Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates

Handle URI:
http://hdl.handle.net/10754/622188
Title:
Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates
Authors:
Boopathi, Pon Arunachalam; Subudhi, Amit; Middha, Sheetal; Acharya, Jyoti; Mugasimangalam, Raja Chinnadurai; Kochar, Sanjay Kumar; Kochar, Dhanpat Kumar; Das, Ashis
Abstract:
High density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.
KAUST Department:
Pathogen Genomics Laboratory
Citation:
Boopathi PA, Subudhi AK, Middha S, Acharya J, Mugasimangalam RC, et al. (2016) Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates. Acta Tropica 164: 438–447. Available: http://dx.doi.org/10.1016/j.actatropica.2016.10.002.
Publisher:
Elsevier BV
Journal:
Acta Tropica
Issue Date:
9-Oct-2016
DOI:
10.1016/j.actatropica.2016.10.002
Type:
Article
ISSN:
0001-706X
Sponsors:
We thank all the patients and technical workers for their participation in and support of this project. P.A.B. acknowledges Project Assistantship from Department of Biotechnology (DBT), New Delhi, India, Basic Scientific Research fellowship from University Grant Commission, New Delhi, India and Research Fellowship from Birla Institute of Technology and Science, Pilani, Rajasthan, India. A.K.S. acknowledges Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), New Delhi, India and Project Assistantship from Department of Biotechnology (DBT), New Delhi, India. A.K.D., S.K.K. and D.K.K. acknowledges Department of Biotechnology (DBT), New Delhi, India for the financial support through the grant BT/PR7520/BRB/10/481/2006 and Birla Institute of Technology and Science, Pilani, India and S.P. Medical college, Bikaner, India for providing the required infrastructural facilities during this study. We thank the PlasmoDB team for making the genome of the Sal I strain available. Genotypic Technology Pvt. Ltd., Bangalore, India is also acknowledged for the microarray hybridization services provided. We also acknowledge Dr. Shilpi Garg for her help in correction of the manuscript.
Additional Links:
http://www.sciencedirect.com/science/article/pii/S0001706X16307823
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Full metadata record

DC FieldValue Language
dc.contributor.authorBoopathi, Pon Arunachalamen
dc.contributor.authorSubudhi, Amiten
dc.contributor.authorMiddha, Sheetalen
dc.contributor.authorAcharya, Jyotien
dc.contributor.authorMugasimangalam, Raja Chinnaduraien
dc.contributor.authorKochar, Sanjay Kumaren
dc.contributor.authorKochar, Dhanpat Kumaren
dc.contributor.authorDas, Ashisen
dc.date.accessioned2017-01-02T08:42:36Z-
dc.date.available2017-01-02T08:42:36Z-
dc.date.issued2016-10-09en
dc.identifier.citationBoopathi PA, Subudhi AK, Middha S, Acharya J, Mugasimangalam RC, et al. (2016) Design, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolates. Acta Tropica 164: 438–447. Available: http://dx.doi.org/10.1016/j.actatropica.2016.10.002.en
dc.identifier.issn0001-706Xen
dc.identifier.doi10.1016/j.actatropica.2016.10.002en
dc.identifier.urihttp://hdl.handle.net/10754/622188-
dc.description.abstractHigh density oligonucleotide microarrays have been used on Plasmodium vivax field isolates to estimate whole genome expression. However, no microarray platform has been experimentally optimized for studying the transcriptome of field isolates. In the present study, we adopted both bioinformatics and experimental testing approaches to select best optimized probes suitable for detecting parasite transcripts from field samples and included them in designing a custom 15K P. vivax microarray. This microarray has long oligonucleotide probes (60 mer) that were in-situ synthesized onto glass slides using Agilent SurePrint technology and has been developed into an 8X15K format (8 identical arrays on a single slide). Probes in this array were experimentally validated and represents 4180 P. vivax genes in sense orientation, of which 1219 genes have also probes in antisense orientation. Validation of the 15K array by using field samples (n =14) has shown 99% of parasite transcript detection from any of the samples. Correlation analysis between duplicate probes (n = 85) present in the arrays showed perfect correlation (r(2) = 0.98) indicating the reproducibility. Multiple probes representing the same gene exhibited similar kind of expression pattern across the samples (positive correlation, r >= 0.6). Comparison of hybridization data with the previous studies and quantitative real-time PCR experiments were performed to highlight the microarray validation procedure. This array is unique in its design, and results indicate that the array is sensitive and reproducible. Hence, this microarray could be a valuable functional genomics tool to generate reliable expression data from P. vivax field isolates. (C) 2016 Published by Elsevier B.V.en
dc.description.sponsorshipWe thank all the patients and technical workers for their participation in and support of this project. P.A.B. acknowledges Project Assistantship from Department of Biotechnology (DBT), New Delhi, India, Basic Scientific Research fellowship from University Grant Commission, New Delhi, India and Research Fellowship from Birla Institute of Technology and Science, Pilani, Rajasthan, India. A.K.S. acknowledges Senior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), New Delhi, India and Project Assistantship from Department of Biotechnology (DBT), New Delhi, India. A.K.D., S.K.K. and D.K.K. acknowledges Department of Biotechnology (DBT), New Delhi, India for the financial support through the grant BT/PR7520/BRB/10/481/2006 and Birla Institute of Technology and Science, Pilani, India and S.P. Medical college, Bikaner, India for providing the required infrastructural facilities during this study. We thank the PlasmoDB team for making the genome of the Sal I strain available. Genotypic Technology Pvt. Ltd., Bangalore, India is also acknowledged for the microarray hybridization services provided. We also acknowledge Dr. Shilpi Garg for her help in correction of the manuscript.en
dc.publisherElsevier BVen
dc.relation.urlhttp://www.sciencedirect.com/science/article/pii/S0001706X16307823en
dc.subjectMicroarrayen
dc.subjectPlasmodium vivaxen
dc.subjectUncomplicated malariaen
dc.subjectComplicated malariaen
dc.subjectviren
dc.titleDesign, construction and validation of a Plasmodium vivax microarray for the transcriptome profiling of clinical isolatesen
dc.typeArticleen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalActa Tropicaen
dc.contributor.institutionMolecular Parasitology and Systems Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, Indiaen
dc.contributor.institutionDepartment of Medicine, S.P. Medical College, Bikaner, Rajasthan, Indiaen
dc.contributor.institutionGenotypic Technology Pvt. Ltd., Bangalore, Indiaen
dc.contributor.institutionRajasthan University of Health Sciences, Jaipur, Rajasthan, Indiaen
kaust.authorSubudhi, Amiten
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