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Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies

Andrea Ganna, Donghwan Lee, Erik Ingelsson, Yudi Pawitan
2014 Briefings in Bioinformatics  
We refer to this proportion as rediscovery rate (RDR). In high-throughput studies, the RDR is a function of false-positive rate and power in both the training and validation samples.  ...  In this article, we review common approaches to determine statistical thresholds for validation and describe the factors influencing the proportion of significant findings from a 'training' sample that  ...  DISCUSSION It is a common and recommended practice in biomedical research to validate significant findings in a different population from the one where the findings were initially assessed.  ... 
doi:10.1093/bib/bbu033 pmid:25256289 fatcat:gjc2vx3ri5eupoair4uscnv44a

Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach

Swetansu Pattnaik, Srividya Vaidyanathan, Durgad G. Pooja, Sa Deepak, Binay Panda, Paolo Provero
2012 PLoS ONE  
Although NGS platforms provide a cost-effective way to discover genome-wide variants from a single experiment, variants discovered by NGS need follow up validation due to the high error rates associated  ...  Biologists often lack the requisite training to deal with the huge amount of data produced by NGS runs and face difficulty in choosing from the list of freely available analytical tools for NGS data analysis  ...  Kuriakose, Mazumdar Shaw Cancer Centre, Narayana Hrudayalaya, Bangalore for providing us with the human tissue samples. Author Contributions Conceived and designed the experiments: BP.  ... 
doi:10.1371/journal.pone.0030080 pmid:22238694 pmcid:PMC3253117 fatcat:m3awmc47jvb5noea52qr2pfn44

Simple multi-trait analysis identifies novel loci associated with growth and obesity measures [article]

Xia Shen, Xiao Wang, Zheng Ning, Yakov Tsepilov, Masoud Shirali, Blair H. Smith, Lynne J. Hocking, Sandosh Padmanabhan, Caroline Hayward, David J. Porteous, Yudi Pawitan, Chris S. Haley (+1 others)
2015 bioRxiv   pre-print
The novel variants had an enriched rediscovery rate in the replication cohort.  ...  Our results provide new important insights into the biological mechanisms underlying anthropometric traits and emphasize the value of combining multiple correlated phenotypes in genomic studies.  ...  Rediscovery rate estimation for assessing 264 the validation of significant findings in high-throughput studies. Brief. Bioinformatics 265 (2014). doi:10.1093/bib/bbu033 266 16. Dalmas, E. et al.  ... 
doi:10.1101/022269 fatcat:b7gaom6tbbf55pbfokr4xaxgsi

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing

Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
2020 Frontiers in Genetics  
In this study, we assess the reproducibility of 9 tools for differential expression analysis in scRNA-seq data.  ...  Instead of comparing the performance across all genes, we compare the methods in terms of the rediscovery rates (RDRs) of top-ranked genes, separately for highly and lowly expressed genes.  ...  In high-throughput studies, the RDR is determined by both the false positive rate (FPR) and power (Ganna et al., 2014) , so it is a convenient and easily understood metric for the comparison of methods  ... 
doi:10.3389/fgene.2019.01331 pmid:32010190 pmcid:PMC6979262 fatcat:fg4zowxiybarjd3hojlnuvjnqa

HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions

Jake Y. Chen, Ragini Pandey, Thanh M. Nguyen
2017 BMC Genomics  
Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine.  ...  Conclusions: While the underlying data for HAPPI-2 are integrated from a diverse data sources, the new HAPPI-2 release represents a good balance between data coverage and data quality of human PPIs, making  ...  TN performed the data coverage and quality evaluations, and helped strengthen the research methodology used in this study. All authors read and approved the final manuscript.  ... 
doi:10.1186/s12864-017-3512-1 pmid:28212602 pmcid:PMC5314692 fatcat:5vv4bc7w7jeebgmp2pm7qgyguy

Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes

Vassily Trubetskoy, Alex Rodriguez, Uptal Dave, Nicholas Campbell, Emily L. Crawford, Edwin H. Cook, James S. Sutcliffe, Ian Foster, Ravi Madduri, Nancy J. Cox, Lea K. Davis
2014 Computer applications in the biosciences : CABIOS  
Motivation: The development of cost-effective next-generation sequencing methods has spurred the development of high-throughput bioinformatics tools for detection of sequence variation.  ...  CGES yielded the fewest total variant calls (N CGES =139 897), the highest Ts/Tv ratio (3.02), the lowest Mendelian error rate across all genotypes (0.028%), the highest rediscovery rate from the Exome  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the individuals who participated in research at the Autism Center for Excellence (University  ... 
doi:10.1093/bioinformatics/btu591 pmid:25270638 pmcid:PMC4287941 fatcat:r4lafeebbfc4ldg3mnyou6wpdq

Flipping the odds of drug development success through human genomics [article]

Aroon Dinesh Hingorani, Valerie Kuan, Chris Finan, Felix A. Kruger, Anna Gaulton, Sandesh Chopade, Reecha Sofat, Raymond J. MacAllister, John Overington, Harry Hemingway, Spiros Denaxas, David Prieto-Merino (+1 others)
2017 bioRxiv   pre-print
Errors in drug target specification contribute to the extremely high rates of drug development failure.  ...  Integrating knowledge of genes that encode druggable targets with those that influence susceptibility to common disease has the potential to radically improve the probability of drug development success  ...  The high 'failure rate' (i.e. high rate of null associations) in GWAS reflects the much more stringent in this type of study design, which results in a much lower and much higher .  ... 
doi:10.1101/170142 fatcat:52ebttd6ozdvbm67rl6n6zobki

Congestion-Adaptive and Delay-Sensitive Multirate Routing Protocol in MANETs: A Cross-Layer Approach

Mahadev A. Gawas, Lucy J. Gudino, K. R Anupama
2019 Journal of Computer Networks and Communications  
The performance of the CADM protocol is comprehensively assessed through the simulation, which highlights the advantages of our cross-layer mechanism.  ...  The protocol discovers multiple node-disjoint routes and facilitates optimal data rates between the links based on the estimated delay to admit a flow with the certain delay requirement in multirate MANETs  ...  Conflicts of Interest e authors declare that there are no conflicts of interest regarding the publication of this paper.  ... 
doi:10.1155/2019/6826984 fatcat:uustw3en4be47epeirounrpoli

Association mapping and genomic prediction for resistance to sudden death syndrome in early maturing soybean germplasm

Yong Bao, James E. Kurle, Grace Anderson, Nevin D. Young
2015 Molecular breeding  
A ninefold cross-validation scheme was used to assess the prediction accuracy of GS for SDS resistance.  ...  The objectives of this study were to identify loci underlying variation in plant responses to SDS through association mapping (AM) and to assess prediction accuracy of genomic selection (GS) in a panel  ...  Acknowledgments We thank Colin Zumwalde, John Lencowski, Erin Walch, Adam Barbeau, Dante Leyva, Marissa Scherven, and other members of Soybean Pathology Lab at University of Minnesota for conducting the  ... 
doi:10.1007/s11032-015-0324-3 pmid:25999779 pmcid:PMC4434860 fatcat:eaqii5vmlzddjf5i3odwinyxpi

Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines

J. Greshock, J. Cheng, D. Rusnak, A. M. Martin, R. Wooster, T. Gilmer, K. Lee, B. L. Weber, T. Zaks
2008 Molecular Cancer Therapeutics  
This study shows that biomarkers predictive for lapatinib sensitivity, including the previously described copy number gains of EGFR and HER2, can be discovered using novel genomic assays in an unbiased  ...  Furthermore, these results show the utility of DNA copy number profiles in pharmacogenomic studies. [Mol Cancer Ther 2008;7(4):935 -43]  ...  Acknowledgments We thank the Discovery Technology Group at GlaxoSmithKline for all gene expression assay work.  ... 
doi:10.1158/1535-7163.mct-07-2072 pmid:18413807 fatcat:2n2hymuhlrdqlee4thrw6slgoi

Efficient and Consistent Path Loss Model for Mobile Network Simulation

Seon Yeong Han, Nael B. Abu-Ghazaleh, Dongman Lee
2016 IEEE/ACM Transactions on Networking  
We use measurements to validate the accuracy of the model for a number of scenarios. We also show that there is substantial impact on simulation behavior when path loss is modeled accurately.  ...  Path loss is the stationary component of the channel model affected by the shadowing in the environment.  ...  Even in a simple two-hop scenario, the use of spatially coherent models can result in significant difference in estimated throughput over existing models when there is only 10dBm difference in path loss  ... 
doi:10.1109/tnet.2015.2431852 fatcat:edwcjrdvsndcrdavlfxvg5qye4

Investigating Meta-Approaches for Reconstructing Gene Networks in a Mammalian Cellular Context

Azree Nazri, Pietro Lio, Philippe Rouet
2012 PLoS ONE  
The output of state-of-the-art reverse-engineering methods for biological networks is often based on the fitting of a mathematical model to the data.  ...  Here, we focus on an alternative approach for combining the information contained within such an ensemble of inconsistent gene networks called meta-analysis, to make more accurate predictions and to estimate  ...  These results highlight the need for a computational approach that integrates the inconsistent information from variable high-throughput studies.  ... 
doi:10.1371/journal.pone.0028713 pmid:22253694 pmcid:PMC3253778 fatcat:ledsrsmmknhgdi3wqyelw4u24y

Erratum: A map of human genome variation from population-scale sequencing

2011 Nature  
Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms.  ...  From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 28 per base pair per generation.  ...  of the project for storing and sharing high-throughput sequencing data.  ... 
doi:10.1038/nature09991 fatcat:7hgi4rxmnjhm5poqexxxx5bl4i

Genomic Medicine: New Frontiers and New Challenges

M. D. Pasic, S. Samaan, G. M. Yousef
2013 Clinical Chemistry  
the risk of "incidental findings" in genetic testing.  ...  for enrollment in clinical trials, and development of new targeted therapies, especially for metastatic tumors that are refractory to treatment.  ...  Revolutionary improvements in the analytical tools required for personalized medicine have accompanied the introduction of high-throughput technologies.  ... 
doi:10.1373/clinchem.2012.184622 pmid:23284016 fatcat:ou7qenog35chrlih6yrrvpkqty

Biosequence Similarity Search on the Mercury System

Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Arpith Jacob, Joseph Lancaster
2007 Journal of VLSI Signal Processing Systems for Signal, Image and Video Technology  
Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high-volume, high-throughput data movement off a data store  ...  The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database.  ...  Though we have shown significant speedup for stage 1 in firmware (refer toTable 5), the overall speedup is limited to a factor of 5 to 8.  ... 
doi:10.1007/s11265-007-0087-0 pmid:18846267 pmcid:PMC2564817 fatcat:6zsefgb7ubcrtaw5pmjy7u4tje
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