to the individual protein domains to identify signals.</p><p><strong>Results: </strong>The domain co-occurrence network was constructed for the human proteome based on PFAM domains in proteins. Highly connected domains in the central cores were identified using the k-core decomposition technique. Here we show that these domains were found to be more evolutionarily conserved than the peripheral domains. The somatic mutations for ovarian, breast and prostate cancer diseases were obtained from the TCGA database. We mapped the somatic mutations to the individual protein domains and the local false discovery rate was used to identify significantly mutated domains in each cancer type. Significantly mutated domains were found to be enriched in cancer disease pathways. However, we found that the inner cores of the DCN did not contain any of the significantly mutated domains. We observed that the inner core protein domains are highly conserved and these domains co-exist in large numbers with other protein domains.</p><p><strong>Conclusion: </strong>Mutations and domain co-occurrence networks provide a framework for understanding hierarchal designs in protein function from a network perspective. This study provides evidence that a majority of protein domains in the inner core of the DCN have a lower mutation frequency and that protein domains present in the peripheral regions of the k-core contribute more heavily to the disease. These findings may contribute further to drug development.</p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-015-0016-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33127643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Copy number variation analysis based on AluScan sequences.","authors":"Jian-Feng Yang,&nbsp;Xiao-Fan Ding,&nbsp;Lei Chen,&nbsp;Wai-Kin Mat,&nbsp;Michelle Zhi Xu,&nbsp;Jin-Fei Chen,&nbsp;Jian-Min Wang,&nbsp;Lin Xu,&nbsp;Wai-Sang Poon,&nbsp;Ava Kwong,&nbsp;Gilberto Ka-Kit Leung,&nbsp;Tze-Ching Tan,&nbsp;Chi-Hung Yu,&nbsp;Yue-Bin Ke,&nbsp;Xin-Yun Xu,&nbsp;Xiao-Yan Ke,&nbsp;Ronald Cw Ma,&nbsp;Juliana Cn Chan,&nbsp;Wei-Qing Wan,&nbsp;Li-Wei Zhang,&nbsp;Yogesh Kumar,&nbsp;Shui-Ying Tsang,&nbsp;Shao Li,&nbsp;Hong-Yang Wang,&nbsp;Hong Xue","doi":"10.1186/s13336-014-0015-z","DOIUrl":"https://doi.org/10.1186/s13336-014-0015-z","url":null,"abstract":"<p><strong>Background: </strong>AluScan combines inter-Alu PCR using multiple Alu-based primers with opposite orientations and next-generation sequencing to capture a huge number of Alu-proximal genomic sequences for investigation. Its requirement of only sub-microgram quantities of DNA facilitates the examination of large numbers of samples. However, the special features of AluScan data rendered difficult the calling of copy number variation (CNV) directly using the calling algorithms designed for whole genome sequencing (WGS) or exome sequencing.</p><p><strong>Results: </strong>In this study, an AluScanCNV package has been assembled for efficient CNV calling from AluScan sequencing data employing a Geary-Hinkley transformation (GHT) of read-depth ratios between either paired test-control samples, or between test samples and a reference template constructed from reference samples, to call the localized CNVs, followed by use of a GISTIC-like algorithm to identify recurrent CNVs and circular binary segmentation (CBS) to reveal large extended CNVs. To evaluate the utility of CNVs called from AluScan data, the AluScans from 23 non-cancer and 38 cancer genomes were analyzed in this study. The glioma samples analyzed yielded the familiar extended copy-number losses on chromosomes 1p and 9. Also, the recurrent somatic CNVs identified from liver cancer samples were similar to those reported for liver cancer WGS with respect to a striking enrichment of copy-number gains in chromosomes 1q and 8q. When localized or recurrent CNV-features capable of distinguishing between liver and non-liver cancer samples were selected by correlation-based machine learning, a highly accurate separation of the liver and non-liver cancer classes was attained.</p><p><strong>Conclusions: </strong>The results obtained from non-cancer and cancerous tissues indicated that the AluScanCNV package can be employed to call localized, recurrent and extended CNVs from AluScan sequences. Moreover, both the localized and recurrent CNVs identified by this method could be subjected to machine-learning selection to yield distinguishing CNV-features that were capable of separating between liver cancers and other types of cancers. Since the method is applicable to any human DNA sample with or without the availability of a paired control, it can also be employed to analyze the constitutional CNVs of individuals.</p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13336-014-0015-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32949209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform","authors":"Mercedeh Movassagh, P. Mudvari, M. Kokkinaki, N. Edwards, N. Golestaneh, A. Horvath","doi":"10.1186/2043-9113-4-14","DOIUrl":"https://doi.org/10.1186/2043-9113-4-14","url":null,"abstract":"","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2043-9113-4-14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65700448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Semi-automated literature mining to identify putative biomarkers of disease from multiple biofluids.","authors":"Rick Jordan,&nbsp;Shyam Visweswaran,&nbsp;Vanathi Gopalakrishnan","doi":"10.1186/2043-9113-4-13","DOIUrl":"https://doi.org/10.1186/2043-9113-4-13","url":null,"abstract":"<p><strong>Background: </strong>Computational methods for mining of biomedical literature can be useful in augmenting manual searches of the literature using keywords for disease-specific biomarker discovery from biofluids. In this work, we develop and apply a semi-automated literature mining method to mine abstracts obtained from PubMed to discover putative biomarkers of breast and lung cancers in specific biofluids.</p><p><strong>Methodology: </strong>A positive set of abstracts was defined by the terms 'breast cancer' and 'lung cancer' in conjunction with 14 separate 'biofluids' (bile, blood, breastmilk, cerebrospinal fluid, mucus, plasma, saliva, semen, serum, synovial fluid, stool, sweat, tears, and urine), while a negative set of abstracts was defined by the terms '(biofluid) NOT breast cancer' or '(biofluid) NOT lung cancer.' More than 5.3 million total abstracts were obtained from PubMed and examined for biomarker-disease-biofluid associations (34,296 positive and 2,653,396 negative for breast cancer; 28,355 positive and 2,595,034 negative for lung cancer). Biological entities such as genes and proteins were tagged using ABNER, and processed using Python scripts to produce a list of putative biomarkers. Z-scores were calculated, ranked, and used to determine significance of putative biomarkers found. Manual verification of relevant abstracts was performed to assess our method's performance.</p><p><strong>Results: </strong>Biofluid-specific markers were identified from the literature, assigned relevance scores based on frequency of occurrence, and validated using known biomarker lists and/or databases for lung and breast cancer [NCBI's On-line Mendelian Inheritance in Man (OMIM), Cancer Gene annotation server for cancer genomics (CAGE), NCBI's Genes & Disease, NCI's Early Detection Research Network (EDRN), and others]. The specificity of each marker for a given biofluid was calculated, and the performance of our semi-automated literature mining method assessed for breast and lung cancer.</p><p><strong>Conclusions: </strong>We developed a semi-automated process for determining a list of putative biomarkers for breast and lung cancer. New knowledge is presented in the form of biomarker lists; ranked, newly discovered biomarker-disease-biofluid relationships; and biomarker specificity across biofluids.</p>","PeriodicalId":73663,"journal":{"name":"Journal of clinical bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2043-9113-4-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32800197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}