An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations

We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effec...

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Autores principales: Tan, John C, Miller, Becky A, Tan, Asako, Patel, Jigar J, Cheeseman, Ian H, Anderson, Tim JC, Manske, Magnus, Maslen, Gareth, Kwiatkowski, Dominic P, Ferdig, Michael T
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218861/
https://www.ncbi.nlm.nih.gov/pubmed/21477297
http://dx.doi.org/10.1186/gb-2011-12-4-r35
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author Tan, John C
Miller, Becky A
Tan, Asako
Patel, Jigar J
Cheeseman, Ian H
Anderson, Tim JC
Manske, Magnus
Maslen, Gareth
Kwiatkowski, Dominic P
Ferdig, Michael T
author_facet Tan, John C
Miller, Becky A
Tan, Asako
Patel, Jigar J
Cheeseman, Ian H
Anderson, Tim JC
Manske, Magnus
Maslen, Gareth
Kwiatkowski, Dominic P
Ferdig, Michael T
author_sort Tan, John C
collection PubMed
description We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.
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spelling pubmed-32188612012-04-08 An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations Tan, John C Miller, Becky A Tan, Asako Patel, Jigar J Cheeseman, Ian H Anderson, Tim JC Manske, Magnus Maslen, Gareth Kwiatkowski, Dominic P Ferdig, Michael T Genome Biol Method We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination. BioMed Central 2011 2011-04-08 /pmc/articles/PMC3218861/ /pubmed/21477297 http://dx.doi.org/10.1186/gb-2011-12-4-r35 Text en Copyright ©2011 Tan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Tan, John C
Miller, Becky A
Tan, Asako
Patel, Jigar J
Cheeseman, Ian H
Anderson, Tim JC
Manske, Magnus
Maslen, Gareth
Kwiatkowski, Dominic P
Ferdig, Michael T
An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title_full An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title_fullStr An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title_full_unstemmed An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title_short An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations
title_sort optimized microarray platform for assaying genomic variation in plasmodium falciparum field populations
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218861/
https://www.ncbi.nlm.nih.gov/pubmed/21477297
http://dx.doi.org/10.1186/gb-2011-12-4-r35
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