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Toward better understanding of artifacts in variant calling from high-coverage samples

Heng Li
2014 Computer applications in the biosciences : CABIOS  
However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of  ...  We estimated that the error rate of raw genotype calls is as high as 1 in 10-15kb, but the error rate of post-filtered calls is reduced to 1 in 100-200kb without significant compromise on the sensitivity  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btu356 pmid:24974202 pmcid:PMC4271055 fatcat:hbbiuj5rdvg7be65h2kjzktgje

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals

Anthony Youzhi Cheng, Yik-Ying Teo, Rick Twee-Hee Ong
2014 Computer applications in the biosciences : CABIOS  
It is thus unclear how these variant calling methods would fare for a dataset of $100 samples from a population not part of the 1 KGP that have been sequenced at various coverage depths.  ...  If study samples are sequenced at a high coverage depth such as 30Â, CASAVA has the highest variant accuracy as compared with the other variant callers assessed.  ...  and the Office of Deputy President (Research and Technology) from the National University of Singapore.  ... 
doi:10.1093/bioinformatics/btu067 pmid:24558117 fatcat:fnlpej3xlnbjdcu2dmz2avtzky

Subclonal variant calling with multiple samples and prior knowledge

M. Gerstung, E. Papaemmanuil, P. J. Campbell
2014 Bioinformatics  
We show that our algorithm has a high accuracy of calling cancer mutations and demonstrate that the detected clonal and subclonal variants have important prognostic consequences.  ...  Motivation: Targeted resequencing of cancer genes in large cohorts of patients is important to understand the biological and clinical consequences of mutations.  ...  to call variants with high specificity and sensitivity.  ... 
doi:10.1093/bioinformatics/btt750 pmid:24443148 pmcid:PMC3998123 fatcat:byqbfhd3i5h4fjehqa2rsyyk24

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair [article]

Ivo Buchhalter, Barbara Hutter, Tyler S Alioto, Timothy A Beck, Paul C Boutros, Benedikt Brors, Adam P Butler, Sasithorn Chotewutmontri, Robert E Denroche, Sophia Derdak, Nicolle Diessl, Lars Feuerbach (+34 others)
2014 bioRxiv   pre-print
This benchmarking exercise has highlighted several fundamental parameters to consider in this regard, which will allow for better optimization and planning of both basic and translational studies.  ...  To become part of routine clinical care, high-throughput sequencing must be globally compatible and comparable.  ...  Acknowledgements We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services.  ... 
doi:10.1101/013177 fatcat:phhmnaxptrg67bvrjsewfvsq7e

From next-generation resequencing reads to a high-quality variant data set

S P Pfeifer
2016 Heredity  
To tap the full potential of high-throughput sequencing, a thorough understanding of the data produced as well as the available methodologies is required.  ...  analyses and provide general guidelines and recommendations for producing high-quality single-nucleotide polymorphism data sets from raw reads by highlighting several sophisticated reference-based methods  ...  In general, study design plays an important role in variant calling and genotyping: more specific variant calls and more accurate genotype estimations can be obtained by using high coverage sequence data  ... 
doi:10.1038/hdy.2016.102 pmid:27759079 pmcid:PMC5234474 fatcat:aunsu43nt5hv5e32gkotekiu5a

Towards best practice in cancer mutation detection with whole-genome and whole-exome sequencing [article]

Wenming Xiao
2019 bioRxiv   pre-print
We identified artifacts of C>A mutations in WES due to sample and library processing and highlighted limitations of bioinformatics tools for artifact detection and removal.By examining the interactions  ...  AbstractClinical applications of precision oncology require accurate tests that can distinguish cancer-specific mutations from errors introduced at each step of next generation sequencing (NGS).  ...  Laufey Amundadottir of the Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), for the sponsorship and the usage of the NIH Biowulf cluster  ... 
doi:10.1101/626440 fatcat:sxskeoedlbbgblt6xjdjcmo4bm

Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers

Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel
2017 BMC Bioinformatics  
Conclusions: The choice of well-performing tools for alignment and variant calling is crucial for the correct interpretation of exome sequencing data obtained from mixed samples, and common pipelines are  ...  The comparison was done as a function of variant allele frequencies and coverage. Our analysis revealed that deepSNV and JointSNVMix2 perform very well, especially in the low-frequency range.  ...  In the case that the coverage in the cancer sample was more than 200×, the variant is labelled high coverage.  ... 
doi:10.1186/s12859-016-1417-7 pmid:28049408 pmcid:PMC5209852 fatcat:7qx3yr4w55hbzoa34lkhy5vvwm

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing [article]

Roger Ros-Freixedes, Mara Battagin, Martin Johnsson, Gregor Gorjanc, Alan J Mileham, Steve D Rounsley, John Hickey
2018 bioRxiv   pre-print
With the proliferation of cost-effective low-coverage sequencing there is a need to understand the impact of these errors and bias on resulting genotype calls.  ...  However, pruning of alternative haplotypes supported by a number of reads below a predefined threshold, a default and desired step for removing potential sequencing errors in high-coverage data, introduced  ...  Acknowledgements This work has made use of the resources provided by the Edinburgh Compute and 541 Data Facility (ECDF) (http://www.ecdf.ed.ac.uk/). 542 543  ... 
doi:10.1101/358085 fatcat:qsik5xvkizgdda4a34aephgzge

Validation of Next Generation Sequencing Cancer Panels for Clinical Somatic Mutation Profiling-- Identification of Source of Variations and Artifacts using FFPE Tissues

Ken CN Chang, Yun Zhao
2014 Journal of Next Generation Sequencing & Applications  
Helen Fernandez of Cornell Medical College for helpful discussions, Jason Hughes of Merck Research Labs in helping to set up data processing pipeline, and John Thompson of Merck Research Labs for training  ...  The C to T artifact mutation calls from formalin-fixed paraffin-embedded (FFPE) tissue samples observed in this study together with high C to A artifact mutation calls from acoustic shearing of intact  ...  As shown in our Illumina data set using replicates from same sample different library preparations, many variant calls with extremely high quality (high coverage or high Q score) were not repeatable.  ... 
doi:10.4172/2469-9853.1000109 fatcat:rgbcd7vum5edvbigddr2scltae

Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac

Michel Plüss, Anna M. Kopps, Irene Keller, Janine Meienberg, Sylvan M. Caspar, Nicolo Dubacher, Rémy Bruggmann, Manfred Vogel, Gabor Matyas
2017 Proceedings of the National Academy of Sciences of the United States of America  
Nat Biotechnol 34:374-376. 8 Li H (2014) Toward better understanding of artifacts in variant calling from high-coverage samples.  ...  To largely reduce systematic errors and alignment artifacts, we limited our benchmarking of whole-genome variant calling to the coding part of the high-confidence BED file of GIAB 3.3 (https://github.com  ... 
doi:10.1073/pnas.1713830114 pmid:28916731 pmcid:PMC5635930 fatcat:le72gmamq5clfcfyvw2ao27goe

CODEX: a normalization and copy number variation detection method for whole exome sequencing

Yuchao Jiang, Derek A. Oldridge, Sharon J. Diskin, Nancy R. Zhang
2015 Nucleic Acids Research  
Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from exome sequencing is challenging due to the high level of biases and artifacts.  ...  High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases.  ...  Better understanding of the genetics of CNVassociated diseases requires accurate CNV detection.  ... 
doi:10.1093/nar/gku1363 pmid:25618849 pmcid:PMC4381046 fatcat:mdu7jsadzjdexp575kqijbnnvi

The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors

Zubin H. Patel, Leah C. Kottyan, Sara Lazaro, Marc S. Williams, David H. Ledbetter, hbGerard Tromp, Andrew Rupert, Mojtaba Kohram, Michael Wagner, Ammar Husami, Yaping Qian, C. Alexander Valencia (+4 others)
2014 Frontiers in Genetics  
The trio strategy allowed us to identify variants in the proband that could not have been inherited from the parents (Mendelian errors) and would most likely indicate sequencing artifacts.  ...  Filtering the variants on these measurements removed ∼95% of the Mendelian errors while retaining 80% of the called variants. These filters were applied independently.  ...  We are grateful for support from the US Department of Veterans Affairs, the Department of Defense (PR094002), and the National Institutes of Health (HG006828, HG006382, AI024717, AI083194, AR048929, AR049084  ... 
doi:10.3389/fgene.2014.00016 pmid:24575121 pmcid:PMC3921572 fatcat:5xn6kgj2vjbt7n2nfh5btfbv5q

Intratumor genetic heterogeneity in squamous cell carcinoma of the oral cavity

Dan P. Zandberg, Luke J. Tallon, Sushma Nagaraj, Lisa K. Sadzewicz, Yuji Zhang, Maxwell B. Strome, Xuechu E. Zhao, Kranthi Vavikolanu, Xiaoyu Zhang, John C. Papadimitriou, Fleesie A. Hubbard, Søren M. Bentzen (+2 others)
2019 Head and Neck  
We sought to evaluate intratumor heterogeneity in squamous cell carcinoma of the oral cavity (OCC) and specifically determine the effect of physical separation and histologic differentiation within the  ...  CONFLICT OF INTEREST Dr Strome is a cofounder, consultant, and stockholder in Gliknik Inc., a biotechnology company.  ...  He receives research support from Pfizer and Gliknik through sponsored research agreements through the University of Maryland, Baltimore.  ... 
doi:10.1002/hed.25719 pmid:30869813 fatcat:yxvl5tqsbncnnf56byivzioije

Reducing INDEL calling errors in whole genome and exome sequencing data

Han Fang, Yiyang Wu, Giuseppe Narzisi, Jason A ORawe, Laura T Jimenez Barrón, Julie Rosenbaum, Michael Ronemus, Ivan Iossifov, Michael C Schatz, Gholson J Lyon
2014 Genome Medicine  
However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.  ...  We also developed a classification scheme based on the coverage and composition to rank high and low quality INDEL calls.  ...  Acknowledgements The laboratory of GJL is supported in part by funds from the Stanley Institute for Cognitive Genomics at Cold Spring Harbor Laboratory (CSHL).  ... 
doi:10.1186/s13073-014-0089-z pmid:25426171 pmcid:PMC4240813 fatcat:fqaqythm6vdzpbcvrfukixe22u

The Isolated in Utero Environment Is Conducive to the Emergence of RNA and DNA Virus Variants

Daniel Udenze, Ivan Trus, Henry Munyanduki, Nathalie Berube, Uladzimir Karniychuk
2021 Viruses  
This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge.  ...  These findings should encourage further studies on virus evolution in placenta and fetuses, to better understand how virus variants emerge and how in utero viral evolution affects congenital virus transmission  ...  Conflicts of Interest: The authors declare no conflict of interest. Viruses 2021, 13, 1827  ... 
doi:10.3390/v13091827 pmid:34578408 pmcid:PMC8473323 fatcat:qkqhpwk5lvfbpdcshtl5nudtwu
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