Quantifying replication slippage error in Cryptosporidium metabarcoding studies

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dc.citation.volumeAccepted manuscript
dc.contributor.authorKnox MA
dc.contributor.authorBiggs PJ
dc.contributor.authorGarcia-R JC
dc.contributor.authorHayman DTS
dc.coverage.spatialUnited States
dc.date.accessioned2024-02-18T23:49:17Z
dc.date.accessioned2024-07-25T06:40:59Z
dc.date.available2024-02-08
dc.date.available2024-02-18T23:49:17Z
dc.date.available2024-07-25T06:40:59Z
dc.date.issued2024-02-08
dc.description.abstractGenetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesised Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios and sequenced them using next generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.
dc.description.confidentialfalse
dc.format.paginationjiae065-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/38330464
dc.identifier.citationKnox MA, Biggs PJ, Garcia-R JC, Hayman DTS. (2024). Quantifying replication slippage error in Cryptosporidium metabarcoding studies.. J Infect Dis. Accepted manuscript. (pp. jiae065-).
dc.identifier.doi10.1093/infdis/jiae065
dc.identifier.eissn1537-6613
dc.identifier.elements-typejournal-article
dc.identifier.issn0022-1899
dc.identifier.pii7603955
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70665
dc.languageeng
dc.publisherOxford University Press on behalf of the Infectious Diseases Society of America
dc.publisher.urihttps://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiae065/7603955
dc.relation.isPartOfJ Infect Dis
dc.rights(c) 2024 The Author/s
dc.rightsCC BY 4.0
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectCryptosporidium hominis
dc.subjectCryptosporidium parvum
dc.subjectPCR slippage
dc.subjectSTR
dc.subjectdada2
dc.subjectrepeat region
dc.titleQuantifying replication slippage error in Cryptosporidium metabarcoding studies
dc.typeJournal article
pubs.elements-id486362
pubs.organisational-groupOther
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