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Identification of missing variants by combining multiple analytic pipelines

Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers (+3 others)
2018 BMC Bioinformatics  
It is well-known that there are discrepancies between variants called by different pipelines, and that using a single pipeline always misses true variants exclusively identifiable by other pipelines.  ...  Nonetheless, it is common practice today to call variants by one pipeline due to computational cost and assume that false negative calls are a small percent of total.  ...  Availability of data and materials The data that support the findings of this study are available from the Alzheimer's Disease Sequencing Project but restrictions apply to the availability of these data  ... 
doi:10.1186/s12859-018-2151-0 pmid:29661148 pmcid:PMC5902939 fatcat:gb7v6iylm5b67gcnj2mouslsxq

RAPIDSNPs: A new computational pipeline for rapidly identifying key genetic variants reveals previously unidentified SNPs that are significantly associated with individual platelet responses

Bajuna Rashid Salehe, Chris Ian Jones, Giuseppe Di Fatta, Liam James McGuffin, Gualtiero I. Colombo
2017 PLoS ONE  
Our new pipeline provides an important step towards addressing the problem of 'missing heritability' through enhanced detection of key genetic variants (SNPs) that are associated with continuous complex  ...  of whole genome variants.  ...  Acknowledgments The authors thank the Institute of Finance Management under the ministry of finance (MoF) of the Tanzanian Government for studentship funding (to BRS) and Bloodomics project supported by  ... 
doi:10.1371/journal.pone.0175957 pmid:28441463 pmcid:PMC5404774 fatcat:63l3qgpiorhmxk7htx3lmhviwe

The Role of New Sequencing Technology in Identifying Rare Mutations in New Susceptibility Genes for Cancer

Melissa C. Southey
2013 Current Genetic Medicine Reports  
to the identification of new cancer susceptibility genes.  ...  The search for new cancer susceptibility genes is no longer limited by sequencing technology; theoretically, MPS can be advantageous to studies searching for genetic variation responsible for cancer predisposition  ...  the likelihood of identifying functionally relevant genetic variants in the same genes in multiple families by combining MPS data [7] (COMPLEXO; http://www.path.unimelb.edu. au/research/labs/southey  ... 
doi:10.1007/s40142-013-0021-7 fatcat:srpenqpi3rbrxi7xbyl2k43gu4

A survey of tools for variant analysis of next-generation genome sequencing data

S. Pabinger, A. Dander, M. Fischer, R. Snajder, M. Sperk, M. Efremova, B. Krabichler, M. R. Speicher, J. Zschocke, Z. Trajanoski
2013 Briefings in Bioinformatics  
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  ...  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  ...  A viable alternative is the use of complete analytical pipelines capable of analyzing all steps starting from raw sequences to a set of identified and annotated variants.  ... 
doi:10.1093/bib/bbs086 pmid:23341494 pmcid:PMC3956068 fatcat:zcunpg3i7bfrvhm5dixp6r6ofq

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

Neil A. Miller, Emily G. Farrow, Margaret Gibson, Laurel K. Willig, Greyson Twist, Byunggil Yoo, Tyler Marrs, Shane Corder, Lisa Krivohlavek, Adam Walter, Josh E. Petrikin, Carol J. Saunders (+9 others)
2015 Genome Medicine  
We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h.  ...  Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes  ...  Comparison of the sensitivity and accuracy of all nucleotide variant calls. B. Comparison of the accuracy of variants that were uniquely called by the GSNAP/GATK-VQSR.  ... 
doi:10.1186/s13073-015-0221-8 pmid:26419432 pmcid:PMC4588251 fatcat:povwyqatyfampefkxxm3xrhk6y

Whole Exome Sequencing Data Analysis Algorithms in Cancer Diagnostics [chapter]

Áron Bartha, Balázs Gyorffy
2020 Prime Archives in Cancer Research  
Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment.  ...  The identification of homologous recombination deficiency enables the use of PARP inhibitors.  ...  The utilization of combined pipelines can successfully filter the false positive hits and provide a platform for the customization of variant calling pipelines for the designated research objective.  ... 
doi:10.37247/pacr.1.2020.5 fatcat:fb3xwm2drbhqhinmehksj3dgai

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies

Matthew A. Field, Vicky Cho, T. Daniel Andrews, Chris C. Goodnow, Yan W. Asmann
2015 PLoS ONE  
A diversity of tools is available for identification of variants from genome sequence data.  ...  This analysis confirms previous work showing that combining variant calls of multiple tools results in the best quality resultant variant set, for either specificity or sensitivity, depending on whether  ...  We also would like to thank Queensland Institute of Medical Research for access to the melanoma cell line generated as part of the larger Australian Melanoma Genome Project. Author Contributions  ... 
doi:10.1371/journal.pone.0143199 pmid:26600436 pmcid:PMC4658170 fatcat:st7unva2lnaopcjmjkiqzb345m

A clinically validated whole genome pipeline for structural variant detection and analysis

Nir Neerman, Gregory Faust, Naomi Meeks, Shira Modai, Limor Kalfon, Tzipora Falik-Zaccai, Alexander Kaplun
2019 BMC Genomics  
Analytical and clinical sensitivity and specificity of the pipeline has been validated using analysis of Genome in a Bottle reference genomes and known positive samples confirmed by orthogonal sequencing  ...  Using a combination of breakpoint analysis of split and discordant reads, and read depth analysis, the pipeline identifies structural variants down to single base pair resolution.  ...  About this supplement This article has been published as part of BMC Genomics Volume 20 Supplement 8, 2019: Proceedings of VarI-COSI 2018: identification and annotation of genetic variants in the context  ... 
doi:10.1186/s12864-019-5866-z pmid:31307387 pmcid:PMC6631445 fatcat:j7dlfydjobdubdrv736spitrv4

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review

Emma Graham, Jessica Lee, Magda Price, Maja Tarailo-Graovac, Allison Matthews, Udo Engelke, Jeffrey Tang, Leo A. J. Kluijtmans, Ron A. Wevers, Wyeth W. Wasserman, Clara D. M. van Karnebeek, Sara Mostafavi
2018 Journal of Inherited Metabolic Disease  
and prioritization of variants causing IEMs.  ...  , causation is often difficult to establish due to the number of plausible variants.  ...  Numerous strategies have been developed to reduce missing values through a group of analytic techniques called missing value imputation (MVI).  ... 
doi:10.1007/s10545-018-0139-6 pmid:29721916 pmcid:PMC5959954 fatcat:rhhdodn4wnapzhbi2746j7xdlq

Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology

Bartha, Győrffy
2019 Cancers  
Variant calling algorithms for SNVs range from standalone tools to machine learning-based combined pipelines. Tools for CNV detection compare the number of reads aligned to a dedicated segment.  ...  The identification of homologous recombination deficiency enables the use of PARP inhibitors.  ...  The utilization of combined pipelines can successfully filter the false positive hits and provide a platform for the customization of variant calling pipelines for the designated research objective.  ... 
doi:10.3390/cancers11111725 pmid:31690036 pmcid:PMC6895801 fatcat:s3lnry4r3ffqbeorfnuiigobtm

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research  ...  Commonly used approaches in these efforts are currently limited by the 3 i's - integration, interpretation, and insights.  ...  To improve imputation accuracy, a recent novel multi-omics imputation approach that integrates multiple correlated omics datasets by combining estimates of missing values from individual omics datasets  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools

Carlos A Garcia-Prieto, Francisco Martínez-Jiménez, Alfonso Valencia, Eduard Porta-Pardo, Can Alkan
2022 Bioinformatics  
Moreover, the Consensus of three calling strategy to combine the output of multiple variant calling tools, a very widely used strategy by the research community, can lead to the loss of some cancer driver  ...  Results Here we quantify the impact of variant calling decisions by comparing the results obtained in three important analyses of cancer genomics data (identification of cancer driver genes, quantification  ...  During MC3, many groups worked together to define a clear and unique strategy to combine the output of multiple variant calling tools.  ... 
doi:10.1093/bioinformatics/btac306 pmid:35512388 fatcat:i5kfc7th4bgbno6lzf2wdudigu

Genomic Analysis of Historical Cases with Positive Newborn Screens for Short-Chain Acyl-CoA Dehydrogenase Deficiency Shows That a Validated Second-Tier Biochemical Test Can Replace Future Sequencing

Aashish N. Adhikari, Robert J. Currier, Hao Tang, Coleman T. Turgeon, Robert L. Nussbaum, Rajgopal Srinivasan, Uma Sunderam, Pui-Yan Kwok, Steven E. Brenner, Dimitar Gavrilov, Jennifer M. Puck, Renata Gallagher
2020 International Journal of Neonatal Screening  
Analyte testing for SCADD in blood and urine, including newborn screening (NBS) using tandem mass spectrometry (MS/MS) on dried blood spots (DBSs), is complicated by the presence of two relatively common  ...  Short-chain acyl-CoA dehydrogenase deficiency (SCADD) is a rare autosomal recessive disorder of β-oxidation caused by pathogenic variants in the ACADS gene.  ...  The California Department of Public Health is not responsible for the results or conclusions drawn by the authors of this publication.  ... 
doi:10.3390/ijns6020041 pmid:32802992 pmcid:PMC7423011 fatcat:tw3socklafgetjdujwqqqsjhhy

Technical Performance of a 430-Gene Preventative Genomics Assay to Identify Multiple Variant Types Associated with Adult-Onset Monogenic Conditions, Susceptibility Loci, and Pharmacogenetic Insights

Ari Silver, Gabriel A. Lazarin, Maxwell Silver, Meghan Miller, Michael Jansen, Christine Wechsberg, Erin Dekanek, Stav Grossfeld, Tim Herpel, Dinura Gunatilake, Alexander Bisignano, Malgorzata Jaremko
2022 Journal of Personalized Medicine  
The custom-designed target enrichment capture and bioinformatics pipelines interrogate multiple variant types, including single nucleotide variants, insertions/deletions (indels), copy number variants,  ...  While not currently in widespread usage, technological advances in genetic analysis overcome barriers to access by enabling less labor-intensive and more cost-efficient means to discover variants of clinical  ...  Acknowledgments: We would like to acknowledge Hudson Schertz for his contributions in designing and professionalizing many of the figures in the manuscript.  ... 
doi:10.3390/jpm12050667 fatcat:sscqezbtzzewffs3ydmmrwubxe

Targeted next generation sequencing for newborn screening of Menkes disease

Richard B. Parad, Stephen G. Kaler, Evan Mauceli, Tanya Sokolsky, Ling Yi, Arindam Bhattacharjee
2020 Molecular Genetics and Metabolism Reports  
For certain medically-actionable conditions, however, NBS is limited by the absence of reliable biochemical signatures amenable to detection by current platforms.  ...  The algorithm correctly identified pathogenic ATP7A variants, including missense, nonsense, small insertions/deletions, and large copy number variants, in 21/22 (95.5%) of subjects, one of whom had inconclusive  ...  RP was supported by a National Institutes of Health Grant (U19HD077671). We thank the BabySeq project Executive Committee and Ozge Ceyhan-Birsoy for review and sharing of ATP7A data.  ... 
doi:10.1016/j.ymgmr.2020.100625 pmid:32714836 pmcid:PMC7378272 fatcat:ikknskoz5fhexprhotaqb34vka
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