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Copy Number Variation detection from 1000 Genomes project exon capture sequencing data

Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert, Alexander E Urban, Michael P Snyder, Gabor T Marth
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
However there has been little attention devoted to Copy Number Variation (CNV) detection from exome capture datasets despite the potentially high impact of CNVs in exonic regions on protein function.  ...  Results: As members of the 1000 Genomes Project analysis effort, we investigated 697 samples in which 931 genes were targeted and sampled with 454 or Illumina paired-end sequencing.  ...  Acknowledgements This work was supported by National Human Genome Research Institute grants R01-HG004719 and RC2-HG005552.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-13-305">doi:10.1186/1471-2105-13-305</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23157288">pmid:23157288</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3563612/">pmcid:PMC3563612</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/if4sty6pr5arbepj64i5tppjo4">fatcat:if4sty6pr5arbepj64i5tppjo4</a> </span>
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CoNVEX: copy number variation estimation in exome sequencing data using HMM

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Here, we propose an HMM to detect CNV in cancer exome data. We used modified data from 1000 Genomes project to evaluate the performance of the proposed method.  ...  One of the main types of genetic variations in cancer is Copy Number Variations (CNV).  ...  We used resources from both University of Melbourne and Peter MacCallum Cancer Centre for data processing and analysis. This work is partially funded by Australian Research Council (grant DP1096296).  ... 
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CONTRA: copy number analysis for targeted resequencing

Jason Li, Richard Lupat, Kaushalya C. Amarasinghe, Ella R. Thompson, Maria A. Doyle, Georgina L. Ryland, Richard W. Tothill, Saman K. Halgamuge, Ian G. Campbell, Kylie L. Gorringe
<span title="2012-04-02">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Results: We present a method for CNV detection for TR data, including whole-exome capture data.  ...  Motivation: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify diseasecausing variants, a robust method for copy number variation (CNV) analysis  ...  The exome sequencing data (.bam files) were obtained from the 1000 genomes project website. The CNV genotype profiles were obtained from the HapMap website.  ... 
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Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2

Romina D'Aurizio, Tommaso Pippucci, Lorenzo Tattini, Betti Giusti, Marco Pellegrini, Alberto Magi
<span title="2016-08-09">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
To evaluate the performance of our novel tool we use it for analysing two WES data sets, a population data set sequenced by the 1000 Genomes Project and a tumor data set made of bladder cancer samples.  ...  Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation that have been proved to be associated with many disease states.  ...  Real for providing the tumor data used in the study.  ... 
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Identification of copy number variants from exome sequence data

Pubudu Samarakoon, Hanne Sorte, Bjørn Kristiansen, Tove Skodje, Ying Sheng, Geir E Tjønnfjord, Barbro Stadheim, Asbjørg Stray-Pedersen, Olaug Rødningen, Robert Lyle
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task.  ...  the 1000 genomes project and 9 exomes from primary immunodeficiency patients.  ...  Exome sequencing was performed by the Norwegian Sequencing Centre.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-661">doi:10.1186/1471-2164-15-661</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25102989">pmid:25102989</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4132917/">pmcid:PMC4132917</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/izvswlq7ynf7ldnb2gy7ainr2m">fatcat:izvswlq7ynf7ldnb2gy7ainr2m</a> </span>
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EXCAVATOR: detecting copy number variants from whole-exome sequencing data

Alberto Magi, Lorenzo Tattini, Ingrid Cifola, Romina D'Aurizio, Matteo Benelli, Eleonora Mangano, Cristina Battaglia, Elena Bonora, Ants Kurg, Marco Seri, Pamela Magini, Betti Giusti (+5 others)
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data.  ...  EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states.  ...  Acknowledgements We gratefully acknowledge the financial support of the Cariplo Foundation grant number 2006_0771 for genomic, epigenetic and transcriptional analysis of cancer by next-generation sequencing  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2013-14-10-r120">doi:10.1186/gb-2013-14-10-r120</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24172663">pmid:24172663</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4053953/">pmcid:PMC4053953</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sqwcrdwwvvgdlfwjjqe6cpxrxi">fatcat:sqwcrdwwvvgdlfwjjqe6cpxrxi</a> </span>
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CODEX: a normalization and copy number variation detection method for whole exome sequencing

Yuchao Jiang, Derek A. Oldridge, Sharon J. Diskin, Nancy R. Zhang
<span title="2015-01-23">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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.  ...  CODEX is compared to existing methods on a population analysis of HapMap samples from the 1000 Genomes Project, and shown to be more accurate on three microarray-based validation data sets.  ...  the 1000 Genomes Project data set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1363">doi:10.1093/nar/gku1363</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25618849">pmid:25618849</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4381046/">pmcid:PMC4381046</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdu7jsadzjdexp575kqijbnnvi">fatcat:mdu7jsadzjdexp575kqijbnnvi</a> </span>
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CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson, Nancy R. Zhang
<span title="2018-11-26">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that  ...  We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent.  ...  Acknowledgements We thank Bradley Garman and Bradley Wubbenhorst for providing the casecontrol melanoma dataset from the samples collected and studied at the Wistar Institute in the laboratory of Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-018-1578-y">doi:10.1186/s13059-018-1578-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30477554">pmid:30477554</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aiwxwdtfffap7d3btijhrxxpzm">fatcat:aiwxwdtfffap7d3btijhrxxpzm</a> </span>
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Detection of internal exon deletion with exon Del

Yan Guo, Shilin Zhao, Brian D Lehmann, Quanhu Sheng, Timothy M Shaver, Thomas P Stricker, Jennifer A Pietenpol, Yu Shyr
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Such deletions have potentially significant biological meaning, and they are often too short to be considered copy number variation.  ...  We tested ExonDel on exome sequencing data generated from 16 breast cancer cell lines and identified both novel and known IEDs.  ...  The TCGA data was downloaded with approved request 14085-3 from dbGAP of NIH. We would also like to thank Margot Bjoring for editorial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-332">doi:10.1186/1471-2105-15-332</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25322818">pmid:25322818</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4288651/">pmcid:PMC4288651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2d3w3ue62vf3let7qqag2dbaoa">fatcat:2d3w3ue62vf3let7qqag2dbaoa</a> </span>
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Copy number variation detection and genotyping from exome sequence data

N. Krumm, P. H. Sudmant, A. Ko, B. J. O'Roak, M. Malig, B. P. Coe, A. R. Quinlan, D. A. Nickerson, E. E. Eichler
<span title="2012-05-14">2012</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
and specificity from exome sequencing data.  ...  of genic copy number variation.  ...  Copy number variation detection from exome data Genome Research 1529 www.genome.org number.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.138115.112">doi:10.1101/gr.138115.112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22585873">pmid:22585873</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3409265/">pmcid:PMC3409265</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sc7psfvmsbbxrls6pohpbxq5du">fatcat:sc7psfvmsbbxrls6pohpbxq5du</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302211454/http://pdfs.semanticscholar.org/a241/d391263dff286d9b19803e6156c50a387d36.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a2/41/a241d391263dff286d9b19803e6156c50a387d36.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.138115.112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3409265" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing [article]

Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N Anastopoulos, Katherine L Nathanson, Nancy R Zhang
<span title="2017-10-30">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods, but suffers from biases and artifacts that  ...  We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent.  ...  Copy number variation detection and genotyping from exome sequence data. MC, Owen MJ, et al: Discovery and statistical genotyping of copy-number variation 544 from whole-exome sequencing depth.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/211698">doi:10.1101/211698</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/olj26gryqfgtphwwuarh4fmwle">fatcat:olj26gryqfgtphwwuarh4fmwle</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723153905/https://www.biorxiv.org/content/biorxiv/early/2017/11/13/211698.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/ab/f0ab151e73ed1b162bc9bd344a0faca16b77077c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/211698"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

SMN1 copy‐number and sequence variant analysis from next‐generation sequencing data

Daniel Lopez‐Lopez, Carlos Loucera, Rosario Carmona, Virginia Aquino, Josefa Salgado, Sara Pasalodos, María Miranda, Ángel Alonso, Joaquín Dopazo
<span title="2020-10-14">2020</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2vzjuzyygveinhd4ab2ux34qv4" style="color: black;">Human Mutation</a> </i> &nbsp;
Here, we present SMAca, the first python tool to detect SMA carriers and estimate the absolute SMN1 copy-number using NGS data.  ...  This tool has been validated with a cohort of 326 samples from the Navarra 1000 Genomes Project (NAGEN1000). SMAca was developed with a focus on execution speed and easy installation.  ...  DATA AVAILABILITY STATEMENT The data that support the findings of this study are available from Navarra 1000 Genomes project (NAGEN1000).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.24120">doi:10.1002/humu.24120</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33058415">pmid:33058415</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ifxi7opbdvbirk5xvlb4nt34fe">fatcat:ifxi7opbdvbirk5xvlb4nt34fe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718060652/https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/humu.24120" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/c0/3bc001de289e3575313d7d5733e33f4a6a6811d0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/humu.24120"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a>

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

Jarupon Fah Sathirapongsasuti, Hane Lee, Basil A. J. Horst, Georg Brunner, Alistair J. Cochran, Scott Binder, John Quackenbush, Stanley F. Nelson
<span title="2011-08-09">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Motivation: The ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point  ...  Results: We present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the  ...  However, the cost and analytical complexity of sequencing still limit the number of whole genomes that can be sequenced in any single project (Teer and Mullikin, 2010) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr462">doi:10.1093/bioinformatics/btr462</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21828086">pmid:21828086</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3179661/">pmcid:PMC3179661</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/id6oyvnr5bg35kfpjrmr2bfquq">fatcat:id6oyvnr5bg35kfpjrmr2bfquq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302213833/http://pdfs.semanticscholar.org/aa21/180d7453b2e776cc18600825c86e845c422d.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/aa/21/aa21180d7453b2e776cc18600825c86e845c422d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr462"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179661" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment

Valentina S. Vysotskaia, Gregory J. Hogan, Genevieve M. Gould, Xin Wang, Alex D. Robertson, Kevin R. Haas, Mark R. Theilmann, Lindsay Spurka, Peter V. Grauman, Henry H. Lai, Diana Jeon, Genevieve Haliburton (+8 others)
<span title="2017-02-23">2017</span> <i title="PeerJ"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyfkjqp7sva5bbnwatk5zazi7q" style="color: black;">PeerJ</a> </i> &nbsp;
Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36  ...  Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test.  ...  Counsyl sequence data for 36 genes were compared to reference data obtained from the 1000 Genomes Projects.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.3046">doi:10.7717/peerj.3046</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28243543">pmid:28243543</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5326550/">pmcid:PMC5326550</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v6qei7tcvjgpvb7chbg6knuqom">fatcat:v6qei7tcvjgpvb7chbg6knuqom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922112151/https://peerj.com/articles/3046.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/9b/be9b879fcef15e24c1fbbaadafc2b96987b074f3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7717/peerj.3046"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326550" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grassPanicum virgatum

Joseph Evans, Jeongwoon Kim, Kevin L. Childs, Brieanne Vaillancourt, Emily Crisovan, Aruna Nandety, Daniel J. Gerhardt, Todd A. Richmond, Jeffrey A. Jeddeloh, Shawn M. Kaeppler, Michael D. Casler, C. Robin Buell
<span title="2014-08-11">2014</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eyeekm765nepfjifdg2zcmtf2y" style="color: black;">The Plant Journal</a> </i> &nbsp;
.; and Buell, C Robin, "Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum" (2014).  ...  Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.  ...  We are grateful to Jeremy Schmutz of the Department of Energy JGI for his work on the switchgrass genome.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tpj.12601">doi:10.1111/tpj.12601</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24947485">pmid:24947485</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4309430/">pmcid:PMC4309430</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bsdh4meijbd2tawqxtkf5f3t5i">fatcat:bsdh4meijbd2tawqxtkf5f3t5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502042716/https://digitalcommons.unl.edu/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=2525&amp;context=usdaarsfacpub" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/67/b9/67b98d031c01967ace8204a0ca3385bd0ac8fea0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tpj.12601"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309430" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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