A tiling array-based comparative genomic hybridization approach to predict copy number variations between Plasmodium falciparum field isolates from the Indian Sub-continent Article Swipe
Isha Pandey
,
Ramandeep Kaur
,
Amit Kumar Subudhi
,
P.A. Boopathi
,
Raja C. Mugasimangalam
,
Sudha N. Rao
,
Mohammed Aiyaz
,
Sanjay Kumar Kochar
,
Dhanpat Kumar Kochar
,
Ashis Das
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.14599.1
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.12688/f1000research.14599.1
Background: There are several techniques to analyse copy number variation in both research and clinical settings, such as whole genome amplification (sWGA), SNP arrays and one of the most commonly used techniques, array based comparative genomic hybridization (aCGH). In the latter, copy number comparison is obtained between differentially labelled target and reference DNAs by measuring ratio of fluorescence intensity of probes indicating loss or gain in the chromosomal region. Methods: Here we carry out a comparative analysis between two Plasmodium falciparum parasite isolates (Pf-isolate-2 and Pf-isolate-1) causing malaria using array CGH. The array contains approximately 418,577, 60mer custom-designed probes with an average probe spacing of 56 bp. The significant major variations (amplifications and deletions) copy number variations (CNV) in Pf-isolate-2 (Pf-2) in comparison with Pf-isolate-1 (Pf-1), are reported. Results: CNVs have been seen in all the chromosomes in Pf-2, most of the deletions have been seen mostly in sub-telomeric and telomeric regions of the chromosomes that comprises of variant surface antigen family genes. Apart from the subtelomeric regions other parts of the chromosomes have also shown CNVs. Novel variations , like continuous amplification of 28kb region (249817-278491) of chromosome-8, which covers for 3 genes two of which codes for conserved Plasmodium proteins with unknown function (MAL8P1.139, PF08_0122) and tRNA pseudouridine synthase, putative (PF08_0123). Amplifications in regions harboring genes like GTP cyclohydrolase I (GCH-1, PFL1155W) and ribosomal protein, L24, putative (PFL1150C) of chromosome 12 were seen. Conclusion: Other than known variations reported earlier, some novel variations have also been seen in the chromosomes of Pf-2. This is an experimental case study reporting major amplifications and deletions in Pf-isolate-2 in comparison with Pf-isolate-1 using a tiling array based comparative genomic hybridization approach.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.12688/f1000research.14599.1
- https://f1000research.com/articles/7-1033/v1/pdf
- OA Status
- gold
- Cited By
- 2
- References
- 48
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2836261058
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2836261058Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.12688/f1000research.14599.1Digital Object Identifier
- Title
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A tiling array-based comparative genomic hybridization approach to predict copy number variations between Plasmodium falciparum field isolates from the Indian Sub-continentWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2018Year of publication
- Publication date
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2018-07-09Full publication date if available
- Authors
-
Isha Pandey, Ramandeep Kaur, Amit Kumar Subudhi, P.A. Boopathi, Raja C. Mugasimangalam, Sudha N. Rao, Mohammed Aiyaz, Sanjay Kumar Kochar, Dhanpat Kumar Kochar, Ashis DasList of authors in order
- Landing page
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https://doi.org/10.12688/f1000research.14599.1Publisher landing page
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https://f1000research.com/articles/7-1033/v1/pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
- OA URL
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https://f1000research.com/articles/7-1033/v1/pdfDirect OA link when available
- Concepts
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Biology, Copy-number variation, Genetics, Comparative genomic hybridization, Genome, Chromosome, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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2Total citation count in OpenAlex
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2021: 1, 2019: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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