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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2007
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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. |
format | Text |
id | pubmed-2048665 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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