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VarScan: variant detection in massively parallel sequencing of individual and pooled samples

Daniel C. Koboldt, Ken Chen, Todd Wylie, David E. Larson, Michael D. McLellan, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Li Ding
2009 Computer applications in the biosciences : CABIOS  
We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples.  ...  Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease.  ...  ACKNOWLEDGEMENTS We thank Stephen Daiger and colleagues at the University of Texas HSC Houston; David Dooling, Scott Smith, Erica Sodergren, Bob Fulton and Rachel Abbott of the Washington University Genome  ... 
doi:10.1093/bioinformatics/btp373 pmid:19542151 pmcid:PMC2734323 fatcat:3t22knnitbb2rcgpsotaxafgty

A Review of Bioinformatics Model and Computational Software of Next Generation Sequencing

Jalilah Arijah Mohd Kamarudin, Afnizanfaizal Abdullah, Roselina Sallehuddin
2019 International Journal of Innovative Computing  
These computational software and bioinformatics model are differentiating into three types of bioinformatics analysis stages including alignment, variant calling and filtering and annotation.  ...  In this paper, the description on functionalities, source type and website of the program or software are provided.  ...  VarScan also companionable in both individual and pooled samples which results for effectively variant calls data of several sequencing platform.  ... 
doi:10.11113/ijic.v9n1.217 fatcat:hi3g4qblefgu3ae4vmtjyml6ym

A statistical method for the detection of variants from next-generation resequencing of DNA pools

V. Bansal
2010 Bioinformatics  
Detection of rare variants from pooled sequencing represents a different challenge than detection of variants from individual sequencing.  ...  The massive capacity of next-generation sequencers can be harnessed for sequencing specific genomic regions in hundreds to thousands of individuals.  ...  ACKNOWLEDGEMENTS I would like to thank Dr Nicholas Schork for supporting this work, members of SGM who generated the sequence data used in this paper and Dr.  ... 
doi:10.1093/bioinformatics/btq214 pmid:20529923 pmcid:PMC2881398 fatcat:2lvrxuubtjcstff2v5lzb2nsmm

Detection of somatic mutations in tumors using unaligned clonal sequencing data

Kate M Sutton, Laura A Crinnion, David Wallace, Sally Harrison, Paul Roberts, Christopher M Watson, Alexander F Markham, David T Bonthron, Philip Quirke, Ian M Carr
2014 Laboratory Investigation  
Owing to the heterogeneous nature of tumors, a somatic mutation may be present in only a subset of cells, necessitating the use of quantitative techniques to detect rare variants.  ...  However, the large volumes of sequence data present significant difficulties when applying NGS for the detection of somatic mutations.  ...  With the advent of massively parallel sequencing technologies, it has become comparatively trivial to generate the required amount of sequence data to detect somatic mutations in a quantifiable manner.  ... 
doi:10.1038/labinvest.2014.96 pmid:25068661 fatcat:vkptaf4q3rfhhckvtah3why3vy

Detailed evaluation of cancer sequencing pipelines in different microenvironments and heterogeneity levels

2021 Turkish Journal of Biology  
We observed significant discrepancy in variant calls among tested pipelines for different heterogeneity levels in real and simulated samples with overall high specificity and low sensitivity.  ...  This suggests that adhering to a single pipeline is not optimal for cancer sequencing analysis and sample heterogeneity should be considered in algorithm optimization.  ...  We utilized the same exome regions in the real dataset and pooled all the variants detected by any of our pipelines in the real samples.  ... 
doi:10.3906/biy-2008-8 pmid:33907494 pmcid:PMC8068765 fatcat:r4a4bclflncrjarlt6azl2ionu

Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster

F. A. Santoni, P. Makrythanasis, S. Nikolaev, M. Guipponi, D. Robyr, A. Bottani, S. E. Antonarakis
2014 Genome Research  
The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation  ...  Moreover, massive whole-exome sequencing of tumors has provided significant advances in the understanding of cancer development through the recognition of somatic driver variants.  ...  Acknowledgments We thank Ximena Bonilla, Teresa Didonna, and Sam Lukowsky for useful comments and discussions.  ... 
doi:10.1101/gr.163832.113 pmid:24389049 pmcid:PMC3912425 fatcat:anxdskx5xrdyjg4q5wal3o33ia

Identification of Disease-Causing Mutations in Autosomal Dominant Retinitis Pigmentosa (adRP) Using Next-Generation DNA Sequencing

Sara J. Bowne, Lori S. Sullivan, Daniel C. Koboldt, Li Ding, Robert Fulton, Rachel M. Abbott, Erica J. Sodergren, David G. Birch, Dianna H. Wheaton, John R. Heckenlively, Qin Liu, Eric A. Pierce (+2 others)
2011 Investigative Ophthalmology and Visual Science  
To determine whether massively parallel next-generation DNA sequencing offers rapid and efficient detection of disease-causing mutations in patients with monogenic inherited diseases.  ...  More than 9000 sequence variants were identified and analyzed, to assess the likelihood of pathogenicity.  ...  Acknowledgments The authors thank Gita Dangol, Kaylie Webb, and Joe Ray for technical assistance.  ... 
doi:10.1167/iovs.10-6180 pmid:20861475 pmcid:PMC3053293 fatcat:cjwxdpaqxbbfjdqebhhoqoovui

High-throughput discovery of rare insertions and deletions in large cohorts

F. L. M. Vallania, T. E. Druley, E. Ramos, J. Wang, I. Borecki, M. Province, R. D. Mitra
2010 Genome Research  
By leveraging the massively parallel output of second-generation DNA sequencing, pooled-sample sequencing allows fast and accurate detection of rare variants in thousands of samples at a fraction of time  ...  Experimental and computational pipeline for detection of indels and substitutions in large pooled DNA samples: DNA samples from a selected group of patients are individually pooled in a complex mixture  ... 
doi:10.1101/gr.109157.110 pmid:21041413 pmcid:PMC2989997 fatcat:2bhcl3juvjgszgv4hy2skdbkky

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

Xutao Deng
2011 BMC Bioinformatics  
The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks.  ...  It supports both paired-end reads and single reads generated on most sequencing platforms; it runs on all major types of computers; it supports arbitrary genome assemblies for arbitrary organisms; and  ...  Kun Qu and Dr. Richard Jove of City of Hope for providing testing data and computing facilities for the trio family exome-Seq study.  ... 
doi:10.1186/1471-2105-12-267 pmid:21714929 pmcid:PMC3148209 fatcat:rkc3mnme3fhynjk4fjxyl6k6ee

MICADo – Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method

Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, Jonas Bergh, Macha Nikolski
2016 Frontiers in Genetics  
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible  ...  MICADo analyses NGS reads for each sample within the context of the data of the whole cohort in order to capture the differences between specificities of the sample with respect to the cohort.  ...  Computational Science for assistance with massively parallel sequencing.  ... 
doi:10.3389/fgene.2016.00214 pmid:28008336 pmcid:PMC5143680 fatcat:ay4y4dl25bhevneyz5evlk6wxe

Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking

Federica Fazzini, Liane Fendt, Sebastian Schönherr, Lukas Forer, Bernd Schöpf, Gertraud Streiter, Jamie Lee Losso, Anita Kloss-Brandstätter, Florian Kronenberg, Hansi Weissensteiner
2021 International Journal of Molecular Sciences  
Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies.  ...  In total, 48 samples were sequenced on Illumina MiSeq.  ...  Introduction One of the most precious benefits of massive parallel sequencing (MPS) technologies in the field of mitochondrial DNA (mtDNA) research is the increase in sensitivity for detecting heteroplasmy  ... 
doi:10.3390/ijms22020935 pmid:33477827 pmcid:PMC7832847 fatcat:2oaeysr5kzcuxb22zstgfmvli4

Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments

Victor Missirian, Luca Comai, Vladimir Filkov
2011 BMC Bioinformatics  
TILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals.  ...  It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data  ...  Acknowledgments This work was supported in part by NSF Plant Genome award DBI-0822383, TRPGR: Efficient identification of induced mutations in crop species by ultra-high throughput DNA sequencing.  ... 
doi:10.1186/1471-2105-12-287 pmid:21756356 pmcid:PMC3150297 fatcat:pekvcatn75g6hk5s26qxdlspwe

Diagnosis of Fanconi Anemia: Mutation Analysis by Next-Generation Sequencing

Najim Ameziane, Daoud Sie, Stefan Dentro, Yavuz Ariyurek, Lianne Kerkhoven, Hans Joenje, Josephine C. Dorsman, Bauke Ylstra, Johan J. P. Gille, Erik A. Sistermans, Johan P. de Winter
2012 Anemia  
Here we describe and validate a comprehensive protocol for the molecular diagnosis of FA, based on massively parallel sequencing.  ...  A valid FA diagnosis requires the detection of pathogenic mutations in a FA gene and/or a positive result from a chromosomal breakage test.  ...  To assess the performance of the custom target kit and the massively parallel sequencing method, we selected FA samples with a spectrum of different types of known variations ( Table 1 ).  ... 
doi:10.1155/2012/132856 pmid:22720145 pmcid:PMC3374947 fatcat:4jn7hvnwbravvnu23zlkrz7rm4

SpeedSeq: ultra-fast personal genome analysis and interpretation

Colby Chiang, Ryan M Layer, Gregory G Faust, Michael R Lindberg, David B Rose, Erik P Garrison, Gabor T Marth, Aaron R Quinlan, Ira M Hall
2015 Nature Methods  
SpeedSeq accomplishes read alignment, duplicate removal, variant detection and functional annotation of a 50X human genome in <24 hours, even using one low-cost server.  ...  SpeedSeq offers competitive or superior performance to current methods for detecting germline and somatic single nucleotide variants (SNVs), indels, and structural variants (SVs) and includes novel functionality  ...  We added new features to GEMINI that enable proper SV annotation and interpretation of variants in cancer samples.  ... 
doi:10.1038/nmeth.3505 pmid:26258291 pmcid:PMC4589466 fatcat:aqxgevgtajc4tedt5xoyidhx44

Whole-exome sequencing reveals recurrent somatic mutation networks in cancer

Xiaoping Liu, Jiguang Wang, Luonan Chen
2013 Cancer Letters  
also can avoid low coverage or lowly recurrent on disease samples in contrast to individual driver genes.  ...  The whole-exome sequencing information can reflect the mutations of the protein-coding region in the genome and depict the causal relationship between the mutations and phenotypes.  ...  Acknowledgments This work was supported by the National Natural Science Foundation of China under Grants Nos. 91029301, 61134013 and 61072149; and by the Chief Scientist Program of Shanghai Institutes  ... 
doi:10.1016/j.canlet.2012.11.002 pmid:23153794 fatcat:angjidrzlfa4fhnnb7anqnhcai
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