Quantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.

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dc.citation.issue1
dc.citation.volume230
dc.contributor.authorKnox MA
dc.contributor.authorBiggs PJ
dc.contributor.authorGarcia-R JC
dc.contributor.authorHayman DTS
dc.coverage.spatialUnited States
dc.date.accessioned2024-08-07T03:02:07Z
dc.date.available2024-08-07T03:02:07Z
dc.date.issued2024-07-15
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 synthesized 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.edition.editionJuly 2024
dc.format.paginatione144-e148
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/39052741
dc.identifier.citationKnox MA, Biggs PJ, Garcia-R JC, Hayman DTS. (2024). Quantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.. J Infect Dis. 230. 1. (pp. e144-e148).
dc.identifier.doi10.1093/infdis/jiae065
dc.identifier.eissn1537-6613
dc.identifier.elements-typejournal-article
dc.identifier.issn0022-1899
dc.identifier.pii7720881
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/71221
dc.languageeng
dc.publisherOxford University Press
dc.publisher.urihttps://academic.oup.com/jid/article/230/1/e144/7603955#476157190
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.subjectShort Tandem Repeat
dc.subjectdada2
dc.subjectCryptosporidium
dc.subjectHumans
dc.subjectDNA Replication
dc.subjectDNA, Protozoan
dc.subjectHigh-Throughput Nucleotide Sequencing
dc.subjectDNA Barcoding, Taxonomic
dc.subjectCryptosporidiosis
dc.subjectGenetic Variation
dc.titleQuantifying Replication Slippage Error in Cryptosporidium Metabarcoding Studies.
dc.typeJournal article
pubs.elements-id490948
pubs.organisational-groupOther
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