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Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes

Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a nove...

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Autores principales: van Orsouw, Nathalie J., Hogers, René C. J., Janssen, Antoine, Yalcin, Feyruz, Snoeijers, Sandor, Verstege, Esther, Schneiders, Harrie, van der Poel, Hein, van Oeveren, Jan, Verstegen, Harold, van Eijk, Michiel J. T.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2048665/
https://www.ncbi.nlm.nih.gov/pubmed/18000544
http://dx.doi.org/10.1371/journal.pone.0001172
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author van Orsouw, Nathalie J.
Hogers, René C. J.
Janssen, Antoine
Yalcin, Feyruz
Snoeijers, Sandor
Verstege, Esther
Schneiders, Harrie
van der Poel, Hein
van Oeveren, Jan
Verstegen, Harold
van Eijk, Michiel J. T.
author_facet van Orsouw, Nathalie J.
Hogers, René C. J.
Janssen, Antoine
Yalcin, Feyruz
Snoeijers, Sandor
Verstege, Esther
Schneiders, Harrie
van der Poel, Hein
van Oeveren, Jan
Verstegen, Harold
van Eijk, Michiel J. T.
author_sort van Orsouw, Nathalie J.
collection PubMed
description Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP® with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave® assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.
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spelling pubmed-20486652007-11-14 Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes van Orsouw, Nathalie J. Hogers, René C. J. Janssen, Antoine Yalcin, Feyruz Snoeijers, Sandor Verstege, Esther Schneiders, Harrie van der Poel, Hein van Oeveren, Jan Verstegen, Harold van Eijk, Michiel J. T. PLoS One Research Article Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP® with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave® assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information. Public Library of Science 2007-11-14 /pmc/articles/PMC2048665/ /pubmed/18000544 http://dx.doi.org/10.1371/journal.pone.0001172 Text en van Orsouw et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
van Orsouw, Nathalie J.
Hogers, René C. J.
Janssen, Antoine
Yalcin, Feyruz
Snoeijers, Sandor
Verstege, Esther
Schneiders, Harrie
van der Poel, Hein
van Oeveren, Jan
Verstegen, Harold
van Eijk, Michiel J. T.
Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title_full Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title_fullStr Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title_full_unstemmed Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title_short Complexity Reduction of Polymorphic Sequences (CRoPS™): A Novel Approach for Large-Scale Polymorphism Discovery in Complex Genomes
title_sort complexity reduction of polymorphic sequences (crops™): a novel approach for large-scale polymorphism discovery in complex genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2048665/
https://www.ncbi.nlm.nih.gov/pubmed/18000544
http://dx.doi.org/10.1371/journal.pone.0001172
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