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Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

F. Favero, T. Joshi, A. M. Marquard, N. J. Birkbak, M. Krzystanek, Q. Li, Z. Szallasi, A. C. Eklund
2014 Annals of Oncology  
Figure 2 . 2 Comparison of cellularity and ploidy estimates and copy number profiles derived from exome sequence to those derived from SNP array and testing on simulated data.  ...  One advantage of SNP arrays over exome sequencing is the genomic coverage. SNP arrays are often designed to both determine SNP genotypes and detect copy number changes.  ...  disclosure The authors have declared no conflicts of interest. references Methods: We conducted simulations in order to obtain a better understanding of how the NSABP B20 and SWOG 8814 results would have  ... 
doi:10.1093/annonc/mdu479 pmid:25319062 pmcid:PMC4269342 fatcat:nriemk5jbnenrpj7vmx4pb2tkm

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

A. Alkodsi, R. Louhimo, S. Hautaniemi
2014 Briefings in Bioinformatics  
Here, we have compared ten SCNA detection algorithms in both simulated and primary tumor deep sequencing data.  ...  Although several algorithms have been developed to detect SCNAs from whole-genome and whole-exome sequencing data, their relative performance has not been studied.  ...  The results published here are in part based upon data generated by The Cancer Genome Atlas pilot project established by the NCI and NHGRI.  ... 
doi:10.1093/bib/bbu004 pmid:24599115 fatcat:cvl45nz7wjczrg2ujyzouq4yly

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

Juan R González, Benjamín Rodríguez-Santiago, Alejandro Cáceres, Roger Pique-Regi, Nathaniel Rothman, Stephen J Chanock, Lluís Armengol, Luis A Pérez-Jurado
2011 BMC Bioinformatics  
The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.  ...  The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.  ...  the NIH, NCI (to SJC and NR) and the Asociación Española Contra el Cáncer (AECC) (to FXR and LAP-J).  ... 
doi:10.1186/1471-2105-12-166 pmid:21586113 pmcid:PMC3118168 fatcat:63gq5fo6fvdbredgpzeamhawuy

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data

Lingyang Xu, Yali Hou, Derek Bickhart, Jiuzhou Song, George Liu
2013 Microarrays  
Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them.  ...  Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome.  ...  CNVs can be identified using various approaches, including comparative genomic hybridization (CGH) arrays, SNP arrays, and DNA sequencing.  ... 
doi:10.3390/microarrays2030171 pmid:27605188 pmcid:PMC5003459 fatcat:47sbjm4g4vasncnwyc756hijne

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection [article]

Xizhi Luo, Fei Qin, Guoshuai Cai, Feifei Xiao
2020 bioRxiv   pre-print
This new segmentation algorithm has a wide scope of application with next-generation sequencing data analysis and single-cell sequencing analysis.  ...  To generate more accurate CNVs, we therefore proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic correlation (i.e., LD).  ...  Acknowledgements We thank the reviewers in advance for their thoughtful and insightful comments.  ... 
doi:10.1101/2020.04.08.032680 fatcat:ecjk6olyhnc5bina2wzr6yqhvy

AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data

Lei Bao, Minya Pu, Karen Messer
2014 Computer applications in the biosciences : CABIOS  
As deep sequencing of the exome or genome has become routine for characterization of tumor samples, in this work, we aim to develop a simple and robust algorithm to infer purity, ploidy and absolute copy  ...  Results: A simulation study shows that estimates have reasonable accuracy, and that the algorithm is robust against the presence of segmentation errors and subclonal populations.  ...  Recall that the two algorithms are using independent sets of data, exome sequencing data for AbsCN-seq and SNP array data for ABSOLUTE, and so this performance appears to be reasonable.  ... 
doi:10.1093/bioinformatics/btt759 pmid:24389661 fatcat:2k7kz26einekzf54evp4gasba4

SLMSuite: a suite of algorithms for segmenting genomic profiles

Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio, Alberto Magi
2017 BMC Bioinformatics  
We apply our method to the analysis of synthetic genomic profiles and real whole genome sequencing data and we demonstrate that it outperforms the state of the art circular binary segmentation algorithm  ...  Results: Here we introduce SLMSuite, a collection of algorithms, based on shifting level models (SLM), to segment genomic profiles from array and SGS experiments.  ...  Funding AM was supported by Italian Ministry of Health, Young Investigators Award, Project GR-2011-02352026 Detecting copy number variants from whole-exome sequencing data applied to acute myeloid leukemias  ... 
doi:10.1186/s12859-017-1734-5 pmid:28659129 pmcid:PMC5490196 fatcat:xpsw3zbcmjasbjgjqvshrgzbwu

ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients

Vinay Varadan, Salendra Singh, Arman Nosrati, Lakshmeswari Ravi, James Lutterbaugh, Jill S. Barnholtz-Sloan, Sanford D. Markowitz, Joseph E. Willis, Kishore Guda
2015 Genome Medicine  
ENVE achieved high concordance with orthogonal sCNA assessments across two colorectal cancer (CRC) WES datasets, and consistently outperformed a best-in-class algorithm, Control-FREEC.  ...  Reliable detection of somatic copy-number alterations (sCNAs) in tumors using whole-exome sequencing (WES) remains challenging owing to technical (inherent noise) and sample-associated variability in WES  ...  The results published here are in part based upon data generated by The Cancer Genome Atlas (TCGA) project established by the NCI and NHGRI.  ... 
doi:10.1186/s13073-015-0192-9 pmid:26269717 pmcid:PMC4534088 fatcat:livwnoqu6rfopbnlyislutkwiu

The Role of Constitutional Copy Number Variants in Breast Cancer

Logan Walker, George Wiggins, John Pearson
2015 Microarrays  
Technical challenges remain in determining the location and distribution of CNVs across the human genome due to the accuracy of computational prediction algorithms and resolution of the array data.  ...  In this review, we explore current and future application of SNP array technology to assess rare and common CNVs in association with breast cancer risk in humans.  ...  Molecular technologies used to profile DNA copy number, such as microarrays (SNP-based arrays and comparative genomic hybridisation) and next-generation sequencing, have led to the identification of more  ... 
doi:10.3390/microarrays4030407 pmid:27600231 pmcid:PMC4996380 fatcat:rhtkxuncvjaxzm2xsh42gy7d2y

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

B. L. Browning, S. R. Browning
2013 Genetics  
To investigate the properties of Refined IBD, we simulate SNP data from a model with recent superexponential population growth that is designed to match United Kingdom data.  ...  The second step (refinement) evaluates candidate segments with a probabilistic approach to assess the evidence for IBD.  ...  A full list of the investigators who contributed to the generation of the data is available from www.wtccc.org.uk.  ... 
doi:10.1534/genetics.113.150029 pmid:23535385 pmcid:PMC3664855 fatcat:vdxtuyfto5cahgdq6ldpno33ce

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

Tianwei Yu, Hui Ye, Wei Sun, Ker-Chau Li, Zugen Chen, Sharoni Jacobs, Dione K Bailey, David T Wong, Xiaofeng Zhou
2007 BMC Bioinformatics  
To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required.  ...  Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level.  ...  Abbreviations SNP, single nucleotide polymorphism; CNA, copy number aberration; FASeg, fragment assembling segmentation; CGH, comparative genomic hybridization; aCGH, array comparative genomic hybridization  ... 
doi:10.1186/1471-2105-8-145 pmid:17477871 pmcid:PMC1868765 fatcat:diouf6arkffeva7gnmarompoya

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens [article]

Haoyang Cai, Nitin Kumar, Homayoun C Bagheri, Christian von Mering, Mark Robinson, Michael Baudis
2014 biorxiv/medrxiv   pre-print
Conclusions Through a large-scale analysis of oncogenomic array data sets, this study characterized features associated with genomic aberrations patterns, compatible to the spectrum of "chromothripsis"  ...  We also report evidence that these genomic events may be correlated with patient age, stage and survival rate.  ...  Acknowledgements The authors would like to thank Henrik Bengtsson and Ni Ai for useful discussions.  ... 
doi:10.1101/001776 fatcat:2q72t4yabrcglcf3ofxj34an4u

Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens

Haoyang Cai, Nitin Kumar, Homayoun C Bagheri, Christian von Mering, Mark D Robinson, Michael Baudis
2014 BMC Genomics  
Conclusions: Through a large-scale analysis of oncogenomic array data sets, this study characterized features associated with genomic aberrations patterns, compatible to the spectrum of "chromothripsis  ...  We also report evidence that these genomic events may be correlated with patient age, stage and survival rate.  ...  Acknowledgements The authors would like to thank Henrik Bengtsson and Ni Ai for useful discussions.  ... 
doi:10.1186/1471-2164-15-82 pmid:24476156 pmcid:PMC3909908 fatcat:2ufcrrq4q5dj3motjfujig7ppi

BMI-CNV: A Bayesian framework for multiple genotyping platforms detection of copy number variation [article]

Xizhi Luo, Guoshuai Cai, Alexander C Mclain, Christopher I Amos, Bo Cai, Feifei Xiao
2021 bioRxiv   pre-print
Fortunately, samples have been previously sequenced by other genotyping platforms, such as SNP array.  ...  By applying to the matched 1000 genomes project and HapMap project data, we showed that BMI-CNV accurately detected common variants.  ...  Acknowledgements We thank the reviewers in advance for their helpful and insightful suggestions and comments. We also acknowledge the support from the international TRICL consortium.  ... 
doi:10.1101/2021.06.22.449433 fatcat:k6yor2pxbnar5lmznz47u3ocz4

PennCNV in whole-genome sequencing data

Leandro de Araújo Lima, Kai Wang
2017 BMC Bioinformatics  
To assess the performance of PennCNV original algorithm for array data in whole genome sequencing data, we processed mapping (BAM) files to extract coverage, representing log R ratio (LRR) of signal intensity  ...  The use of high-throughput sequencing data has improved the results of genomic analysis due to the resolution of mapping algorithms.  ...  Acknowledgements The authors thank the lab members for helpful comments and suggestions.  ... 
doi:10.1186/s12859-017-1802-x pmid:28984186 pmcid:PMC5629549 fatcat:haczzc2f7rfobehbwxn5cs6vya
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