A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Filters
Identification of missing variants by combining multiple analytic pipelines
2018
BMC Bioinformatics
Preserved Fulltext
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
2017
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2013
Current Genetic Medicine Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Genome Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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]
2020
Prime Archives in Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2015
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2019
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Journal of Inherited Metabolic Disease
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2019
Cancers
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Journal of Molecular Endocrinology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2022
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2020
International Journal of Neonatal Screening
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2022
Journal of Personalized Medicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2020
Molecular Genetics and Metabolism Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 9,630 results