Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-08

AUTHORS

Erin N Smith, Kristen Jepsen, Mahdieh Khosroheidari, Laura Z Rassenti, Matteo D’Antonio, Emanuela M Ghia, Dennis A Carson, Catriona HM Jamieson, Thomas J Kipps, Kelly A Frazer

ABSTRACT

Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution. More... »

PAGES

420

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13059-014-0420-4

DOI

http://dx.doi.org/10.1186/s13059-014-0420-4

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1012204991

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/25103687


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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-014-0420-4'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-014-0420-4'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-014-0420-4'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-014-0420-4'


 

This table displays all metadata directly associated to this object as RDF triples.

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