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Comparing the performance of selected variant callers using synthetic data and genome segmentation

Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks, Daoud Meerzaman
2018 BMC Bioinformatics  
genome provides an effective and economical way to compare data analyzed by variant callers with ground truth.  ...  In this study we employed four synthetic data sets (variants with known mutations spiked into specific genomic locations) of increasing complexity to assess the sensitivity, specificity, and balanced accuracy  ...  QC, CN, and DM engaged in data-analysis planning. MH designed the data-analysis pipeline and provided the data sets. XB and YH performed data analysis. YH proposed the segmentation analysis.  ... 
doi:10.1186/s12859-018-2440-7 fatcat:27neka6fendmro544lpffe3mam

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data

Yu Fan, Liu Xi, Daniel S. T. Hughes, Jianjun Zhang, Jianhua Zhang, P. Andrew Futreal, David A. Wheeler, Wenyi Wang
2016 Genome Biology  
We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequencing.  ...  of the tumor and normal tissue at each reference base.  ...  Acknowledgments We thank the ICGC PCAWG for use of the ICGC Pilot-63 data and Kyle Ellrott from UCSC for generating the MuSE calls presented in Fig. 3d . We thank Dr. John N.  ... 
doi:10.1186/s13059-016-1029-6 pmid:27557938 pmcid:PMC4995747 fatcat:jd25bdlts5gz5bgan32k7p53ke

New synthetic-diploid benchmark for accurate variant calling evaluation [article]

Heng Li, Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura D Gauthier, Benjamin Neale, Daniel MacArthur
2017 bioRxiv   pre-print
Constructed from the consensus of multiple variant callers based on short-read data, existing benchmark datasets for evaluating variant calling accuracy are biased toward easy regions accessible by known  ...  This benchmark provides a more accurate and less biased estimate of the error rate of small variant calls in a realistic context.  ...  Syndip is the first benchmark dataset that does not heavily depend on short-read data and short-read variant callers, and thus more honestly reflects the true accuracy of such variant callers.  ... 
doi:10.1101/223297 fatcat:gc2bgedjrranxisp4jhld3wym4

Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software

Daniel L. Cameron, Leon Di Stefano, Anthony T. Papenfuss
2019 Nature Communications  
We characterise the impact on performance of event size and type, sequencing characteristics, and genomic context, and analyse the efficacy of ensemble calling and calibration of variant quality scores  ...  In recent years, many software packages for identifying structural variants (SVs) using whole-genome sequencing data have been released.  ...  We next set out to determine the overall performance of callers using four cell line datasets with orthogonal validation data: NA12878, HG002, and CHM1 and CHM13 separately and merged as a synthetic diploid  ... 
doi:10.1038/s41467-019-11146-4 pmid:31324872 pmcid:PMC6642177 fatcat:3fin3kowobfipdypybcwr7lzse

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

Wouter De Coster, Peter De Rijk, Arne De Roeck, Tim De Pooter, Svenn D'Hert, Mojca Strazisar, Kristel Sleegers, Christine Van Broeckhoven
2019 Genome Research  
structural variant calling tools, as well as a comparison with the performance of structural variant calling from short-read sequencing data.  ...  We sequenced the genome of the Yoruban reference individual NA19240 on the long-read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline  ...  assistance in using NanoSV and interpreting its output, Fritz Sedlazeck for assistance in using Sniffles and SURVIVOR, and Mark Chaisson for releasing the SV calls of NA19240.  ... 
doi:10.1101/gr.244939.118 pmid:31186302 pmcid:PMC6633254 fatcat:4okys7ot5rahdfcymihzd3yjmu

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

Chang Xu
2018 Computational and Structural Biotechnology Journal  
We will review the reference materials, datasets, and performance metrics that have been used in the benchmarking studies.  ...  This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications.  ...  At potential mutation sites (high LOD score), another model selection is performed in normal to compare the wide-type model M 0 and the heterozygous model M 0.5 .  ... 
doi:10.1016/j.csbj.2018.01.003 pmid:29552334 pmcid:PMC5852328 fatcat:zfe7b6ja2ne3pa3hlxhr3qms2q

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Konstantinos Karagiannis, Malcolm Moos, Sean Smith, Luis Santana-Quintero, Chunlin Xiao, Michael Colgan, Huixiao Hong, Marghoob Mohiyuddin, Wenming Xiao
2022 Genome Biology  
real scenarios, for example, a model trained on a combination of real and spike-in mutations had the highest average performance.  ...  Results In this study, we use the first comprehensive and well-characterized somatic reference data sets from the SEQC2 consortium to investigate best practices for using a deep learning framework in cancer  ...  Rebecca Kusko of the Immuneering Corporation for manuscript polishing and Dr. Daniel P. Cooke of the University of Oxford for providing data sets for NA12878.BRCA and NA24631.PACA.  ... 
doi:10.1186/s13059-021-02592-9 pmid:34996510 pmcid:PMC8740374 fatcat:do5bxuuv7vd3nmsl3735tox23y

Comparing multi- and single-sample variant calls to improve variant call sets from deep coverage whole-genome sequencing data [article]

Suyash S. Shringarpure, Rasika A. Mathias, Ryan D Hernandez, Timothy D. O'Connor, Zachary A. Szpiech, Raul Torres, Francisco M. De La Vega, Carlos D. Bustamante, Kathleen C. Barnes, Margaret A. Taub
2016 bioRxiv   pre-print
At a False Positive Rate of 5%, our method determines true positive rates of 97.5%, 95% and 99% on variant calls obtained using Illumina's single-sample caller CASAVA, Real Time Genomics' multisample variant  ...  caller, and the GATK Unified Genotyper, respectively.  ...  Acknowledgments Funding for this study was provided by National Institutes of Health (NIH) R01HL104608.  ... 
doi:10.1101/078642 fatcat:oe5xtcmjsnau7ny6akf2zi474e

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi (+10 others)
2018 Genome Biology  
Whole-genome sequencing of tumors can allow exhaustive identification of the specific structural variants present in an individual cancer, facilitating both clinical diagnostics and the discovery of novel  ...  Rigorous performance evaluation of somatic structural variant detection methods has been challenged by the lack of gold standards, extensive resource requirements, and difficulties arising from the need  ...  Availability of data and materials Sequence files are available at the Sequence Read Archive (SRA) under accession number SRP042948.  ... 
doi:10.1186/s13059-018-1539-5 pmid:30400818 pmcid:PMC6219177 fatcat:ytg6g3eodfdkbovexsshxvnfey

Best practices for variant calling in clinical sequencing

Daniel C. Koboldt
2020 Genome Medicine  
I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection.  ...  Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance.  ...  Cottrell, Peter White, and other members of the Steve and Cindy Institute for Genomic Medicine at Nationwide Children's Hospital.  ... 
doi:10.1186/s13073-020-00791-w pmid:33106175 fatcat:qpa42hvyqbg6nobonl7wzcwef4

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome [article]

Wouter De Coster, Arne De Roeck, Tim De Pooter, Svenn D'Hert, Peter De Rijk, Mojca Strazisar, Kristel Sleegers, Christine Van Broeckhoven
2018 bioRxiv   pre-print
The aligner Minimap2 and structural variant caller Sniffles are both the most accurate and the most computationally efficient tools in our study.  ...  We sequenced the Yoruban NA19240 genome on the Oxford Nanopore PromethION for benchmarking and evaluation of recently published aligners and structural variant calling tools.  ...  for assistance in using NanoSV and interpreting its output, Fritz Sedlazeck for assistance in using Sniffles and SURVIVOR and Mark Chaisson for releasing the SV calls of NA19240.  ... 
doi:10.1101/434118 fatcat:gpqwcgxfybcl5bcrzy3ilu7owa

Accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling for sequencing data [article]

Yu Fan, Liu Xi, Daniel S. T. Hughes, Jianjun Zhang, Jianhua Zhang, P. Andrew Futreal, David A. Wheeler, Wenyi Wang
2016 bioRxiv   pre-print
We demonstrate the accuracy of MuSE in calling subclonal mutations in the context of large-scale tumor sequencing projects using whole exome and whole genome sequence.  ...  of the tumor and normal tissue at each reference base.  ...  Acknowledgements We thank the ICGC PCAWG for use of the ICGC Pilot-63 data and Kyle Ellrott from UCSC for generating the MuSE calls presented in Figure 3d . We thank Dr. John N.  ... 
doi:10.1101/055467 fatcat:r4iuc24rgza6fhy7b3ed5wbw7u

Reliability of algorithmic somatic copy number alteration detection from targeted capture data

Nora Rieber, Regina Bohnert, Ulrike Ziehm, Gunther Jansen, Alfonso Valencia
2017 Bioinformatics  
To investigate the accuracy of SCNA detection algorithms on simulated and clinical tumor samples, the precision and sensitivity of four SCNA callers were measured using 50 simulated whole exome and 50  ...  Results: On synthetic exome and panel data, VarScan2 mostly called false positives, whereas Control-FREEC was precise (>90% correct calls) at the cost of low sensitivity (<40% detected).  ...  Acknowledgements The results published here are in part based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/.  ... 
doi:10.1093/bioinformatics/btx284 pmid:28472276 pmcid:PMC5870863 fatcat:4askx7fzvvcmjhbr5st2zvf7h4

Accurate detection of structural variation is hard [article]

Kyle Lesack, Grace M Mariene, Erik C. Andersen, James D. Wasmuth
2022 bioRxiv   pre-print
Moreover, the performance of these tools for predicting variants in non-human genomes is less certain, as most tools were developed and benchmarked using data from the human genome.  ...  To evaluate the use of long-read data for the validation of short-read predictions, the agreement between predictions from a short-read ensemble learning method and long-read tools were compared.  ...  These changes that span large segments of the genome (e.g., > 100 bp) are termed structural variants (SVs) and include .  ... 
doi:10.1101/2022.03.11.483485 fatcat:nwwdoahc6fdpjixtlwzyupmnd4

A thesaurus of genetic variation for interrogation of repetitive genomic regions

Claudia Kerzendorfer, Tomasz Konopka, Sebastian M.B. Nijman
2015 Nucleic Acids Research  
We apply the technique to whole genome datasets and establish that called variants in low mappability regions annotated using the thesaurus can be experimentally validated.  ...  We then extend the analysis to a large panel of exomes to show that the annotation technique opens possibilities to study variation in hereto hidden and understudied parts of the genome.  ...  ACKNOWLEDGEMENT We thank members of CeMM for comments and discussions.  ... 
doi:10.1093/nar/gkv178 pmid:25820428 pmcid:PMC4446415 fatcat:eu65id4e6fdothqkzoq73fateq
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